Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 1339/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSA2dist 1.8.0 (landing page) Kristian K Ullrich
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.8.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MSA2dist_1.8.0.tar.gz |
StartedAt: 2024-07-22 02:34:50 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 02:39:01 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 250.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSA2dist.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MSA2dist_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MSA2dist.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘MSA2dist/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSA2dist’ version ‘1.8.0’ * 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: libs 5.4Mb * 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 ... 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 5.856 0.857 10.897 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/MSA2dist.Rcheck/00check.log’ for details.
MSA2dist.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MSA2dist ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘MSA2dist’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c GY94.cpp -o GY94.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c KaKs.cpp -o KaKs.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c LPB93.cpp -o LPB93.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c LWL85.cpp -o LWL85.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c MSMA.cpp -o MSMA.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c MYN.cpp -o MYN.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c NG86.cpp -o NG86.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c YN00.cpp -o YN00.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c base.cpp -o base.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_KaKs.cpp -o rcpp_KaKs.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_distSTRING.cpp -o rcpp_distSTRING.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_pairwiseDeletionAA.cpp -o rcpp_pairwiseDeletionAA.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_pairwiseDeletionDNA.cpp -o rcpp_pairwiseDeletionDNA.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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") Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) Computing: [========================================] 100% (done) [ FAIL 0 | WARN 0 | SKIP 0 | PASS 176 ] > > proc.time() user system elapsed 80.858 12.008 95.297
MSA2dist.Rcheck/MSA2dist-Ex.timings
name | user | system | elapsed | |
AAMatrix-data | 0.003 | 0.000 | 0.003 | |
GENETIC_CODE_TCAG | 0.006 | 0.000 | 0.006 | |
aa2selfscore | 0.290 | 0.004 | 0.294 | |
aabin2aastring | 0.038 | 0.000 | 0.038 | |
aastring2aabin | 0.188 | 0.012 | 0.200 | |
aastring2aln | 0.144 | 0.016 | 0.159 | |
aastring2dist | 1.056 | 0.032 | 1.087 | |
addmask2string | 0.674 | 0.048 | 0.722 | |
addpop2string | 0.182 | 0.016 | 0.198 | |
addpos2string | 0.095 | 0.012 | 0.107 | |
addregion2string | 0.584 | 0.016 | 0.600 | |
aln2aastring | 0.141 | 0.000 | 0.141 | |
aln2dnastring | 0.020 | 0.000 | 0.021 | |
cds2aa | 0.623 | 0.024 | 0.647 | |
cds2codonaln | 0.416 | 0.004 | 0.419 | |
cdsstring2codonaln | 0.206 | 0.004 | 0.210 | |
codon2numberAMBIG | 0.000 | 0.001 | 0.002 | |
codon2numberTCAG | 0.000 | 0.002 | 0.001 | |
codonmat2pnps | 0.041 | 0.001 | 0.041 | |
codonmat2xy | 5.856 | 0.857 | 10.897 | |
compareCodons | 0.041 | 0.008 | 0.050 | |
dnabin2dnastring | 0.023 | 0.007 | 0.032 | |
dnastring2aln | 0.006 | 0.007 | 0.014 | |
dnastring2codonmat | 0.039 | 0.003 | 0.043 | |
dnastring2dist | 0.186 | 0.036 | 0.221 | |
dnastring2dnabin | 0.015 | 0.000 | 0.016 | |
dnastring2kaks | 1.088 | 0.586 | 1.849 | |
getmask | 0.494 | 0.144 | 0.234 | |
getpos | 0.054 | 0.028 | 0.082 | |
globalDeletion | 0.02 | 0.00 | 0.02 | |
granthamMatrix | 0.004 | 0.000 | 0.004 | |
hiv-data | 0.024 | 0.004 | 0.028 | |
indices2kaks | 1.140 | 0.449 | 1.770 | |
iupac-data | 0.350 | 0.149 | 0.123 | |
iupacMatrix | 0.000 | 0.002 | 0.002 | |
makePostalignedSeqs | 1.229 | 0.113 | 1.342 | |
pal2nal | 1.029 | 0.116 | 1.144 | |
popinteger | 0.187 | 0.008 | 0.195 | |
popnames | 0.182 | 0.009 | 0.192 | |
rcpp_KaKs | 0.038 | 0.006 | 0.044 | |
rcpp_distSTRING | 0.028 | 0.004 | 0.033 | |
rcpp_pairwiseDeletionAA | 0.154 | 0.003 | 0.157 | |
rcpp_pairwiseDeletionDNA | 0.020 | 0.004 | 0.024 | |
region | 0.192 | 0.008 | 0.199 | |
regionused | 0.160 | 0.008 | 0.167 | |
string2region | 0.445 | 0.008 | 0.452 | |
subString | 0.017 | 0.000 | 0.017 | |
uptriidx | 0.000 | 0.001 | 0.001 | |