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BioC 3.0: CHECK report for groHMM on perceval

This page was generated on 2015-04-10 10:00:39 -0700 (Fri, 10 Apr 2015).

Package 405/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.0.2
Minho Chae, W. Lee Kraus
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/groHMM
Last Changed Rev: 96298 / Revision: 102249
Last Changed Date: 2014-10-31 12:24:01 -0700 (Fri, 31 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: groHMM
Version: 1.0.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch groHMM_1.0.2.tar.gz
StartedAt: 2015-04-10 02:30:07 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:35:10 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 302.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: groHMM.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch groHMM_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/groHMM.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘groHMM/DESCRIPTION’ ... OK
* this is package ‘groHMM’ version ‘1.0.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘MASS’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘GenomicAlignments’
  ‘rtracklayer’ ‘parallel’
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 ... [30s/32s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
 NOTE
Authors@R field gives more than one person with maintainer role:
  Minho Chae <minho.chae@gmail.com> [aut, cre]
  W Lee Kraus <lee.kraus@utsouthwestern.edu> [aut, cre]
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘S4Vectors’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
combineTranscripts: no visible global function definition for ‘Rle’
combineTranscripts: no visible global function definition for
  ‘seqlevels<-’
combineTranscripts: no visible global function definition for
  ‘seqlevels’
detectTranscripts: no visible global function definition for ‘Rle’
getLIValues: no visible global function definition for ‘Rle’
getTxDensity : <anonymous>: no visible global function definition for
  ‘Rle’
metaGene: no visible global function definition for ‘seqlevels<-’
metaGene: no visible global function definition for ‘seqlevels’
metaGene: no visible global function definition for ‘Rle’
metaGene_foreachChrom: no visible global function definition for ‘Rle’
readBed: no visible global function definition for ‘Rle’
samplingMetaGene : <anonymous>: no visible global function definition
  for ‘Rle’
samplingMetaGene: no visible global function definition for ‘Rle’
windowAnalysis : <anonymous>: no visible global function definition for
  ‘seqlevels<-’
windowAnalysis : <anonymous>: no visible global function definition for
  ‘Rle’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getCores’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/groHMM.Rcheck/00check.log’
for details.

groHMM.Rcheck/00install.out:

* installing *source* package ‘groHMM’ ...
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c AnnotateProbes.c -o AnnotateProbes.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c DecayAlgorithm.c -o DecayAlgorithm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c MLEfit.c -o MLEfit.o
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c RegisterRRoutines.c -o RegisterRRoutines.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Windowing.c -o Windowing.o
Windowing.c: In function ‘WindowAnalysis’:
Windowing.c:147: warning: unused variable ‘II’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hmmEM.c -o hmmEM.o
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hmmFwBw.c -o hmmFwBw.o
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function ‘SStatsNormExp’:
hmmMiscFunctions.c:385: warning: unused variable ‘wi’
hmmMiscFunctions.c: In function ‘UpdateNormExp’:
hmmMiscFunctions.c:418: warning: unused variable ‘epsilon’
hmmMiscFunctions.c: At top level:
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hmmViterbi.c -o hmmViterbi.o
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/groHMM.Rcheck/groHMM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (groHMM)

groHMM.Rcheck/groHMM-Ex.timings:

nameusersystemelapsed
breakTranscriptsOnGenes0.9070.0050.912
combineTranscripts0.4130.0080.420
detectTranscripts1.9420.0331.976
evaluateHMMInAnnotations0.2090.0020.213
getTxDensity0.0210.0000.021
limitToXkb0.1120.0010.113
makeConsensusAnnotations0.0010.0000.001
metaGene0.1740.0220.196
pausingIndex1.2370.0271.263
polymeraseWave2.9900.0833.073
runMetaGene0.0210.0000.022
windowAnalysis0.7820.0370.822
writeWiggle0.3610.0460.407