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CHECK report for groHMM on malbec1

This page was generated on 2019-04-16 11:50:56 -0400 (Tue, 16 Apr 2019).

Package 686/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.16.0
Anusha Nagari , Tulip Nandu , W. Lee Kraus
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/groHMM
Branch: RELEASE_3_8
Last Commit: 218ef0f
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: groHMM
Version: 1.16.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings groHMM_1.16.0.tar.gz
StartedAt: 2019-04-16 00:28:24 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:31:50 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 205.4 seconds
RetCode: 0
Status:  OK 
CheckDir: groHMM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings groHMM_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/groHMM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.0’
* 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-3.8-bioc/meat/groHMM.Rcheck/00check.log’
for details.



Installation output

groHMM.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL groHMM
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘groHMM’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.8-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:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hmmEM.c -o hmmEM.o
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;
               ^
In file included from hmmEM.c:51:0:
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmFwBw.c:46:0:
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
gcc -I"/home/biocbuild/bbs-3.8-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]
   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:36:0,
                 from hmmMiscFunctions.c:44:
hmmMiscFunctions.c: 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;
               ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmViterbi.c:49:0:
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
gcc -shared -L/home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (groHMM)

Tests output


Example timings

groHMM.Rcheck/groHMM-Ex.timings

nameusersystemelapsed
breakTranscriptsOnGenes0.5000.0040.503
combineTranscripts0.2080.0040.212
detectTranscripts0.9720.0201.065
evaluateHMMInAnnotations0.1040.0000.104
getCores000
getTxDensity0.0160.0000.016
limitToXkb0.0560.0000.057
makeConsensusAnnotations000
metaGene0.10.00.1
pausingIndex0.3640.0080.372
polymeraseWave1.3080.0161.357
runMetaGene0.0160.0000.018
windowAnalysis0.3240.0040.328
writeWiggle0.3320.0040.337