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 12:07 -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 908/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
groHMM 1.40.3 (landing page) Tulip Nandu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the groHMM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/groHMM.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: groHMM |
Version: 1.40.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:groHMM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings groHMM_1.40.3.tar.gz |
StartedAt: 2024-12-20 21:34:56 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 21:38:47 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 230.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: groHMM.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:groHMM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings groHMM_1.40.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/groHMM.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘groHMM/DESCRIPTION’ ... OK * this is package ‘groHMM’ version ‘1.40.3’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'MASS', 'parallel', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'GenomicAlignments', 'rtracklayer' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘groHMM’ can be installed ... WARNING Found the following significant warnings: hmmMiscFunctions.c:236:49: warning: format specifies type 'int' but the argument has type 'double' [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/groHMM.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives no person with maintainer role, valid email address and non-empty name. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/groHMM.Rcheck/00check.log’ for details.
groHMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL groHMM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘groHMM’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AnnotateProbes.c -o AnnotateProbes.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DecayAlgorithm.c -o DecayAlgorithm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MLEfit.c -o MLEfit.o MLEfit.c:260:25: warning: variable 'cnt' set but not used [-Wunused-but-set-variable] int maxn = 2*n_x+1, cnt=0; ^ In file included from MLEfit.c:43: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RegisterRRoutines.c -o RegisterRRoutines.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Windowing.c -o Windowing.o Windowing.c:146:6: warning: unused variable 'II' [-Wunused-variable] int II = 0; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmEM.c -o hmmEM.o In file included from hmmEM.c:50: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmFwBw.c -o hmmFwBw.o In file included from hmmFwBw.c:45: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o hmmMiscFunctions.c:236:49: warning: format specifies type 'int' but the argument has type 'double' [-Wformat] Assertion about to fail! logPP= %d\n", logPP); ~~ ^~~~~ %f hmmMiscFunctions.c:384:10: warning: unused variable 'wi' [-Wunused-variable] double wi, *newEx; ^ hmmMiscFunctions.c:417:10: warning: unused variable 'epsilon' [-Wunused-variable] double epsilon=0.00001; ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmViterbi.c -o hmmViterbi.o In file included from hmmViterbi.c:48: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 2 warnings generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-groHMM/00new/groHMM/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 (groHMM)
groHMM.Rcheck/groHMM-Ex.timings
name | user | system | elapsed | |
breakTranscriptsOnGenes | 0.522 | 0.016 | 0.537 | |
combineTranscripts | 0.233 | 0.012 | 0.247 | |
detectTranscripts | 1.241 | 0.020 | 1.262 | |
evaluateHMMInAnnotations | 0.088 | 0.000 | 0.089 | |
getCores | 0.000 | 0.001 | 0.001 | |
getTxDensity | 0.014 | 0.000 | 0.015 | |
limitToXkb | 0.061 | 0.000 | 0.061 | |
makeConsensusAnnotations | 0.000 | 0.000 | 0.001 | |
metaGene | 0.084 | 0.000 | 0.085 | |
pausingIndex | 0.243 | 0.014 | 0.257 | |
polymeraseWave | 0.353 | 0.041 | 0.402 | |
runMetaGene | 0.008 | 0.000 | 0.008 | |
windowAnalysis | 0.143 | 0.016 | 0.160 | |
writeWiggle | 0.200 | 0.019 | 0.219 | |