Anusha Nagari
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/groHMM |
| Branch: RELEASE_3_9 |
| Last Commit: 991c027 |
| Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:05:39 -0400 (Wed, 16 Oct 2019).
| Package 720/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| groHMM 1.18.0 Anusha Nagari
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: groHMM |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings groHMM_1.18.0.tar.gz |
| StartedAt: 2019-10-16 02:12:25 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:16:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 220.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: groHMM.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings groHMM_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/groHMM.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.18.0’ * 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-3.9-bioc/meat/groHMM.Rcheck/00check.log’ for details.
groHMM.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL groHMM
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:0:
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,
^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.9-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]
int II = 0;
^~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:51:0:
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:36:0,
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;
^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-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]
for(k=1; k
groHMM.Rcheck/groHMM-Ex.timings
| name | user | system | elapsed | |
| breakTranscriptsOnGenes | 0.538 | 0.016 | 0.555 | |
| combineTranscripts | 0.200 | 0.044 | 0.244 | |
| detectTranscripts | 0.434 | 0.016 | 0.978 | |
| evaluateHMMInAnnotations | 0.107 | 0.000 | 0.107 | |
| getCores | 0 | 0 | 0 | |
| getTxDensity | 0.015 | 0.000 | 0.015 | |
| limitToXkb | 0.062 | 0.000 | 0.062 | |
| makeConsensusAnnotations | 0 | 0 | 0 | |
| metaGene | 0.114 | 0.000 | 0.114 | |
| pausingIndex | 0.454 | 0.008 | 0.479 | |
| polymeraseWave | 1.344 | 0.020 | 1.508 | |
| runMetaGene | 0.008 | 0.000 | 0.008 | |
| windowAnalysis | 0.334 | 0.008 | 0.346 | |
| writeWiggle | 0.351 | 0.004 | 0.356 | |