Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 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 1316/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
motifcounter 1.30.0 (landing page) Wolfgang Kopp
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 motifcounter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifcounter.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: motifcounter |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.30.0.tar.gz |
StartedAt: 2024-12-20 06:21:02 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:27:48 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 406.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: motifcounter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘motifcounter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘motifcounter’ version ‘1.30.0’ * 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 ... NOTE Found the following hidden files and directories: .zenodo.json These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘motifcounter’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... 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 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 simulateClumpSizeDist 18.606 0.480 19.462 scoreDistEmpirical 5.315 0.075 5.452 motifEnrichment 5.109 0.036 5.182 * 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-3.20-bioc/meat/motifcounter.Rcheck/00check.log’ for details.
motifcounter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifcounter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘motifcounter’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rbackground.c -o Rbackground.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rcombinatorial.c -o Rcombinatorial.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rcompoundpoisson.c -o Rcompoundpoisson.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rminmaxscore.c -o Rminmaxscore.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Roption.c -o Roption.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Roverlap.c -o Roverlap.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rscore1d.c -o Rscore1d.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rsequence.c -o Rsequence.o Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable] int mins, maxs, noscores; ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rsimulate.c -o Rsimulate.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c background.c -o background.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c combinatorial.c -o combinatorial.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c compoundpoisson.c -o compoundpoisson.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c markovchain.c -o markovchain.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c markovchain_single.c -o markovchain_single.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c matrix.c -o matrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c mdist_register.c -o mdist_register.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c minmaxscore.c -o minmaxscore.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c overlap.c -o overlap.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c score1d.c -o score1d.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c score2d.c -o score2d.o score2d.c:597:15: warning: variable 'p0' set but not used [-Wunused-but-set-variable] double p, p0 = 0.0, p1 = 0.0, ptmp; ^ score2d.c:597:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable] double p, p0 = 0.0, p1 = 0.0, ptmp; ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c scorefunctions.c -o scorefunctions.o scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable] int j, i, index, cindex, ds; ^ scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable] int s, index, cindex; ^ scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable] int s, index, cindex; ^ 3 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c sequence.c -o sequence.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c simulate.c -o simulate.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-motifcounter/00new/motifcounter/libs ** R ** 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 (motifcounter)
motifcounter.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(motifcounter) > > test_check("motifcounter") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ] > > proc.time() user system elapsed 188.332 3.271 197.374
motifcounter.Rcheck/motifcounter-Ex.timings
name | user | system | elapsed | |
clumpSizeDist | 0.355 | 0.013 | 0.373 | |
combinatorialDist | 0.484 | 0.032 | 0.521 | |
compoundPoissonDist | 0.368 | 0.040 | 0.443 | |
computeClumpStartProb | 0.244 | 0.005 | 0.250 | |
generateDNAString | 0.190 | 0.005 | 0.199 | |
generateDNAStringSet | 0.278 | 0.004 | 0.284 | |
hitStrand | 0.192 | 0.023 | 0.217 | |
lenSequences | 0.188 | 0.029 | 0.219 | |
markovModel | 0.224 | 0.006 | 0.232 | |
motifAndBackgroundValid | 0.175 | 0.003 | 0.182 | |
motifEnrichment | 5.109 | 0.036 | 5.182 | |
motifHitProfile | 0.164 | 0.007 | 0.173 | |
motifHits | 0.180 | 0.007 | 0.190 | |
motifValid | 0.003 | 0.001 | 0.004 | |
motifcounter-package | 1.601 | 0.037 | 1.666 | |
motifcounterOptions | 0.000 | 0.000 | 0.001 | |
normalizeMotif | 0.003 | 0.001 | 0.005 | |
numMotifHits | 1.339 | 0.018 | 1.389 | |
probOverlapHit | 0.279 | 0.008 | 0.290 | |
readBackground | 0.181 | 0.004 | 0.189 | |
revcompMotif | 0.003 | 0.002 | 0.004 | |
scoreDist | 0.178 | 0.004 | 0.183 | |
scoreDistBf | 0.203 | 0.003 | 0.207 | |
scoreDistEmpirical | 5.315 | 0.075 | 5.452 | |
scoreHistogram | 0.450 | 0.022 | 0.478 | |
scoreHistogramSingleSeq | 0.192 | 0.021 | 0.214 | |
scoreProfile | 0.969 | 0.011 | 0.990 | |
scoreSequence | 0.178 | 0.007 | 0.187 | |
scoreStrand | 0.184 | 0.005 | 0.190 | |
scoreThreshold | 0.187 | 0.003 | 0.191 | |
sigLevel | 0.001 | 0.000 | 0.001 | |
simulateClumpSizeDist | 18.606 | 0.480 | 19.462 | |
simulateNumHitsDist | 3.917 | 0.062 | 4.158 | |