Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the groHMM package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 813/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
groHMM 1.26.0 (landing page) Anusha Nagari
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.26.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings groHMM_1.26.0.tar.gz |
StartedAt: 2021-10-14 10:05:51 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:09:04 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 192.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: groHMM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings groHMM_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/groHMM.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘groHMM/DESCRIPTION’ ... OK * this is package ‘groHMM’ version ‘1.26.0’ * 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 for sufficient/correct file permissions ... 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 * 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 files in ‘vignettes’ ... OK * checking examples ... 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/groHMM.Rcheck/00check.log’ for details.
groHMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL groHMM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘groHMM’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AnnotateProbes.c -o AnnotateProbes.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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] 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"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Windowing.c -o Windowing.o Windowing.c: In function ‘WindowAnalysis’: Windowing.c:147:6: warning: unused variable ‘II’ [-Wunused-variable] 147 | int II = 0; | ^~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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] 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, from hmmEM.c:51: 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"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmFwBw.c -o hmmFwBw.o hmmFwBw.c: In function ‘forward’: hmmFwBw.c:143:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 143 | 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’ 146 | 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] 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, from hmmFwBw.c:46: 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"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmMiscFunctions.c -o hmmMiscFunctions.o hmmMiscFunctions.c: In function ‘SStatsNormExp’: hmmMiscFunctions.c:385:10: warning: unused variable ‘wi’ [-Wunused-variable] 385 | double wi, *newEx; | ^~ hmmMiscFunctions.c: In function ‘UpdateNormExp’: hmmMiscFunctions.c:418:10: warning: unused variable ‘epsilon’ [-Wunused-variable] 418 | 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] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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] 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, from hmmViterbi.c:49: 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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/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 | 1.100 | 0.032 | 1.132 | |
combineTranscripts | 0.519 | 0.051 | 0.570 | |
detectTranscripts | 0.270 | 0.023 | 0.296 | |
evaluateHMMInAnnotations | 0.132 | 0.000 | 0.132 | |
getCores | 0.000 | 0.000 | 0.001 | |
getTxDensity | 0.023 | 0.000 | 0.023 | |
limitToXkb | 0.093 | 0.000 | 0.093 | |
makeConsensusAnnotations | 0 | 0 | 0 | |
metaGene | 0.111 | 0.000 | 0.110 | |
pausingIndex | 0.263 | 0.012 | 0.275 | |
polymeraseWave | 1.466 | 0.028 | 1.498 | |
runMetaGene | 0.058 | 0.000 | 0.068 | |
windowAnalysis | 0.305 | 0.019 | 0.349 | |
writeWiggle | 0.323 | 0.012 | 0.383 | |