Jianhong Ou
| Snapshot Date: 2024-11-29 13:40 -0500 (Fri, 29 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/enhancerHomologSearch |
| git_branch: devel |
| git_last_commit: 672f113 |
| git_last_commit_date: 2024-11-18 15:43:30 -0500 (Mon, 18 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-30 12:47 -0500 (Sat, 30 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4461 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4403 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 636/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| enhancerHomologSearch 1.13.1 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the enhancerHomologSearch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/enhancerHomologSearch.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: enhancerHomologSearch |
| Version: 1.13.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:enhancerHomologSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings enhancerHomologSearch_1.13.1.tar.gz |
| StartedAt: 2024-11-29 21:41:22 -0500 (Fri, 29 Nov 2024) |
| EndedAt: 2024-11-29 21:56:40 -0500 (Fri, 29 Nov 2024) |
| EllapsedTime: 917.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: enhancerHomologSearch.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:enhancerHomologSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings enhancerHomologSearch_1.13.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/enhancerHomologSearch.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘enhancerHomologSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enhancerHomologSearch’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘enhancerHomologSearch’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
Enhancers-class.Rd: BSgenome-class, GRanges-class, lgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
conservedMotifs 91.732 17.032 110.856
searchTFBPS 71.844 15.459 122.226
saveAlignments 10.544 0.719 21.527
getENCODEdata 4.662 0.604 18.918
alignmentOne 4.914 0.091 5.023
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/enhancerHomologSearch.Rcheck/00check.log’
for details.
enhancerHomologSearch.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL enhancerHomologSearch
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘enhancerHomologSearch’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/alignment/Alignment.cpp -o ClustalW/alignment/Alignment.o
ClustalW/alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable]
SeqArray::iterator posToAddTo = sectionToRealign.begin();
^
In file included from ClustalW/alignment/Alignment.cpp:25:
In file included from ClustalW/alignment/Alignment.h:41:
In file included from ClustalW/alignment/Sequence.h:21:
In file included from ClustalW/alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/alignment/../general/UserParameters.h:22:
In file included from ClustalW/alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/alignment/../general/Utility.h:15:
In file included from ClustalW/alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o
In file included from ClustalW/alignment/AlignmentOutput.cpp:27:
In file included from ClustalW/alignment/AlignmentOutput.h:24:
In file included from ClustalW/alignment/Alignment.h:41:
In file included from ClustalW/alignment/Sequence.h:21:
In file included from ClustalW/alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/alignment/../general/UserParameters.h:22:
In file included from ClustalW/alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/alignment/../general/Utility.h:15:
In file included from ClustalW/alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o
In file included from ClustalW/alignment/ObjectiveScore.cpp:10:
In file included from ClustalW/alignment/ObjectiveScore.h:14:
In file included from ClustalW/alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
In file included from ClustalW/alignment/ObjectiveScore.cpp:10:
ClustalW/alignment/ObjectiveScore.h:40:14: warning: private field 'scale' is not used [-Wunused-private-field]
long scale;
^
ClustalW/alignment/ObjectiveScore.h:41:13: warning: private field 'weightScale' is not used [-Wunused-private-field]
int weightScale;
^
ClustalW/alignment/ObjectiveScore.h:42:13: warning: private field 'sagaGapEx' is not used [-Wunused-private-field]
int sagaGapEx, sagaGapOp;
^
ClustalW/alignment/ObjectiveScore.h:42:24: warning: private field 'sagaGapOp' is not used [-Wunused-private-field]
int sagaGapEx, sagaGapOp;
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o
In file included from ClustalW/alignment/Sequence.cpp:10:
In file included from ClustalW/alignment/Sequence.h:21:
In file included from ClustalW/alignment/../general/userparams.h:8:
In file included from ClustalW/alignment/../general/UserParameters.h:22:
In file included from ClustalW/alignment/../general/utils.h:8:
In file included from ClustalW/alignment/../general/Utility.h:15:
In file included from ClustalW/alignment/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o
In file included from ClustalW/Clustal.cpp:27:
In file included from ./ClustalW/Clustal.h:16:
In file included from ./ClustalW/fileInput/../alignment/../general/clustalw.h:44:
./ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o
In file included from ClustalW/fileInput/ClustalFileParser.cpp:19:
In file included from ClustalW/fileInput/ClustalFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o
In file included from ClustalW/fileInput/EMBLFileParser.cpp:16:
In file included from ClustalW/fileInput/EMBLFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/FileParser.cpp -o ClustalW/fileInput/FileParser.o
ClustalW/fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable]
int n = (*input).inputSeqs.size();
^
In file included from ClustalW/fileInput/FileParser.cpp:14:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/FileReader.cpp -o ClustalW/fileInput/FileReader.o
ClustalW/fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable]
int maxAlnLength; // Get values from the Alignment object.
^
In file included from ClustalW/fileInput/FileReader.cpp:29:
In file included from ClustalW/fileInput/FileReader.h:12:
In file included from ClustalW/fileInput/../alignment/Alignment.h:41:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o
In file included from ClustalW/fileInput/GDEFileParser.cpp:16:
In file included from ClustalW/fileInput/GDEFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o
In file included from ClustalW/fileInput/MSFFileParser.cpp:16:
In file included from ClustalW/fileInput/MSFFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o
In file included from ClustalW/fileInput/PearsonFileParser.cpp:26:
In file included from ClustalW/fileInput/PearsonFileParser.h:14:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o
In file included from ClustalW/fileInput/PIRFileParser.cpp:16:
In file included from ClustalW/fileInput/PIRFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o
In file included from ClustalW/fileInput/RSFFileParser.cpp:16:
In file included from ClustalW/fileInput/RSFFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o
In file included from ClustalW/general/ClustalWResources.cpp:14:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o
In file included from ClustalW/general/OutputFile.cpp:10:
In file included from ClustalW/general/utils.h:8:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o
In file included from ClustalW/general/Stats.cpp:16:
In file included from ClustalW/general/../alignment/Alignment.h:41:
In file included from ClustalW/general/../alignment/Sequence.h:21:
In file included from ClustalW/general/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/general/UserParameters.h:22:
In file included from ClustalW/general/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o
In file included from ClustalW/general/SymMatrix.cpp:10:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o
In file included from ClustalW/general/UserParameters.cpp:24:
In file included from ClustalW/general/UserParameters.h:22:
In file included from ClustalW/general/utils.h:8:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/Utility.cpp -o ClustalW/general/Utility.o
ClustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
int n;
^
In file included from ClustalW/general/Utility.cpp:19:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/Help.cpp -o ClustalW/Help.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o
In file included from ClustalW/interface/CommandLineParser.cpp:13:
In file included from ClustalW/interface/CommandLineParser.h:18:
In file included from ClustalW/interface/../Clustal.h:16:
In file included from ClustalW/interface/../general/clustalw.h:44:
./ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/Iteration.cpp -o ClustalW/multipleAlign/Iteration.o
ClustalW/multipleAlign/Iteration.cpp:171:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count;
^
In file included from ClustalW/multipleAlign/Iteration.cpp:13:
In file included from ClustalW/multipleAlign/Iteration.h:8:
In file included from ClustalW/multipleAlign/../tree/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../tree/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o
In file included from ClustalW/multipleAlign/LowScoreSegProfile.cpp:9:
In file included from ClustalW/multipleAlign/LowScoreSegProfile.h:13:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/MSA.cpp -o ClustalW/multipleAlign/MSA.o
ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
^
In file included from ClustalW/multipleAlign/MSA.cpp:16:
In file included from ClustalW/multipleAlign/MSA.h:10:
In file included from ClustalW/multipleAlign/ProfileBase.h:14:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o
In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.cpp:10:
In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.h:11:
In file included from ClustalW/multipleAlign/ProfileAlignAlgorithm.h:10:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.cpp:10:
ClustalW/multipleAlign/MyersMillerProfileAlign.h:61:13: warning: private field 'matrix' is not used [-Wunused-private-field]
int matrix[32][32];
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o
In file included from ClustalW/multipleAlign/ProfileBase.cpp:9:
In file included from ClustalW/multipleAlign/ProfileBase.h:14:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o
In file included from ClustalW/multipleAlign/ProfileStandard.cpp:9:
In file included from ClustalW/multipleAlign/ProfileStandard.h:9:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o
In file included from ClustalW/multipleAlign/ProfileWithSub.cpp:9:
In file included from ClustalW/multipleAlign/ProfileWithSub.h:9:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o
In file included from ClustalW/pairwise/FastPairwiseAlign.cpp:10:
In file included from ClustalW/pairwise/FastPairwiseAlign.h:9:
In file included from ClustalW/pairwise/PairwiseAlignBase.h:10:
In file included from ClustalW/pairwise/../alignment/Alignment.h:41:
In file included from ClustalW/pairwise/../alignment/Sequence.h:21:
In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/pairwise/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/pairwise/../alignment/../general/Utility.h:15:
In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/pairwise/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o
In file included from ClustalW/pairwise/FullPairwiseAlign.cpp:9:
In file included from ClustalW/pairwise/FullPairwiseAlign.h:9:
In file included from ClustalW/pairwise/PairwiseAlignBase.h:10:
In file included from ClustalW/pairwise/../alignment/Alignment.h:41:
In file included from ClustalW/pairwise/../alignment/Sequence.h:21:
In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/pairwise/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/pairwise/../alignment/../general/Utility.h:15:
In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/pairwise/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/substitutionMatrix/SubMatrix.cpp -o ClustalW/substitutionMatrix/SubMatrix.o
ClustalW/substitutionMatrix/SubMatrix.cpp:697:9: warning: variable 'av1' set but not used [-Wunused-but-set-variable]
int av1, av2, av3, min, max;
^
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
int n, llimit, ulimit;
^
ClustalW/substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
char inline1[1024];
^
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
int n, llimit, ulimit;
^
ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
int nmat;
^
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
int n, llimit, ulimit;
^
ClustalW/substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
int maxRes;
^
ClustalW/substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
int maxRes;
^
In file included from ClustalW/substitutionMatrix/SubMatrix.cpp:15:
In file included from ClustalW/substitutionMatrix/SubMatrix.h:28:
In file included from ClustalW/substitutionMatrix/../general/clustalw.h:44:
ClustalW/substitutionMatrix/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
9 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/ClusterTree.cpp -o ClustalW/tree/ClusterTree.o
ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
int rs = 0, rl = 0;
^
ClustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
int rs = 0, rl = 0;
^
ClustalW/tree/ClusterTree.cpp:967:22: warning: variable 'tempSeed' set but not used [-Wunused-but-set-variable]
unsigned int tempSeed;
^
In file included from ClustalW/tree/ClusterTree.cpp:9:
In file included from ClustalW/tree/ClusterTree.h:20:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o
In file included from ClustalW/tree/ClusterTreeOutput.cpp:9:
In file included from ClustalW/tree/ClusterTreeOutput.h:11:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o
In file included from ClustalW/tree/NJTree.cpp:10:
In file included from ClustalW/tree/NJTree.h:11:
In file included from ClustalW/tree/ClusterTreeAlgorithm.h:12:
In file included from ClustalW/tree/../general/clustalw.h:44:
ClustalW/tree/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o
In file included from ClustalW/tree/Tree.cpp:10:
In file included from ClustalW/tree/Tree.h:13:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o
In file included from ClustalW/tree/TreeInterface.cpp:15:
In file included from ClustalW/tree/TreeInterface.h:19:
In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o
In file included from ClustalW/tree/UnRootedClusterTree.cpp:9:
In file included from ClustalW/tree/UnRootedClusterTree.h:8:
In file included from ClustalW/tree/ClusterTree.h:20:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/Node.cpp -o ClustalW/tree/UPGMA/Node.o
In file included from ClustalW/tree/UPGMA/Node.cpp:7:
In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/RootedClusterTree.cpp -o ClustalW/tree/UPGMA/RootedClusterTree.o
In file included from ClustalW/tree/UPGMA/RootedClusterTree.cpp:9:
In file included from ClustalW/tree/UPGMA/RootedClusterTree.h:8:
In file included from ClustalW/tree/UPGMA/../ClusterTree.h:20:
In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41:
In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:21:
In file included from ClustalW/tree/UPGMA/../../general/userparams.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/RootedGuideTree.cpp -o ClustalW/tree/UPGMA/RootedGuideTree.o
In file included from ClustalW/tree/UPGMA/RootedGuideTree.cpp:10:
In file included from ClustalW/tree/UPGMA/RootedGuideTree.h:17:
In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41:
In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:21:
In file included from ClustalW/tree/UPGMA/../../general/userparams.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/RootedTreeOutput.cpp -o ClustalW/tree/UPGMA/RootedTreeOutput.o
In file included from ClustalW/tree/UPGMA/RootedTreeOutput.cpp:9:
In file included from ClustalW/tree/UPGMA/RootedTreeOutput.h:15:
In file included from ClustalW/tree/UPGMA/RootedGuideTree.h:17:
In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41:
In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:21:
In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp -o ClustalW/tree/UPGMA/UPGMAAlgorithm.o
In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.h:6:
In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/aligngivenpath.cpp -o Muscle/aligngivenpath.o
In file included from Muscle/aligngivenpath.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
const unsigned uLengthB = msaB.GetColCount();
^
Muscle/aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
const unsigned uLengthA = msaA.GetColCount();
^
Muscle/aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^
Muscle/aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^
Muscle/aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^
Muscle/aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^
In file included from Muscle/aligngivenpath.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/aligngivenpathsw.cpp -o Muscle/aligngivenpathsw.o
In file included from Muscle/aligngivenpathsw.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
const unsigned uLengthB = msaB.GetColCount();
^
Muscle/aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
const unsigned uLengthA = msaA.GetColCount();
^
Muscle/aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^
Muscle/aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^
Muscle/aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
const unsigned uColA = uPrefixLengthA - 1;
^
Muscle/aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
const unsigned uColB = uPrefixLengthB - 1;
^
In file included from Muscle/aligngivenpathsw.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/aligntwomsas.cpp -o Muscle/aligntwomsas.o
In file included from Muscle/aligntwomsas.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/aligntwomsas.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/aligntwoprofs.cpp -o Muscle/aligntwoprofs.o
In file included from Muscle/aligntwoprofs.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/aligntwoprofs.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/aln.cpp -o Muscle/aln.o
In file included from Muscle/aln.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/aln.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/alpha.cpp -o Muscle/alpha.o
In file included from Muscle/alpha.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/alpha.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/anchors.cpp -o Muscle/anchors.o
In file included from Muscle/anchors.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
^
In file included from Muscle/anchors.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function]
static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
^
Muscle/anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function]
static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/bittraceback.cpp -o Muscle/bittraceback.o
In file included from Muscle/bittraceback.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
char Bits = TraceBack[uLengthA][uLengthB];
^
In file included from Muscle/bittraceback.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function]
static const char *BitsToStr(char Bits)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/blosum62.cpp -o Muscle/blosum62.o
In file included from Muscle/blosum62.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/blosum62.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/blosumla.cpp -o Muscle/blosumla.o
In file included from Muscle/blosumla.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/blosumla.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable]
static float Blosum62LA[20][20] =
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/clust.cpp -o Muscle/clust.o
In file included from Muscle/clust.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/clust.cpp:186:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
const unsigned uClusterCount = GetClusterCount();
^
Muscle/clust.cpp:206:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
const unsigned uClusterCount = GetClusterCount();
^
Muscle/clust.cpp:365:14: warning: unused variable 'dDistLR' [-Wunused-variable]
const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
^
In file included from Muscle/clust.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/cluster.cpp -o Muscle/cluster.o
In file included from Muscle/cluster.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
bool bFound = false;
^
Muscle/cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
double dMaxDist = 0.0;
^
In file included from Muscle/cluster.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function]
static inline float Max(float d1, float d2)
^
Muscle/cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function]
static inline float Mean(float d1, float d2)
^
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/clwwt.cpp -o Muscle/clwwt.o
In file included from Muscle/clwwt.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/clwwt.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/color.cpp -o Muscle/color.o
In file included from Muscle/color.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
+4, -2, +0, -2, -1, -2, +0, -2, -1, -1, -1, -1, -2, -1, -1, -1, +1, +0, +0, -3, -1, -2, -1, // A
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:8:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // B
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:9:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
+0, -3, +9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -1, -2, -4, // C
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:10:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // D
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // E
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:13:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-2, -3, -2, -3, -3, +6, -3, -1, +0, -3, +0, +0, -3, -4, -3, -3, -2, -2, -1, +1, -1, +3, -3, // F
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:14:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
+0, -1, -3, -1, -2, -3, +6, -2, -4, -2, -4, -3, +0, -2, -2, -2, +0, -2, -3, -2, -1, -3, -2, // G
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:15:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-2, -1, -3, -1, +0, -1, -2, +8, -3, -1, -3, -2, +1, -2, +0, +0, -1, -2, -3, -2, -1, +2, +0, // H
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:16:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, -3, -1, -3, -3, +0, -4, -3, +4, -3, +2, +1, -3, -3, -3, -3, -2, -1, +3, -3, -1, -1, -3, // I
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:17:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, -1, -3, -1, +1, -3, -2, -1, -3, +5, -2, -1, +0, -1, +1, +2, +0, -1, -2, -3, -1, -2, +1, // K
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, -4, -1, -4, -3, +0, -4, -3, +2, -2, +4, +2, -3, -3, -2, -2, -2, -1, +1, -2, -1, -1, -3, // L
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, -3, -1, -3, -2, +0, -3, -2, +1, -1, +2, +5, -2, -2, +0, -1, -1, -1, +1, -1, -1, -1, -2, // M
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-2, +1, -3, +1, +0, -3, +0, +1, -3, +0, -3, -2, +6, -2, +0, +0, +1, +0, -3, -4, -1, -2, +0, // N
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, -1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, +7, -1, -2, -1, -1, -2, -4, -1, -3, -1, // P
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, +0, -3, +0, +2, -3, -2, +0, -3, +1, -2, +0, +0, -1, +5, +1, +0, -1, -2, -2, -1, -1, +2, // Q
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, -2, -3, -2, +0, -3, -2, +0, -3, +2, -2, -1, +0, -2, +1, +5, -1, -1, -3, -3, -1, -2, +0, // R
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
+1, +0, -1, +0, +0, -2, +0, -1, -2, +0, -2, -1, +1, -1, +0, -1, +4, +1, -2, -3, -1, -2, +0, // S
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
+0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, +0, -1, -1, -1, +1, +5, +0, -2, -1, -2, -1, // T
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
+0, -3, -1, -3, -2, -1, -3, -3, +3, -2, +1, +1, -3, -2, -2, -3, -2, +0, +4, -3, -1, -1, -2, // V
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-3, -4, -2, -4, -3, +1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3,+11, -1, +2, -3, // W
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, // X
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-2, -3, -2, -3, -2, +3, -3, +2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, +2, -1, +7, -2, // Y
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/color.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // Z
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
In file included from Muscle/color.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function]
static int BlosumScore(char c1, char c2)
^
26 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/cons.cpp -o Muscle/cons.o
In file included from Muscle/cons.cpp:7:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/cons.cpp:7:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/diaglist.cpp -o Muscle/diaglist.o
In file included from Muscle/diaglist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/diaglist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/diffobjscore.cpp -o Muscle/diffobjscore.o
In file included from Muscle/diffobjscore.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
const unsigned uSeqCount = msa.GetSeqCount();
^
Muscle/diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
const unsigned uColCount = msa.GetColCount();
^
In file included from Muscle/diffobjscore.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/diffpaths.cpp -o Muscle/diffpaths.o
In file included from Muscle/diffpaths.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/diffpaths.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/difftrees.cpp -o Muscle/difftrees.o
In file included from Muscle/difftrees.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
const unsigned uLeafCount2 = Tree2.GetLeafCount();
^
In file included from Muscle/difftrees.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/difftreese.cpp -o Muscle/difftreese.o
In file included from Muscle/difftreese.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/difftreese.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/distcalc.cpp -o Muscle/distcalc.o
In file included from Muscle/distcalc.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/distcalc.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/distfunc.cpp -o Muscle/distfunc.o
In file included from Muscle/distfunc.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/distfunc.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/distpwkimura.cpp -o Muscle/distpwkimura.o
In file included from Muscle/distpwkimura.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/distpwkimura.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/domuscle.cpp -o Muscle/domuscle.o
In file included from Muscle/domuscle.cpp:1:
In file included from ./RMuscle.h:4:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
int PNlength = (msaInput->inputSeqs).Length();
^
In file included from Muscle/domuscle.cpp:1:
In file included from ./RMuscle.h:4:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/dosp.cpp -o Muscle/dosp.o
In file included from Muscle/dosp.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/dosp.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/dpreglist.cpp -o Muscle/dpreglist.o
In file included from Muscle/dpreglist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
^
In file included from Muscle/dpreglist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/drawtree.cpp -o Muscle/drawtree.o
In file included from Muscle/drawtree.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/drawtree.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/edgelist.cpp -o Muscle/edgelist.o
In file included from Muscle/edgelist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/edgelist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/enumopts.cpp -o Muscle/enumopts.o
In file included from Muscle/enumopts.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, Amino)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:196:1: note: expanded from here
"Amino"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, DNA)
^~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:199:1: note: expanded from here
"DNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, RNA)
^~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:202:1: note: expanded from here
"RNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(ALPHA)
^~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:18:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, Protein)
^~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:206:1: note: expanded from here
"Protein"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, DNA)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:209:1: note: expanded from here
"DNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, RNA)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:212:1: note: expanded from here
"RNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, Auto)
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:215:1: note: expanded from here
"Auto"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(SEQTYPE)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:25:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, Pseudo)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:219:1: note: expanded from here
"Pseudo"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, MidLongestSpan)
^~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:222:1: note: expanded from here
"MidLongestSpan"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, MinAvgLeafDist)
^~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:225:1: note: expanded from here
"MinAvgLeafDist"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(ROOT)
^~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:31:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMA)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:229:1: note: expanded from here
"UPGMA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMAMax)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:232:1: note: expanded from here
"UPGMAMax"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMAMin)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:235:1: note: expanded from here
"UPGMAMin"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMB)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:238:1: note: expanded from here
"UPGMB"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, NeighborJoining)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:241:1: note: expanded from here
"NeighborJoining"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(CLUSTER)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:39:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(JOIN, NearestNeighbor)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:245:1: note: expanded from here
"NearestNeighbor"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(JOIN, NeighborJoining)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:248:1: note: expanded from here
"NeighborJoining"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(JOIN)
^~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:44:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Min)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:252:1: note: expanded from here
"Min"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Avg)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:255:1: note: expanded from here
"Avg"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Max)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:258:1: note: expanded from here
"Max"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, NeighborJoining)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:261:1: note: expanded from here
"NeighborJoining"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Biased)
^~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:264:1: note: expanded from here
"Biased"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(LINKAGE)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:52:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer6_6)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:268:1: note: expanded from here
"Kmer6_6"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer20_3)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:271:1: note: expanded from here
"Kmer20_3"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer20_4)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:274:1: note: expanded from here
"Kmer20_4"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kbit20_3)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:277:1: note: expanded from here
"Kbit20_3"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer4_6)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:280:1: note: expanded from here
"Kmer4_6"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PctIdKimura)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:283:1: note: expanded from here
"PctIdKimura"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PctIdLog)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:286:1: note: expanded from here
"PctIdLog"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PWKimura)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:289:1: note: expanded from here
"PWKimura"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PWScoreDist)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:292:1: note: expanded from here
"PWScoreDist"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, ScoreDist)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:295:1: note: expanded from here
"ScoreDist"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Edit)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:298:1: note: expanded from here
"Edit"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(DISTANCE)
^~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:66:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, LE)
^~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:302:1: note: expanded from here
"LE"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SP)
^~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:305:1: note: expanded from here
"SP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SV)
^~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:308:1: note: expanded from here
"SV"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SPN)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:311:1: note: expanded from here
"SPN"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(PPSCORE)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:73:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, None)
^~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:315:1: note: expanded from here
"None"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, Henikoff)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:318:1: note: expanded from here
"Henikoff"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, HenikoffPB)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:321:1: note: expanded from here
"HenikoffPB"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, GSC)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:324:1: note: expanded from here
"GSC"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, ClustalW)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:327:1: note: expanded from here
"ClustalW"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, ThreeWay)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:330:1: note: expanded from here
"ThreeWay"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(SEQWEIGHT)
^~~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:82:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SP) // Sum of Pairs of sequences
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:3:1: note: expanded from here
"SP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, DP) // Dynamic Programming score
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:6:1: note: expanded from here
"DP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:9:1: note: expanded from here
"XP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, PS) // sum of Prof-Seq score for all seqs in MSA
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:12:1: note: expanded from here
"PS"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SPF) // sum of pairs, fast approximation
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:15:1: note: expanded from here
"SPF"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:18:1: note: expanded from here
"SPM"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(OBJSCORE)
^~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:91:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Full)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:22:1: note: expanded from here
"Full"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Half)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:25:1: note: expanded from here
"Half"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Ext)
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x) #x, t##_##x,
^~~~~~~~~~~
<scratch space>:28:1: note: expanded from here
"Ext"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(TERMGAPS)
^~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t) 0, 0 };
^~~~
In file included from Muscle/enumopts.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
65 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/enumtostr.cpp -o Muscle/enumtostr.o
In file included from Muscle/enumtostr.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/enumtostr.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/estring.cpp -o Muscle/estring.o
In file included from Muscle/estring.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if (nB > 0)
^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
switch (cType)
^~~~~
Muscle/estring.cpp:397:4: note: remove the 'if' if its condition is always true
if (nB > 0)
^~~~~~~~~~~
Muscle/estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (nA < 0)
^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
switch (cType)
^~~~~
Muscle/estring.cpp:395:8: note: remove the 'if' if its condition is always true
else if (nA < 0)
^~~~~~~~~~~
Muscle/estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (nB < 0)
^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
switch (cType)
^~~~~
Muscle/estring.cpp:386:9: note: remove the 'if' if its condition is always true
else if (nB < 0)
^~~~~~~~~~~
Muscle/estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning
char cType;
^
= '\0'
In file included from Muscle/estring.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function]
static bool CanMultiplyEstrings(const short es1[], const short es2[])
^
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fasta.cpp -o Muscle/fasta.o
In file included from Muscle/fasta.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
unsigned uSeqCount = 0;
^
Muscle/fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
unsigned uColCount = uInsane;
^
In file included from Muscle/fasta.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fasta2.cpp -o Muscle/fasta2.o
In file included from Muscle/fasta2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/fasta2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastclust.cpp -o Muscle/fastclust.o
In file included from Muscle/fastclust.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/fastclust.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastdist.cpp -o Muscle/fastdist.o
In file included from Muscle/fastdist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/fastdist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastdistjones.cpp -o Muscle/fastdistjones.o
In file included from Muscle/fastdistjones.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/fastdistjones.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastdistkbit.cpp -o Muscle/fastdistkbit.o
In file included from Muscle/fastdistkbit.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/fastdistkbit.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastdistkmer.cpp -o Muscle/fastdistkmer.o
In file included from Muscle/fastdistkmer.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
double KD = KimuraDist(EstimatedPctId);
^
In file included from Muscle/fastdistkmer.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastdistmafft.cpp -o Muscle/fastdistmafft.o
In file included from Muscle/fastdistmafft.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
const char *pName1 = s1.GetName();
^
In file included from Muscle/fastdistmafft.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function]
static void ListCount(const unsigned char Count[])
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastdistnuc.cpp -o Muscle/fastdistnuc.o
In file included from Muscle/fastdistnuc.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
const char *pName1 = s1.GetName();
^
In file included from Muscle/fastdistnuc.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable]
static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
^
Muscle/fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function]
static void ListCount(const unsigned char Count[])
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/fastscorepath2.cpp -o Muscle/fastscorepath2.o
In file included from Muscle/fastscorepath2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/fastscorepath2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/finddiags.cpp -o Muscle/finddiags.o
In file included from Muscle/finddiags.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/finddiags.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function]
static char *TupleToStr(int t)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/finddiagsn.cpp -o Muscle/finddiagsn.o
In file included from Muscle/finddiagsn.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/finddiagsn.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function]
static char *TupleToStr(int t)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalign.cpp -o Muscle/glbalign.o
In file included from Muscle/glbalign.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalign.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalign352.cpp -o Muscle/glbalign352.o
In file included from Muscle/glbalign352.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalign352.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbaligndiag.cpp -o Muscle/glbaligndiag.o
In file included from Muscle/glbaligndiag.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbaligndiag.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalignla.cpp -o Muscle/glbalignla.o
In file included from Muscle/glbalignla.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalignla.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalignle.cpp -o Muscle/glbalignle.o
In file included from Muscle/glbalignle.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalignle.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalignns.cpp -o Muscle/glbalignns.o
In file included from Muscle/glbalignns.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalignns.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalignsimple.cpp -o Muscle/glbalignsimple.o
In file included from Muscle/glbalignsimple.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalignsimple.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function]
static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
^
Muscle/glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalignsp.cpp -o Muscle/glbalignsp.o
In file included from Muscle/glbalignsp.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalignsp.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalignspn.cpp -o Muscle/glbalignspn.o
In file included from Muscle/glbalignspn.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalignspn.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalignss.cpp -o Muscle/glbalignss.o
In file included from Muscle/glbalignss.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
const SCORE *ptrRowA = MxRowA[i];
^
Muscle/glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
const unsigned uPrefixCountA = uLengthA + 1;
^
Muscle/glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
const unsigned uPrefixCountB = uLengthB + 1;
^
In file included from Muscle/glbalignss.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function]
static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
^
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o
In file included from Muscle/glbalndimer.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/glbalndimer.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/globals.cpp -o Muscle/globals.o
In file included from Muscle/globals.cpp:6:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/globals.cpp:6:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/globalslinux.cpp -o Muscle/globalslinux.o
In file included from Muscle/globalslinux.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/globalslinux.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/globalsother.cpp -o Muscle/globalsother.o
In file included from Muscle/globalsother.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/globalsother.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/gonnet.cpp -o Muscle/gonnet.o
In file included from Muscle/gonnet.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/gonnet.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable]
static SCORE Gonnet160[20][20] =
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/gotowt.cpp -o Muscle/gotowt.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/henikoffweight.cpp -o Muscle/henikoffweight.o
In file included from Muscle/henikoffweight.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/henikoffweight.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/henikoffweightpb.cpp -o Muscle/henikoffweightpb.o
In file included from Muscle/henikoffweightpb.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/henikoffweightpb.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/html.cpp -o Muscle/html.o
In file included from Muscle/html.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/html.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/hydro.cpp -o Muscle/hydro.o
In file included from Muscle/hydro.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/hydro.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/intmath.cpp -o Muscle/intmath.o
In file included from Muscle/intmath.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/intmath.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/local.cpp -o Muscle/local.o
In file included from Muscle/local.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/local.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/main.cpp -o Muscle/main.o
In file included from Muscle/main.cpp:3:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/main.cpp:3:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/makerootmsa.cpp -o Muscle/makerootmsa.o
In file included from Muscle/makerootmsa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
const unsigned uSeqLength = s.Length();
^
Muscle/makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
const PWPath &Path = Nodes[uNodeIndex].m_Path;
^
Muscle/makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
^
In file included from Muscle/makerootmsa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function]
static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
^
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/makerootmsab.cpp -o Muscle/makerootmsab.o
In file included from Muscle/makerootmsab.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/makerootmsab.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/maketree.cpp -o Muscle/maketree.o
In file included from Muscle/maketree.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/maketree.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/mhack.cpp -o Muscle/mhack.o
In file included from Muscle/mhack.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/mhack.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/mpam200.cpp -o Muscle/mpam200.o
In file included from Muscle/mpam200.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/mpam200.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/msa.cpp -o Muscle/msa.o
In file included from Muscle/msa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/msa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function]
static void FmtChar(char c, unsigned uWidth)
^
Muscle/msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function]
static void FmtInt(unsigned u, unsigned uWidth)
^
Muscle/msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function]
static void FmtInt0(unsigned u, unsigned uWidth)
^
Muscle/msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function]
static void FmtPad(unsigned n)
^
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/msa2.cpp -o Muscle/msa2.o
In file included from Muscle/msa2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/msa2.cpp:479:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
const unsigned uColCountCat = uColCount1 + uColCount2;
^
In file included from Muscle/msa2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/msadistkimura.cpp -o Muscle/msadistkimura.o
In file included from Muscle/msadistkimura.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/msadistkimura.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/msf.cpp -o Muscle/msf.o
In file included from Muscle/msf.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/msf.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function]
static const char *strfind(const char *s, const char *t)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/muscle.cpp -o Muscle/muscle.o
In file included from Muscle/muscle.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/muscle.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/muscleout.cpp -o Muscle/muscleout.o
In file included from Muscle/muscleout.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/muscleout.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/nucmx.cpp -o Muscle/nucmx.o
In file included from Muscle/nucmx.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/nucmx.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/nwdasimple.cpp -o Muscle/nwdasimple.o
In file included from Muscle/nwdasimple.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/nwdasimple.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/nwdasimple2.cpp -o Muscle/nwdasimple2.o
In file included from Muscle/nwdasimple2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/nwdasimple2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/nwdasmall.cpp -o Muscle/nwdasmall.o
In file included from Muscle/nwdasmall.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/nwdasmall.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/nwrec.cpp -o Muscle/nwrec.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/nwsmall.cpp -o Muscle/nwsmall.o
In file included from Muscle/nwsmall.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/nwsmall.cpp:394:14: note: uninitialized use occurs here
TB[i][j] |= Bit;
^~~
Muscle/nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning
char Bit;
^
= '\0'
Muscle/nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/nwsmall.cpp:412:14: note: uninitialized use occurs here
TB[i][j] |= Bit;
^~~
Muscle/nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning
char Bit;
^
= '\0'
Muscle/nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/nwsmall.cpp:430:14: note: uninitialized use occurs here
TB[i][j] |= Bit;
^~~
Muscle/nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning
char Bit;
^
= '\0'
In file included from Muscle/nwsmall.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function]
static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c)
^
Muscle/nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function]
static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c)
^
7 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/objscore.cpp -o Muscle/objscore.o
In file included from Muscle/objscore.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/objscore.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/objscore2.cpp -o Muscle/objscore2.o
In file included from Muscle/objscore2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/objscore2.cpp:65:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
SCORE scoreGaps = 0;
^
Muscle/objscore2.cpp:85:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
bool bRightTermGap = false;
^
Muscle/objscore2.cpp:66:7: warning: unused variable 'bGapping1' [-Wunused-variable]
bool bGapping1 = false;
^
Muscle/objscore2.cpp:70:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
bool bLeftTermGap = false;
^
Muscle/objscore2.cpp:67:7: warning: unused variable 'bGapping2' [-Wunused-variable]
bool bGapping2 = false;
^
Muscle/objscore2.cpp:143:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
bool bLeftTermGap = false;
^
Muscle/objscore2.cpp:158:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
bool bRightTermGap = false;
^
Muscle/objscore2.cpp:317:17: warning: unused variable 'uColCount2' [-Wunused-variable]
const unsigned uColCount2 = msa2.GetColCount();
^
Muscle/objscore2.cpp:496:17: warning: unused variable 'w' [-Wunused-variable]
const WEIGHT w = w1*w2;
^
In file included from Muscle/objscore2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
11 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/objscoreda.cpp -o Muscle/objscoreda.o
In file included from Muscle/objscoreda.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/objscoreda.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/onexception.cpp -o Muscle/onexception.o
In file included from Muscle/onexception.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/onexception.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/options.cpp -o Muscle/options.o
In file included from Muscle/options.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/options.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"in", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"in1", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"in2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"out", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MaxIters", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MaxHours", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"GapOpen", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"GapOpen2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"GapExtend", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"GapExtend2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"GapAmbig", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Center", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SmoothScoreCeil", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MinBestColScore", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MinSmoothScore", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"ObjScore", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SmoothWindow", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"RefineWindow", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"FromWindow", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"ToWindow", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SaveWindow", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"WindowOffset", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"FirstWindow", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"AnchorSpacing", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Log", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"LogA", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MaxTrees", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SUEFF", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Distance", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Distance1", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Distance2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Weight", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Weight1", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Weight2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Cluster", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Cluster1", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Cluster2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Root1", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Root2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Tree1", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Tree2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"UseTree", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"UseTree_NoWarn", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"DiagLength", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"DiagMargin", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"DiagBreak", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Hydro", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"HydroFactor", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SPScore", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SeqType", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MaxMB", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"ComputeWeights", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MaxSubFam", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"ScoreFile", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"TermGaps", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"FASTAOut", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"CLWOut", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"CLWStrictOut", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"HTMLOut", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MSFOut", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"PHYIOut", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"PHYSOut", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:81:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Matrix", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:82:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"DistMx1", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:83:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"DistMx2", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:84:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Weight", 0,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:90:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"LE", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:91:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SP", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SV", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SPN", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Core", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"NoCore", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Diags1", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Diags2", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Diags", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Quiet", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MSF", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Verbose", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Anchors", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"NoAnchors", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Refine", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"RefineW", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"SW", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Profile", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"PPScore", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"ClusterOnly", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Brenner", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Dimer", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"clw", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"clwstrict", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"HTML", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Version", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Stable", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"Group", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"FASTA", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"ProfDB", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"PAS", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"PHYI", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"PHYS", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"TomHydro", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/options.cpp:124:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
"MakeTree", false,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
In file included from Muscle/options.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
103 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/outweights.cpp -o Muscle/outweights.o
In file included from Muscle/outweights.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/outweights.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/pam200mafft.cpp -o Muscle/pam200mafft.o
In file included from Muscle/pam200mafft.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
408, 20, 54, 52, -182, 179, -68, 109, -35, -47, 39, 106, 206, -14, -12, 257, 293, 191, -306, -219, 0, 0, 0, // A
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:10:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
20, 1190, -228, -295, 94, 6, 63, -131, -184, -176, -112, -29, -122, -195, 49, 185, 13, -49, 199, 333, 0, 0, 0, // C
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:11:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
54, -228, 645, 516, -399, 168, 98, -225, 75, -341, -235, 352, -149, 142, -44, 65, 7, -147, -418, -128, 0, 0, 0, // D
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:12:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
52, -295, 516, 630, -460, 145, 45, -225, 195, -307, -222, 186, -121, 299, 54, -10, -36, -130, -366, -285, 0, 0, 0, // E
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:13:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-182, 94, -399, -460, 908, -387, 82, 100, -423, 340, 87, -216, -160, -274, -307, -31, -153, 51, 19, 604, 0, 0, 0, // F
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:14:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
179, 6, 168, 145, -387, 682, -94, -196, -14, -304, -226, 99, -57, -48, 117, 175, 41, -73, -38, -329, 0, 0, 0, // G
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:15:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-68, 63, 98, 45, 82, -94, 786, -185, 164, -72, -132, 258, 86, 388, 277, 55, -15, -197, -181, 488, 0, 0, 0, // H
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:16:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
109, -131, -225, -225, 100, -196, -185, 574, -204, 308, 411, -94, -95, -202, -188, 1, 182, 489, -254, -133, 0, 0, 0, // I
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:17:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-35, -184, 75, 195, -423, -14, 164, -204, 652, -229, -98, 206, -66, 335, 486, 22, 39, -207, -196, -244, 0, 0, 0, // K
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:18:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-47, -176, -341, -307, 340, -304, -72, 308, -229, 611, 389, -203, 73, -66, -150, -49, -21, 259, -46, -9, 0, 0, 0, // L
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:19:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
39, -112, -235, -222, 87, -226, -132, 411, -98, 389, 776, -111, -78, -104, -109, -29, 149, 351, -209, -162, 0, 0, 0, // M
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:20:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
106, -29, 352, 186, -216, 99, 258, -94, 206, -203, -111, 536, -1, 108, 93, 260, 188, -98, -359, 12, 0, 0, 0, // N
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:21:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
206, -122, -149, -121, -160, -57, 86, -95, -66, 73, -78, -1, 756, 142, 25, 241, 159, -55, -353, -206, 0, 0, 0, // P
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:22:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-14, -195, 142, 299, -274, -48, 388, -202, 335, -66, -104, 108, 142, 655, 321, 7, -15, -175, -223, -53, 0, 0, 0, // Q
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:23:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-12, 49, -44, 54, -307, 117, 277, -188, 486, -150, -109, 93, 25, 321, 626, 48, 16, -181, 124, -113, 0, 0, 0, // R
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:24:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
257, 185, 65, -10, -31, 175, 55, 1, 22, -49, -29, 260, 241, 7, 48, 373, 279, 28, -193, -35, 0, 0, 0, // S
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:25:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
293, 13, 7, -36, -153, 41, -15, 182, 39, -21, 149, 188, 159, -15, 16, 279, 442, 163, -323, -170, 0, 0, 0, // T
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:26:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
191, -49, -147, -130, 51, -73, -197, 489, -207, 259, 351, -98, -55, -175, -181, 28, 163, 525, -225, -177, 0, 0, 0, // V
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-306, 199, -418, -366, 19, -38, -181, -254, -196, -46, -209, -359, -353, -223, 124, -193, -323, -225, 1495, 83, 0, 0, 0, // W
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-219, 333, -128, -285, 604, -329, 488, -133, -244, -9, -162, 12, -206, -53, -113, -35, -170, -177, 83, 999, 0, 0, 0, // Y
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:29:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // B
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:30:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // Z
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
Muscle/pam200mafft.cpp:31:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // X
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
In file included from Muscle/pam200mafft.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable]
static float PAM200[23][23] =
^
26 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/params.cpp -o Muscle/params.o
In file included from Muscle/params.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/params.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/phy.cpp -o Muscle/phy.o
In file included from Muscle/phy.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
double dEdgeLength = GetEdgeLength(uNode1, uNode2);
^
In file included from Muscle/phy.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/phy2.cpp -o Muscle/phy2.o
In file included from Muscle/phy2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/phy2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/phy3.cpp -o Muscle/phy3.o
In file included from Muscle/phy3.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
^
Muscle/phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
double dAllMaxDist = -1e20;
^
Muscle/phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
unsigned uMaxTo = NULL_NEIGHBOR;
^
Muscle/phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
unsigned uMaxFrom = NULL_NEIGHBOR;
^
Muscle/phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
const unsigned uLeafCount = tree.GetLeafCount();
^
Muscle/phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
unsigned uMostDistantLeaf = NULL_NEIGHBOR;
^
In file included from Muscle/phy3.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function]
static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
^
9 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/phy4.cpp -o Muscle/phy4.o
In file included from Muscle/phy4.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/phy4.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/phyfromclust.cpp -o Muscle/phyfromclust.o
In file included from Muscle/phyfromclust.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/phyfromclust.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/phyfromfile.cpp -o Muscle/phyfromfile.o
In file included from Muscle/phyfromfile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/phyfromfile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/physeq.cpp -o Muscle/physeq.o
In file included from Muscle/physeq.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/physeq.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/phytofile.cpp -o Muscle/phytofile.o
In file included from Muscle/phytofile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/phytofile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/posgap.cpp -o Muscle/posgap.o
In file included from Muscle/posgap.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/posgap.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/ppscore.cpp -o Muscle/ppscore.o
In file included from Muscle/ppscore.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/ppscore.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/profdb.cpp -o Muscle/profdb.o
In file included from Muscle/profdb.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/profdb.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/profile.cpp -o Muscle/profile.o
In file included from Muscle/profile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/profile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/profilefrommsa.cpp -o Muscle/profilefrommsa.o
In file included from Muscle/profilefrommsa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/profilefrommsa.cpp:248:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
const unsigned uSeqCount = a.GetSeqCount();
^
Muscle/profilefrommsa.cpp:256:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
unsigned uHydrophobicRunLength = 0;
^
In file included from Muscle/profilefrommsa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/progalign.cpp -o Muscle/progalign.o
In file included from Muscle/progalign.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
const unsigned uIterCount = uSeqCount - 1;
^
In file included from Muscle/progalign.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/progress.cpp -o Muscle/progress.o
In file included from Muscle/progress.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/progress.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/progressivealign.cpp -o Muscle/progressivealign.o
In file included from Muscle/progressivealign.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/progressivealign.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/pwpath.cpp -o Muscle/pwpath.o
In file included from Muscle/pwpath.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
^
Muscle/pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
unsigned uEdgeIndex = 0;
^
In file included from Muscle/pwpath.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/readmx.cpp -o Muscle/readmx.o
In file included from Muscle/readmx.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/readmx.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function]
static unsigned MxCharToLetter(char c)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/realigndiffs.cpp -o Muscle/realigndiffs.o
In file included from Muscle/realigndiffs.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/realigndiffs.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/realigndiffse.cpp -o Muscle/realigndiffse.o
In file included from Muscle/realigndiffse.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable]
unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
^
Muscle/realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable]
unsigned uOldRight = OldTree.GetRight(uOld);
^
In file included from Muscle/realigndiffse.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/refine.cpp -o Muscle/refine.o
In file included from Muscle/refine.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/refine.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/refinehoriz.cpp -o Muscle/refinehoriz.o
In file included from Muscle/refinehoriz.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/refinehoriz.cpp:260:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/refinehoriz.cpp:263:56: note: uninitialized use occurs here
RefineHeightParts(msaIn, tree, Internals, bReverse, bRight,
^~~~~~
Muscle/refinehoriz.cpp:251:15: note: initialize the variable 'bRight' to silence this warning
bool bRight;
^
= false
In file included from Muscle/refinehoriz.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/refinesubfams.cpp -o Muscle/refinesubfams.o
In file included from Muscle/refinesubfams.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
const unsigned uNodeCount = tree.GetNodeCount();
^
In file included from Muscle/refinesubfams.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/refinetree.cpp -o Muscle/refinetree.o
In file included from Muscle/refinetree.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/refinetree.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/refinetreee.cpp -o Muscle/refinetreee.o
In file included from Muscle/refinetreee.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/refinetreee.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/refinevert.cpp -o Muscle/refinevert.o
In file included from Muscle/refinevert.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/refinevert.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/refinew.cpp -o Muscle/refinew.o
In file included from Muscle/refinew.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/refinew.cpp:23:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
const unsigned uColCountCat = uColCount1 + uColCount2;
^
Muscle/refinew.cpp:128:13: warning: unused variable 'uOutCols' [-Wunused-variable]
unsigned uOutCols = msaOut.GetColCount();
^
In file included from Muscle/refinew.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/savebest.cpp -o Muscle/savebest.o
In file included from Muscle/savebest.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/savebest.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/scoredist.cpp -o Muscle/scoredist.o
In file included from Muscle/scoredist.cpp:3:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/scoredist.cpp:3:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable]
static const double Dayhoff_CalibrationFactor = 1.3370;
^
Muscle/scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable]
static const double MV_CalibrationFactor = 1.1775;
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/scoregaps.cpp -o Muscle/scoregaps.o
In file included from Muscle/scoregaps.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/scoregaps.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function]
static void FreeGapInfo(GAPINFO *GI)
^
Muscle/scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function]
static SCORE Penalty(unsigned Length, bool Term)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/scorehistory.cpp -o Muscle/scorehistory.o
In file included from Muscle/scorehistory.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/scorehistory.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/scorepp.cpp -o Muscle/scorepp.o
In file included from Muscle/scorepp.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/scorepp.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/seq.cpp -o Muscle/seq.o
In file included from Muscle/seq.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/seq.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/seqvect.cpp -o Muscle/seqvect.o
In file included from Muscle/seqvect.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
return (Seq &) *((Seq *) 0);
^~~~~~~~~~~~
In file included from Muscle/seqvect.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable]
const size_t MAX_FASTA_LINE = 16000;
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/setblosumweights.cpp -o Muscle/setblosumweights.o
In file included from Muscle/setblosumweights.cpp:42:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/setblosumweights.cpp:42:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/setgscweights.cpp -o Muscle/setgscweights.o
In file included from Muscle/setgscweights.cpp:104:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/setgscweights.cpp:104:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/setnewhandler.cpp -o Muscle/setnewhandler.o
In file included from Muscle/setnewhandler.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/setnewhandler.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/spfast.cpp -o Muscle/spfast.o
In file included from Muscle/spfast.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
const unsigned uSeqCount = msa.GetSeqCount();
^
In file included from Muscle/spfast.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function]
static const char *GapTypeToStr(int GapType)
^
Muscle/spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function]
static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/sptest.cpp -o Muscle/sptest.o
In file included from Muscle/sptest.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/sptest.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/stabilize.cpp -o Muscle/stabilize.o
In file included from Muscle/stabilize.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/stabilize.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/subfam.cpp -o Muscle/subfam.o
In file included from Muscle/subfam.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
int NotUsed = system(CmdLine);
^
In file included from Muscle/subfam.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/subfams.cpp -o Muscle/subfams.o
In file included from Muscle/subfams.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/subfams.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function]
static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
^
Muscle/subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function]
static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
^
Muscle/subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function]
static void Relax(DistFunc &DF, unsigned u, unsigned v)
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/sw.cpp -o Muscle/sw.o
In file included from Muscle/sw.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/sw.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/termgaps.cpp -o Muscle/termgaps.o
In file included from Muscle/termgaps.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/termgaps.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/textfile.cpp -o Muscle/textfile.o
In file included from Muscle/textfile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/textfile.cpp:107:6: warning: unused variable 'i' [-Wunused-variable]
int i = fputc(c, m_ptrFile);
^
Muscle/textfile.cpp:120:6: warning: unused variable 'iError' [-Wunused-variable]
int iError = fputs(szLine, m_ptrFile);
^
In file included from Muscle/textfile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/threewaywt.cpp -o Muscle/threewaywt.o
In file included from Muscle/threewaywt.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/threewaywt.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/tomhydro.cpp -o Muscle/tomhydro.o
In file included from Muscle/tomhydro.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/tomhydro.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/traceback.cpp -o Muscle/traceback.o
In file included from Muscle/traceback.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
const unsigned uPrefixCountB = uLengthB + 1;
^
Muscle/traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (EQ(Score, scoreSI))
^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b) (fabs(a-b) < 0.1)
^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/traceback.cpp:186:9: note: remove the 'if' if its condition is always true
else if (EQ(Score, scoreSI))
^~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (EQ(Score, scoreSD))
^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b) (fabs(a-b) < 0.1)
^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/traceback.cpp:150:9: note: remove the 'if' if its condition is always true
else if (EQ(Score, scoreSD))
^~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (EQ(scoreSM, Score))
^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b) (fabs(a-b) < 0.1)
^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/traceback.cpp:112:9: note: remove the 'if' if its condition is always true
else if (EQ(scoreSM, Score))
^~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
char cPrevEdgeType;
^
= '\0'
In file included from Muscle/traceback.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
7 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/tracebackopt.cpp -o Muscle/tracebackopt.o
In file included from Muscle/tracebackopt.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/tracebackopt.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/tracebacksw.cpp -o Muscle/tracebacksw.o
In file included from Muscle/tracebacksw.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
^
Muscle/tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
const unsigned uPrefixCountB = uLengthB + 1;
^
Muscle/tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (EQ(Score, scoreSI))
^~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b) (fabs(a-b) < 0.1)
^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true
else if (EQ(Score, scoreSI))
^~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (EQ(Score, scoreSD))
^~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b) (fabs(a-b) < 0.1)
^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true
else if (EQ(Score, scoreSD))
^~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (EQ(scoreMatch, Score))
^~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b) (fabs(a-b) < 0.1)
^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
cEdgeType = cPrevEdgeType;
^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true
else if (EQ(scoreMatch, Score))
^~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
char cPrevEdgeType;
^
= '\0'
In file included from Muscle/tracebacksw.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/treefrommsa.cpp -o Muscle/treefrommsa.o
In file included from Muscle/treefrommsa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/treefrommsa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/typetostr.cpp -o Muscle/typetostr.o
In file included from Muscle/typetostr.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/typetostr.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/upgma2.cpp -o Muscle/upgma2.o
In file included from Muscle/upgma2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/upgma2.cpp:292:17: note: uninitialized use occurs here
g_Dist[vL] = dtNewDist;
^~~~~~~~~
Muscle/upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning
dist_t dtNewDist;
^
= 0.0
Muscle/upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
0, 2, 14, 14, 20,
^~~~~~~~~~~~~~~~~
{ }
Muscle/upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
2, 0, 14, 14, 20,
^~~~~~~~~~~~~~~~~
{ }
Muscle/upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
14, 14, 0, 4, 20,
^~~~~~~~~~~~~~~~~~
{ }
Muscle/upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
14, 14, 4, 0, 20,
^~~~~~~~~~~~~~~~~~
{ }
Muscle/upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
20, 20, 20, 20, 0,
^~~~~~~~~~~~~~~~~~
{ }
In file included from Muscle/upgma2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
Muscle/upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function]
static void ListState()
^
9 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/usage.cpp -o Muscle/usage.o
In file included from Muscle/usage.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/usage.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/validateids.cpp -o Muscle/validateids.o
In file included from Muscle/validateids.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/validateids.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/vtml2.cpp -o Muscle/vtml2.o
In file included from Muscle/vtml2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from Muscle/vtml2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Muscle/writescorefile.cpp -o Muscle/writescorefile.o
In file included from Muscle/writescorefile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
Muscle/writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
Muscle/writescorefile.cpp:40:12: note: uninitialized use occurs here
dSum += Score;
^~~~~
Muscle/writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning
double Score;
^
= 0.0
In file included from Muscle/writescorefile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RClustalW.cpp -o RClustalW.o
In file included from RClustalW.cpp:2:
In file included from ./RClustalWMain.h:6:
In file included from ./ClustalW/general/clustalw.h:44:
./ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RClustalWMain.cpp -o RClustalWMain.o
In file included from RClustalWMain.cpp:5:
In file included from ./ClustalW/fileInput/../alignment/Alignment.h:41:
In file included from ./ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ./ClustalW/interface/../general/userparams.h:8:
In file included from ./ClustalW/general/UserParameters.h:22:
In file included from ./ClustalW/interface/../general/utils.h:8:
In file included from ./ClustalW/general/Utility.h:15:
In file included from ./ClustalW/interface/../general/clustalw.h:44:
./ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
int firstSeq, numSeqsInSub;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RMuscle.cpp -o RMuscle.o
In file included from RMuscle.cpp:1:
In file included from ./RMuscle.h:4:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp) ((void)0)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e) ((void)0)
^
In file included from RMuscle.cpp:1:
In file included from ./RMuscle.h:4:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ushuffle.c -o ushuffle.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ushuffler.cpp -o ushuffler.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o enhancerHomologSearch.so ClustalW/alignment/Alignment.o ClustalW/alignment/AlignmentOutput.o ClustalW/alignment/ObjectiveScore.o ClustalW/alignment/Sequence.o ClustalW/Clustal.o ClustalW/fileInput/ClustalFileParser.o ClustalW/fileInput/EMBLFileParser.o ClustalW/fileInput/FileParser.o ClustalW/fileInput/FileReader.o ClustalW/fileInput/GDEFileParser.o ClustalW/fileInput/InFileStream.o ClustalW/fileInput/MSFFileParser.o ClustalW/fileInput/PearsonFileParser.o ClustalW/fileInput/PIRFileParser.o ClustalW/fileInput/RSFFileParser.o ClustalW/general/ClustalWResources.o ClustalW/general/DebugLog.o ClustalW/general/InvalidCombination.o ClustalW/general/OutputFile.o ClustalW/general/Stats.o ClustalW/general/SymMatrix.o ClustalW/general/UserParameters.o ClustalW/general/Utility.o ClustalW/general/VectorOutOfRange.o ClustalW/Help.o ClustalW/interface/CommandLineParser.o ClustalW/multipleAlign/Iteration.o ClustalW/multipleAlign/LowScoreSegProfile.o ClustalW/multipleAlign/MSA.o ClustalW/multipleAlign/MyersMillerProfileAlign.o ClustalW/multipleAlign/ProfileBase.o ClustalW/multipleAlign/ProfileStandard.o ClustalW/multipleAlign/ProfileWithSub.o ClustalW/pairwise/FastPairwiseAlign.o ClustalW/pairwise/FullPairwiseAlign.o ClustalW/substitutionMatrix/SubMatrix.o ClustalW/tree/AlignmentSteps.o ClustalW/tree/ClusterTree.o ClustalW/tree/ClusterTreeOutput.o ClustalW/tree/NJTree.o ClustalW/tree/RandomGenerator.o ClustalW/tree/Tree.o ClustalW/tree/TreeInterface.o ClustalW/tree/UnRootedClusterTree.o ClustalW/tree/UPGMA/Node.o ClustalW/tree/UPGMA/RootedClusterTree.o ClustalW/tree/UPGMA/RootedGuideTree.o ClustalW/tree/UPGMA/RootedTreeOutput.o ClustalW/tree/UPGMA/UPGMAAlgorithm.o Muscle/aligngivenpath.o Muscle/aligngivenpathsw.o Muscle/aligntwomsas.o Muscle/aligntwoprofs.o Muscle/aln.o Muscle/alpha.o Muscle/anchors.o Muscle/bittraceback.o Muscle/blosum62.o Muscle/blosumla.o Muscle/clust.o Muscle/cluster.o Muscle/clwwt.o Muscle/color.o Muscle/cons.o Muscle/diaglist.o Muscle/diffobjscore.o Muscle/diffpaths.o Muscle/difftrees.o Muscle/difftreese.o Muscle/distcalc.o Muscle/distfunc.o Muscle/distpwkimura.o Muscle/domuscle.o Muscle/dosp.o Muscle/dpreglist.o Muscle/drawtree.o Muscle/edgelist.o Muscle/enumopts.o Muscle/enumtostr.o Muscle/estring.o Muscle/fasta.o Muscle/fasta2.o Muscle/fastclust.o Muscle/fastdist.o Muscle/fastdistjones.o Muscle/fastdistkbit.o Muscle/fastdistkmer.o Muscle/fastdistmafft.o Muscle/fastdistnuc.o Muscle/fastscorepath2.o Muscle/finddiags.o Muscle/finddiagsn.o Muscle/glbalign.o Muscle/glbalign352.o Muscle/glbaligndiag.o Muscle/glbalignla.o Muscle/glbalignle.o Muscle/glbalignns.o Muscle/glbalignsimple.o Muscle/glbalignsp.o Muscle/glbalignspn.o Muscle/glbalignss.o Muscle/glbalndimer.o Muscle/globals.o Muscle/globalslinux.o Muscle/globalsosx.o Muscle/globalsother.o Muscle/globalswin32.o Muscle/gonnet.o Muscle/gotowt.o Muscle/henikoffweight.o Muscle/henikoffweightpb.o Muscle/html.o Muscle/hydro.o Muscle/intmath.o Muscle/local.o Muscle/main.o Muscle/makerootmsa.o Muscle/makerootmsab.o Muscle/maketree.o Muscle/mhack.o Muscle/mpam200.o Muscle/msa.o Muscle/msa2.o Muscle/msadistkimura.o Muscle/msf.o Muscle/muscle.o Muscle/muscleout.o Muscle/nucmx.o Muscle/nwdasimple.o Muscle/nwdasimple2.o Muscle/nwdasmall.o Muscle/nwrec.o Muscle/nwsmall.o Muscle/objscore.o Muscle/objscore2.o Muscle/objscoreda.o Muscle/onexception.o Muscle/options.o Muscle/outweights.o Muscle/pam200mafft.o Muscle/params.o Muscle/phy.o Muscle/phy2.o Muscle/phy3.o Muscle/phy4.o Muscle/phyfromclust.o Muscle/phyfromfile.o Muscle/physeq.o Muscle/phytofile.o Muscle/posgap.o Muscle/ppscore.o Muscle/profdb.o Muscle/profile.o Muscle/profilefrommsa.o Muscle/progalign.o Muscle/progress.o Muscle/progressivealign.o Muscle/pwpath.o Muscle/readmx.o Muscle/realigndiffs.o Muscle/realigndiffse.o Muscle/refine.o Muscle/refinehoriz.o Muscle/refinesubfams.o Muscle/refinetree.o Muscle/refinetreee.o Muscle/refinevert.o Muscle/refinew.o Muscle/savebest.o Muscle/scoredist.o Muscle/scoregaps.o Muscle/scorehistory.o Muscle/scorepp.o Muscle/seq.o Muscle/seqvect.o Muscle/setblosumweights.o Muscle/setgscweights.o Muscle/setnewhandler.o Muscle/spfast.o Muscle/sptest.o Muscle/stabilize.o Muscle/subfam.o Muscle/subfams.o Muscle/sw.o Muscle/termgaps.o Muscle/textfile.o Muscle/threewaywt.o Muscle/tomhydro.o Muscle/traceback.o Muscle/tracebackopt.o Muscle/tracebacksw.o Muscle/treefrommsa.o Muscle/typetostr.o Muscle/upgma2.o Muscle/usage.o Muscle/validateids.o Muscle/vtml2.o Muscle/writescorefile.o RClustalW.o RClustalWMain.o RcppExports.o RMuscle.o ushuffle.o ushuffler.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-enhancerHomologSearch/00new/enhancerHomologSearch/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (enhancerHomologSearch)
enhancerHomologSearch.Rcheck/tests/runTests.Rout
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> require("enhancerHomologSearch") || stop("unable to load Package:enhancerHomologSearch")
Loading required package: enhancerHomologSearch
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg38") || stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg38")
Loading required package: BSgenome.Hsapiens.UCSC.hg38
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BiocIO
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:BiocIO':
FileForFormat
[1] TRUE
> require("BSgenome.Mmusculus.UCSC.mm10") || stop("unable to load Package:BSgenome.Mmusculus.UCSC.mm10")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
Loading required package: GenomicFeatures
[1] TRUE
> require("BiocParallel") || stop("unable to load BiocParallel")
Loading required package: BiocParallel
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("enhancerHomologSearch")
|
| | 0%
|
|======================================================================| 100%
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
>
> proc.time()
user system elapsed
108.002 16.987 150.989
enhancerHomologSearch.Rcheck/enhancerHomologSearch-Ex.timings
| name | user | system | elapsed | |
| Enhancers-class | 0.026 | 0.001 | 0.027 | |
| alignment | 2.730 | 0.187 | 3.070 | |
| alignmentOne | 4.914 | 0.091 | 5.023 | |
| conservedMotifs | 91.732 | 17.032 | 110.856 | |
| getENCODEdata | 4.662 | 0.604 | 18.918 | |
| motifs | 0.154 | 0.029 | 1.963 | |
| queryEncode | 0.259 | 0.048 | 1.642 | |
| saveAlignments | 10.544 | 0.719 | 21.527 | |
| searchTFBPS | 71.844 | 15.459 | 122.226 | |
| shuffle | 0.152 | 0.021 | 0.179 | |