Jianhong Ou
| Snapshot Date: 2025-02-02 13:40 -0500 (Sun, 02 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/enhancerHomologSearch |
| git_branch: devel |
| git_last_commit: 27b3973 |
| git_last_commit_date: 2025-01-03 09:38:11 -0500 (Fri, 03 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-03 12:37 -0500 (Mon, 03 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4704 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4467 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4478 |
| 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 638/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| enhancerHomologSearch 1.13.2 (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: 1.13.2 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:enhancerHomologSearch.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings enhancerHomologSearch_1.13.2.tar.gz |
| StartedAt: 2025-02-02 21:55:51 -0500 (Sun, 02 Feb 2025) |
| EndedAt: 2025-02-02 22:15:42 -0500 (Sun, 02 Feb 2025) |
| EllapsedTime: 1191.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: enhancerHomologSearch.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:enhancerHomologSearch.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings enhancerHomologSearch_1.13.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/enhancerHomologSearch.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘enhancerHomologSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enhancerHomologSearch’ version ‘1.13.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 15.3Mb
sub-directories of 1Mb or more:
libs 14.1Mb
* 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 loading without being on the library search path ... 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 108.257 30.800 148.720
searchTFBPS 86.553 25.814 122.936
saveAlignments 10.331 0.287 10.619
alignmentOne 5.721 0.138 5.860
getENCODEdata 3.743 0.436 11.395
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/enhancerHomologSearch.Rcheck/00check.log’
for details.
enhancerHomologSearch.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL enhancerHomologSearch
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘enhancerHomologSearch’ ...
** this is package ‘enhancerHomologSearch’ version ‘1.13.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/alignment/Alignment.cpp -o ClustalW/alignment/Alignment.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/FileParser.cpp -o ClustalW/fileInput/FileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/FileReader.cpp -o ClustalW/fileInput/FileReader.o
ClustalW/fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)’:
ClustalW/fileInput/FileReader.cpp:357:54: warning: ‘this’ pointer is null [-Wnonnull]
357 | seqRangeVector = fileParser->getSeqRangeR(1, noSeqs, offendingSeq, input);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ClustalW/fileInput/FileReader.h:16,
from ClustalW/fileInput/FileReader.cpp:29:
ClustalW/fileInput/FileParser.h:44:26: note: in a call to non-static member function ‘std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)’
44 | vector<Sequence> getSeqRangeR(int firstSeq, int num, string *offendingSeq, ClustalWInput *input);
| ^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/Utility.cpp -o ClustalW/general/Utility.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/Help.cpp -o ClustalW/Help.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/Iteration.cpp -o ClustalW/multipleAlign/Iteration.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/MSA.cpp -o ClustalW/multipleAlign/MSA.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/substitutionMatrix/SubMatrix.cpp -o ClustalW/substitutionMatrix/SubMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/ClusterTree.cpp -o ClustalW/tree/ClusterTree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/Node.cpp -o ClustalW/tree/UPGMA/Node.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/RootedClusterTree.cpp -o ClustalW/tree/UPGMA/RootedClusterTree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/RootedGuideTree.cpp -o ClustalW/tree/UPGMA/RootedGuideTree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/RootedTreeOutput.cpp -o ClustalW/tree/UPGMA/RootedTreeOutput.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp -o ClustalW/tree/UPGMA/UPGMAAlgorithm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/aligngivenpath.cpp -o Muscle/aligngivenpath.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/aligngivenpathsw.cpp -o Muscle/aligngivenpathsw.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/aligntwomsas.cpp -o Muscle/aligntwomsas.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/aligntwoprofs.cpp -o Muscle/aligntwoprofs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/aln.cpp -o Muscle/aln.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/alpha.cpp -o Muscle/alpha.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/anchors.cpp -o Muscle/anchors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/bittraceback.cpp -o Muscle/bittraceback.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/blosum62.cpp -o Muscle/blosum62.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/blosumla.cpp -o Muscle/blosumla.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/clust.cpp -o Muscle/clust.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/cluster.cpp -o Muscle/cluster.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/clwwt.cpp -o Muscle/clwwt.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/color.cpp -o Muscle/color.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/cons.cpp -o Muscle/cons.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/diaglist.cpp -o Muscle/diaglist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/diffobjscore.cpp -o Muscle/diffobjscore.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/diffpaths.cpp -o Muscle/diffpaths.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/difftrees.cpp -o Muscle/difftrees.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/difftreese.cpp -o Muscle/difftreese.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/distcalc.cpp -o Muscle/distcalc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/distfunc.cpp -o Muscle/distfunc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/distpwkimura.cpp -o Muscle/distpwkimura.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/domuscle.cpp -o Muscle/domuscle.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/dosp.cpp -o Muscle/dosp.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/dpreglist.cpp -o Muscle/dpreglist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/drawtree.cpp -o Muscle/drawtree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/edgelist.cpp -o Muscle/edgelist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/enumopts.cpp -o Muscle/enumopts.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/enumtostr.cpp -o Muscle/enumtostr.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/estring.cpp -o Muscle/estring.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fasta.cpp -o Muscle/fasta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fasta2.cpp -o Muscle/fasta2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastclust.cpp -o Muscle/fastclust.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastdist.cpp -o Muscle/fastdist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastdistjones.cpp -o Muscle/fastdistjones.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastdistkbit.cpp -o Muscle/fastdistkbit.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastdistkmer.cpp -o Muscle/fastdistkmer.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastdistmafft.cpp -o Muscle/fastdistmafft.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastdistnuc.cpp -o Muscle/fastdistnuc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/fastscorepath2.cpp -o Muscle/fastscorepath2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/finddiags.cpp -o Muscle/finddiags.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/finddiagsn.cpp -o Muscle/finddiagsn.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalign.cpp -o Muscle/glbalign.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalign352.cpp -o Muscle/glbalign352.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbaligndiag.cpp -o Muscle/glbaligndiag.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalignla.cpp -o Muscle/glbalignla.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalignle.cpp -o Muscle/glbalignle.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalignns.cpp -o Muscle/glbalignns.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalignsimple.cpp -o Muscle/glbalignsimple.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalignsp.cpp -o Muscle/glbalignsp.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalignspn.cpp -o Muscle/glbalignspn.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalignss.cpp -o Muscle/glbalignss.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/globals.cpp -o Muscle/globals.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/globalslinux.cpp -o Muscle/globalslinux.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/globalsother.cpp -o Muscle/globalsother.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/gonnet.cpp -o Muscle/gonnet.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/gotowt.cpp -o Muscle/gotowt.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/henikoffweight.cpp -o Muscle/henikoffweight.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/henikoffweightpb.cpp -o Muscle/henikoffweightpb.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/html.cpp -o Muscle/html.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/hydro.cpp -o Muscle/hydro.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/intmath.cpp -o Muscle/intmath.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/local.cpp -o Muscle/local.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/main.cpp -o Muscle/main.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/makerootmsa.cpp -o Muscle/makerootmsa.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/makerootmsab.cpp -o Muscle/makerootmsab.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/maketree.cpp -o Muscle/maketree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/mhack.cpp -o Muscle/mhack.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/mpam200.cpp -o Muscle/mpam200.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/msa.cpp -o Muscle/msa.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/msa2.cpp -o Muscle/msa2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/msadistkimura.cpp -o Muscle/msadistkimura.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/msf.cpp -o Muscle/msf.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/muscle.cpp -o Muscle/muscle.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/muscleout.cpp -o Muscle/muscleout.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/nucmx.cpp -o Muscle/nucmx.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/nwdasimple.cpp -o Muscle/nwdasimple.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/nwdasimple2.cpp -o Muscle/nwdasimple2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/nwdasmall.cpp -o Muscle/nwdasmall.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/nwrec.cpp -o Muscle/nwrec.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/nwsmall.cpp -o Muscle/nwsmall.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/objscore.cpp -o Muscle/objscore.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/objscore2.cpp -o Muscle/objscore2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/objscoreda.cpp -o Muscle/objscoreda.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/onexception.cpp -o Muscle/onexception.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/options.cpp -o Muscle/options.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/outweights.cpp -o Muscle/outweights.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/pam200mafft.cpp -o Muscle/pam200mafft.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/params.cpp -o Muscle/params.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/phy.cpp -o Muscle/phy.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/phy2.cpp -o Muscle/phy2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/phy3.cpp -o Muscle/phy3.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/phy4.cpp -o Muscle/phy4.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/phyfromclust.cpp -o Muscle/phyfromclust.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/phyfromfile.cpp -o Muscle/phyfromfile.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/physeq.cpp -o Muscle/physeq.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/phytofile.cpp -o Muscle/phytofile.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/posgap.cpp -o Muscle/posgap.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/ppscore.cpp -o Muscle/ppscore.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/profdb.cpp -o Muscle/profdb.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/profile.cpp -o Muscle/profile.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/profilefrommsa.cpp -o Muscle/profilefrommsa.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/progalign.cpp -o Muscle/progalign.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/progress.cpp -o Muscle/progress.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/progressivealign.cpp -o Muscle/progressivealign.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/pwpath.cpp -o Muscle/pwpath.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/readmx.cpp -o Muscle/readmx.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/realigndiffs.cpp -o Muscle/realigndiffs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/realigndiffse.cpp -o Muscle/realigndiffse.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/refine.cpp -o Muscle/refine.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/refinehoriz.cpp -o Muscle/refinehoriz.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/refinesubfams.cpp -o Muscle/refinesubfams.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/refinetree.cpp -o Muscle/refinetree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/refinetreee.cpp -o Muscle/refinetreee.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/refinevert.cpp -o Muscle/refinevert.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/refinew.cpp -o Muscle/refinew.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/savebest.cpp -o Muscle/savebest.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/scoredist.cpp -o Muscle/scoredist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/scoregaps.cpp -o Muscle/scoregaps.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/scorehistory.cpp -o Muscle/scorehistory.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/scorepp.cpp -o Muscle/scorepp.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/seq.cpp -o Muscle/seq.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/seqvect.cpp -o Muscle/seqvect.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/setblosumweights.cpp -o Muscle/setblosumweights.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/setgscweights.cpp -o Muscle/setgscweights.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/setnewhandler.cpp -o Muscle/setnewhandler.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/spfast.cpp -o Muscle/spfast.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/sptest.cpp -o Muscle/sptest.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/stabilize.cpp -o Muscle/stabilize.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/subfam.cpp -o Muscle/subfam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/subfams.cpp -o Muscle/subfams.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/sw.cpp -o Muscle/sw.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/termgaps.cpp -o Muscle/termgaps.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/textfile.cpp -o Muscle/textfile.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/threewaywt.cpp -o Muscle/threewaywt.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/tomhydro.cpp -o Muscle/tomhydro.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/traceback.cpp -o Muscle/traceback.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/tracebackopt.cpp -o Muscle/tracebackopt.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/tracebacksw.cpp -o Muscle/tracebacksw.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/treefrommsa.cpp -o Muscle/treefrommsa.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/typetostr.cpp -o Muscle/typetostr.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/upgma2.cpp -o Muscle/upgma2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/usage.cpp -o Muscle/usage.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/validateids.cpp -o Muscle/validateids.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/vtml2.cpp -o Muscle/vtml2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c Muscle/writescorefile.cpp -o Muscle/writescorefile.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c RClustalW.cpp -o RClustalW.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c RClustalWMain.cpp -o RClustalWMain.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c RMuscle.cpp -o RMuscle.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ushuffle.c -o ushuffle.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fpic -g -O2 -DR_NO_REMAP -c ushuffler.cpp -o ushuffler.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/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 -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lpthread -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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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
116.847 24.463 141.337
enhancerHomologSearch.Rcheck/enhancerHomologSearch-Ex.timings
| name | user | system | elapsed | |
| Enhancers-class | 0.031 | 0.005 | 0.036 | |
| alignment | 3.101 | 0.203 | 3.305 | |
| alignmentOne | 5.721 | 0.138 | 5.860 | |
| conservedMotifs | 108.257 | 30.800 | 148.720 | |
| getENCODEdata | 3.743 | 0.436 | 11.395 | |
| motifs | 0.133 | 0.002 | 0.135 | |
| queryEncode | 0.191 | 0.025 | 1.277 | |
| saveAlignments | 10.331 | 0.287 | 10.619 | |
| searchTFBPS | 86.553 | 25.814 | 122.936 | |
| shuffle | 0.123 | 0.004 | 0.128 | |