Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1328/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSA2dist 1.10.1 (landing page) Kristian K Ullrich
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MSA2dist |
Version: 1.10.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MSA2dist_1.10.1.tar.gz |
StartedAt: 2024-11-20 10:10:26 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 10:15:17 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 291.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSA2dist.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MSA2dist_1.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MSA2dist.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSA2dist/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSA2dist’ version ‘1.10.1’ * 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: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: libs 8.7Mb * 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 7.33 1.474 12.541 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MSA2dist.Rcheck/00check.log’ for details.
MSA2dist.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MSA2dist ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘MSA2dist’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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: aarch64-unknown-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 100.790 14.244 116.424
MSA2dist.Rcheck/MSA2dist-Ex.timings
name | user | system | elapsed | |
AAMatrix-data | 0.003 | 0.000 | 0.003 | |
GENETIC_CODE_TCAG | 0.005 | 0.000 | 0.004 | |
aa2selfscore | 0.348 | 0.000 | 0.349 | |
aabin2aastring | 0.045 | 0.008 | 0.054 | |
aastring2aabin | 0.227 | 0.024 | 0.251 | |
aastring2aln | 0.206 | 0.000 | 0.207 | |
aastring2dist | 1.241 | 0.020 | 1.263 | |
addmask2string | 0.675 | 0.020 | 0.696 | |
addpop2string | 0.239 | 0.004 | 0.244 | |
addpos2string | 0.106 | 0.012 | 0.119 | |
addregion2string | 0.655 | 0.012 | 0.668 | |
aln2aastring | 0.188 | 0.007 | 0.196 | |
aln2dnastring | 0.025 | 0.001 | 0.026 | |
cds2aa | 0.821 | 0.023 | 0.846 | |
cds2codonaln | 0.554 | 0.004 | 0.560 | |
cdsstring2codonaln | 0.293 | 0.001 | 0.294 | |
codon2numberAMBIG | 0.000 | 0.000 | 0.001 | |
codon2numberTCAG | 0.001 | 0.000 | 0.001 | |
codonmat2pnps | 0.046 | 0.000 | 0.046 | |
codonmat2xy | 7.330 | 1.474 | 12.541 | |
compareCodons | 0.055 | 0.008 | 0.064 | |
dnabin2dnastring | 0.036 | 0.004 | 0.040 | |
dnastring2aln | 0.021 | 0.004 | 0.025 | |
dnastring2codonmat | 0.048 | 0.012 | 0.060 | |
dnastring2dist | 0.239 | 0.044 | 0.282 | |
dnastring2dnabin | 0.017 | 0.004 | 0.020 | |
dnastring2kaks | 1.452 | 0.787 | 2.367 | |
getmask | 0.639 | 0.157 | 0.294 | |
getpos | 0.082 | 0.004 | 0.086 | |
globalDeletion | 0.027 | 0.004 | 0.031 | |
granthamMatrix | 0.002 | 0.000 | 0.001 | |
hiv-data | 0.028 | 0.003 | 0.031 | |
indices2kaks | 1.594 | 0.632 | 2.552 | |
iupac-data | 0.479 | 0.130 | 0.091 | |
iupacMatrix | 0.001 | 0.000 | 0.001 | |
makePostalignedSeqs | 1.495 | 0.239 | 1.739 | |
pal2nal | 1.196 | 0.072 | 1.270 | |
popinteger | 0.251 | 0.004 | 0.255 | |
popnames | 0.255 | 0.004 | 0.259 | |
rcpp_KaKs | 0.051 | 0.000 | 0.051 | |
rcpp_distSTRING | 0.031 | 0.004 | 0.034 | |
rcpp_pairwiseDeletionAA | 0.223 | 0.000 | 0.224 | |
rcpp_pairwiseDeletionDNA | 0.024 | 0.000 | 0.024 | |
region | 0.252 | 0.016 | 0.269 | |
regionused | 0.237 | 0.000 | 0.237 | |
string2region | 0.650 | 0.008 | 0.659 | |
subString | 0.024 | 0.000 | 0.025 | |
uptriidx | 0.000 | 0.000 | 0.001 | |