Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:46 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE groHMM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 779/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
groHMM 1.22.0 Anusha Nagari
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: groHMM |
Version: 1.22.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:groHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings groHMM_1.22.0.tar.gz |
StartedAt: 2020-10-17 04:43:32 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 04:48:53 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 321.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: groHMM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:groHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings groHMM_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/groHMM.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'groHMM/DESCRIPTION' ... OK * this is package 'groHMM' version '1.22.0' * 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 ... OK * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/groHMM/libs/i386/groHMM.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/groHMM/libs/x64/groHMM.dll': 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. 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed polymeraseWave 0.95 0.1 6.7 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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 'C:/Users/biocbuild/bbs-3.11-bioc/meat/groHMM.Rcheck/00check.log' for details.
groHMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/groHMM_1.22.0.tar.gz && rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=groHMM.buildbin-libdir groHMM_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL groHMM_1.22.0.zip && rm groHMM_1.22.0.tar.gz groHMM_1.22.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 3956k 100 3956k 0 0 37.3M 0 --:--:-- --:--:-- --:--:-- 39.4M install for i386 * installing *source* package 'groHMM' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AnnotateProbes.c -o AnnotateProbes.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DecayAlgorithm.c -o DecayAlgorithm.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MLEfit.c -o MLEfit.o In file included from MLEfit.c:44: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RegisterRRoutines.c -o RegisterRRoutines.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Windowing.c -o Windowing.o Windowing.c: In function 'WindowAnalysis': Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable] int II = 0; ^~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmEM.c -o hmmEM.o In file included from hmmEM.c:51: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36, from hmmEM.c:51: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmFwBw.c -o hmmFwBw.o hmmFwBw.c: In function 'forward': hmmFwBw.c:143:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for(k=1; k<n; k++) ^~~ hmmFwBw.c:146:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' for (k = 0; k<n; k++) { ^~~ In file included from hmmFwBw.c:46: At top level: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36, from hmmFwBw.c:46: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmMiscFunctions.c -o hmmMiscFunctions.o hmmMiscFunctions.c: In function 'SStatsNormExp': hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable] double wi, *newEx; ^~ hmmMiscFunctions.c: In function 'UpdateNormExp': hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable] double epsilon=0.00001; ^~~~~~~ In file included from hmmHeader.h:36, from hmmMiscFunctions.c:44: At top level: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmViterbi.c -o hmmViterbi.o In file included from hmmViterbi.c:49: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36, from hmmViterbi.c:49: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/groHMM.buildbin-libdir/00LOCK-groHMM/00new/groHMM/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'groHMM' finding HTML links ... done RgammaMLE html Rnorm html Rnorm.exp html averagePlot html breakTranscriptsOnGenes html combineTranscripts html countMappableReadsInInterval html detectTranscripts html evaluateHMMInAnnotations html expressedGenes html getCores html getTxDensity html groHMM-package html limitToXkb html makeConsensusAnnotations html metaGene html metaGeneMatrix html metaGene_nL html pausingIndex html polymeraseWave html readBed html runMetaGene html tlsDeming html tlsLoess html tlsSvd html windowAnalysis html writeWiggle html ** 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 install for x64 * installing *source* package 'groHMM' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AnnotateProbes.c -o AnnotateProbes.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DecayAlgorithm.c -o DecayAlgorithm.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MLEfit.c -o MLEfit.o In file included from MLEfit.c:44: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RegisterRRoutines.c -o RegisterRRoutines.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Windowing.c -o Windowing.o Windowing.c: In function 'WindowAnalysis': Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable] int II = 0; ^~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmEM.c -o hmmEM.o In file included from hmmEM.c:51: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36, from hmmEM.c:51: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmFwBw.c -o hmmFwBw.o hmmFwBw.c: In function 'forward': hmmFwBw.c:143:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for(k=1; k<n; k++) ^~~ hmmFwBw.c:146:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' for (k = 0; k<n; k++) { ^~~ In file included from hmmFwBw.c:46: At top level: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36, from hmmFwBw.c:46: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmMiscFunctions.c -o hmmMiscFunctions.o hmmMiscFunctions.c: In function 'SStatsNormExp': hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable] double wi, *newEx; ^~ hmmMiscFunctions.c: In function 'UpdateNormExp': hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable] double epsilon=0.00001; ^~~~~~~ In file included from hmmHeader.h:36, from hmmMiscFunctions.c:44: At top level: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmViterbi.c -o hmmViterbi.o In file included from hmmViterbi.c:49: hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function] static double expSum(double *logValues, int length) { ^~~~~~ hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36, from hmmViterbi.c:49: UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable] static double VERY_LARGE_DOUBLE_VALUE = 1e20; ^~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'groHMM' as groHMM_1.22.0.zip * DONE (groHMM) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'groHMM' successfully unpacked and MD5 sums checked
groHMM.Rcheck/examples_i386/groHMM-Ex.timings
|
groHMM.Rcheck/examples_x64/groHMM-Ex.timings
|