Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-30 11:40 -0400 (Tue, 30 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4690 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4387 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4406 |
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 895/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
groHMM 1.39.0 (landing page) Tulip Nandu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 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: 1.39.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:groHMM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings groHMM_1.39.0.tar.gz |
StartedAt: 2024-07-30 01:41:32 -0400 (Tue, 30 Jul 2024) |
EndedAt: 2024-07-30 01:45:51 -0400 (Tue, 30 Jul 2024) |
EllapsedTime: 259.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: groHMM.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:groHMM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings groHMM_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/groHMM.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'groHMM/DESCRIPTION' ... OK * this is package 'groHMM' version '1.39.0' * 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 whether package 'groHMM' can be installed ... WARNING Found the following significant warnings: hmmMiscFunctions.c:235:37: warning: format '%d' expects argument of type 'int', but argument 2 has type 'double' [-Wformat=] See 'F:/biocbuild/bbs-3.20-bioc/meat/groHMM.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/groHMM/libs/x64/groHMM.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 'F:/biocbuild/bbs-3.20-bioc/meat/groHMM.Rcheck/00check.log' for details.
groHMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL groHMM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'groHMM' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AnnotateProbes.c -o AnnotateProbes.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DecayAlgorithm.c -o DecayAlgorithm.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MLEfit.c -o MLEfit.o In file included from MLEfit.c:43: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RegisterRRoutines.c -o RegisterRRoutines.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Windowing.c -o Windowing.o Windowing.c: In function 'WindowAnalysis': Windowing.c:146:13: warning: unused variable 'II' [-Wunused-variable] 146 | int II = 0; | ^~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmmEM.c -o hmmEM.o In file included from hmmEM.c:50: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmmFwBw.c -o hmmFwBw.o hmmFwBw.c: In function 'forward': hmmFwBw.c:142:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 142 | for(k=1; k<n; k++) | ^~~ hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 145 | for (k = 0; k<n; k++) { | ^~~ In file included from hmmFwBw.c:45: hmmHeader.h: At top level: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmmMiscFunctions.c -o hmmMiscFunctions.o hmmMiscFunctions.c: In function 'SStatsGamma': hmmMiscFunctions.c:235:37: warning: format '%d' expects argument of type 'int', but argument 2 has type 'double' [-Wformat=] 235 | if(!(logPP <= epsilon)) Rprintf("[SSallocGamma] -- \ | ^~~~~~~~~~~~~~~~~~~~ 236 | Assertion about to fail! logPP= %d\n", logPP); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ | | | double hmmMiscFunctions.c: In function 'SStatsNormExp': hmmMiscFunctions.c:384:10: warning: unused variable 'wi' [-Wunused-variable] 384 | double wi, *newEx; | ^~ hmmMiscFunctions.c: In function 'UpdateNormExp': hmmMiscFunctions.c:417:10: warning: unused variable 'epsilon' [-Wunused-variable] 417 | double epsilon=0.00001; | ^~~~~~~ In file included from hmmHeader.h:36, from hmmMiscFunctions.c:43: UsefulValues.h: At top level: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmmViterbi.c -o hmmViterbi.o In file included from hmmViterbi.c:48: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-groHMM/00new/groHMM/libs/x64 ** 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 ** 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 | 0.61 | 0.09 | 0.92 | |
combineTranscripts | 0.34 | 0.00 | 0.35 | |
detectTranscripts | 0.28 | 0.02 | 0.55 | |
evaluateHMMInAnnotations | 0.25 | 0.00 | 0.25 | |
getCores | 0 | 0 | 0 | |
getTxDensity | 0.01 | 0.00 | 0.03 | |
limitToXkb | 0.10 | 0.00 | 0.09 | |
makeConsensusAnnotations | 0 | 0 | 0 | |
metaGene | 0.14 | 0.00 | 0.14 | |
pausingIndex | 0.26 | 0.03 | 0.30 | |
polymeraseWave | 1.39 | 0.11 | 1.56 | |
runMetaGene | 0.04 | 0.00 | 0.03 | |
windowAnalysis | 0.21 | 0.00 | 0.22 | |
writeWiggle | 0.22 | 0.02 | 0.24 | |