Kristian K Ullrich
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MSA2dist |
| git_branch: devel |
| git_last_commit: b5ab038 |
| git_last_commit_date: 2024-11-14 02:08:34 -0500 (Thu, 14 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 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" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1321/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSA2dist 1.11.1 (landing page) Kristian K Ullrich
| 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 | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the MSA2dist package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSA2dist.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: MSA2dist |
| Version: 1.11.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSA2dist_1.11.1.tar.gz |
| StartedAt: 2024-12-23 21:46:13 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 21:50:26 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 253.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSA2dist.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSA2dist_1.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSA2dist.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 ‘MSA2dist/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSA2dist’ version ‘1.11.1’
* 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 ‘MSA2dist’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 ... OK
* 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 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
codonmat2xy 5.576 1.134 5.17
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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/MSA2dist.Rcheck/00check.log’
for details.
MSA2dist.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSA2dist
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MSA2dist’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c GY94.cpp -o GY94.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c KaKs.cpp -o KaKs.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c LPB93.cpp -o LPB93.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c LWL85.cpp -o LWL85.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c MSMA.cpp -o MSMA.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c MYN.cpp -o MYN.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c NG86.cpp -o NG86.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread.h:9:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c YN00.cpp -o YN00.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c base.cpp -o base.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rcpp_KaKs.cpp -o rcpp_KaKs.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rcpp_distSTRING.cpp -o rcpp_distSTRING.o
In file included from rcpp_distSTRING.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread.h:9:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rcpp_pairwiseDeletionAA.cpp -o rcpp_pairwiseDeletionAA.o
In file included from rcpp_pairwiseDeletionAA.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread.h:9:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rcpp_pairwiseDeletionDNA.cpp -o rcpp_pairwiseDeletionDNA.o
In file included from rcpp_pairwiseDeletionDNA.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread.h:9:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MSA2dist.so GY94.o KaKs.o LPB93.o LWL85.o MSMA.o MYN.o NG86.o RcppExports.o YN00.o base.o rcpp_KaKs.o rcpp_distSTRING.o rcpp_pairwiseDeletionAA.o rcpp_pairwiseDeletionDNA.o -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-MSA2dist/00new/MSA2dist/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (MSA2dist)
MSA2dist.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(MSA2dist)
>
> test_check("MSA2dist")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 177 ]
>
> proc.time()
user system elapsed
90.485 18.285 107.488
MSA2dist.Rcheck/MSA2dist-Ex.timings
| name | user | system | elapsed | |
| AAMatrix-data | 0.003 | 0.001 | 0.004 | |
| GENETIC_CODE_TCAG | 0.004 | 0.002 | 0.006 | |
| aa2selfscore | 0.292 | 0.009 | 0.304 | |
| aabin2aastring | 0.041 | 0.002 | 0.043 | |
| aastring2aabin | 0.239 | 0.004 | 0.245 | |
| aastring2aln | 0.165 | 0.004 | 0.170 | |
| aastring2dist | 0.961 | 0.032 | 0.995 | |
| addmask2string | 0.247 | 0.013 | 0.260 | |
| addpop2string | 0.257 | 0.013 | 0.271 | |
| addpos2string | 0.095 | 0.002 | 0.097 | |
| addregion2string | 0.593 | 0.008 | 0.603 | |
| aln2aastring | 0.175 | 0.002 | 0.178 | |
| aln2dnastring | 0.022 | 0.001 | 0.024 | |
| cds2aa | 0.650 | 0.020 | 0.673 | |
| cds2codonaln | 0.419 | 0.005 | 0.425 | |
| cdsstring2codonaln | 0.245 | 0.006 | 0.253 | |
| codon2numberAMBIG | 0.001 | 0.001 | 0.001 | |
| codon2numberTCAG | 0.000 | 0.001 | 0.002 | |
| codonmat2pnps | 0.039 | 0.001 | 0.040 | |
| codonmat2xy | 5.576 | 1.134 | 5.170 | |
| compareCodons | 0.043 | 0.005 | 0.047 | |
| dnabin2dnastring | 0.023 | 0.003 | 0.026 | |
| dnastring2aln | 0.012 | 0.002 | 0.014 | |
| dnastring2codonmat | 0.045 | 0.004 | 0.048 | |
| dnastring2dist | 0.178 | 0.027 | 0.206 | |
| dnastring2dnabin | 0.018 | 0.001 | 0.019 | |
| dnastring2kaks | 1.768 | 1.055 | 2.450 | |
| getmask | 0.237 | 0.042 | 0.281 | |
| getpos | 0.118 | 0.017 | 0.137 | |
| globalDeletion | 0.020 | 0.001 | 0.022 | |
| globalDeletionAA | 0.198 | 0.006 | 0.205 | |
| granthamMatrix | 0.001 | 0.003 | 0.004 | |
| hiv-data | 0.025 | 0.001 | 0.026 | |
| indices2kaks | 1.989 | 1.022 | 2.870 | |
| iupac-data | 0.074 | 0.028 | 0.103 | |
| iupacMatrix | 0.001 | 0.001 | 0.002 | |
| makePostalignedSeqs | 1.222 | 0.178 | 1.412 | |
| pal2nal | 0.865 | 0.072 | 0.941 | |
| popinteger | 0.221 | 0.027 | 0.250 | |
| popnames | 0.217 | 0.005 | 0.225 | |
| rcpp_KaKs | 0.051 | 0.002 | 0.053 | |
| rcpp_distSTRING | 0.028 | 0.003 | 0.032 | |
| rcpp_pairwiseDeletionAA | 0.182 | 0.007 | 0.191 | |
| rcpp_pairwiseDeletionDNA | 0.016 | 0.003 | 0.019 | |
| region | 0.234 | 0.005 | 0.241 | |
| regionused | 0.218 | 0.004 | 0.224 | |
| string2region | 0.564 | 0.019 | 0.585 | |
| subString | 0.020 | 0.001 | 0.020 | |
| uptriidx | 0.001 | 0.000 | 0.001 | |