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Package 511/609HostnameOS / ArchBUILDCHECKBUILD BIN
rnaSeqMap 2.12.0
Michal Okoniewski
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/rnaSeqMap
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: rnaSeqMap
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rnaSeqMap_2.12.0.tar.gz
StartedAt: 2013-03-25 01:08:45 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:12:36 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 230.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rnaSeqMap.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/rnaSeqMap.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rnaSeqMap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rnaSeqMap' version '2.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'rnaSeqMap' can be installed ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
  /Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
See '/Users/biocbuild/bbs-2.11-bioc/meat/rnaSeqMap.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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 ... NOTE
qq_derivative_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F):
  partial argument match of 'plot' to 'plot.it'
qq_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F): partial
  argument match of 'plot' to 'plot.it'
bam2sig: no visible global function definition for 'dbGetQuery'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/rnaSeqMap.Rcheck/00check.log'
for details.

rnaSeqMap.Rcheck/00install.out:

* installing *source* package 'rnaSeqMap' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Rinit.c -o Rinit.o
In file included from Rinit.c:3:
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c gcoverage.c -o gcoverage.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c ghistogram.c -o ghistogram.o
ghistogram.c: In function 'ghistogram':
ghistogram.c:31: warning: operation on 'k' may be undefined
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c regionmining.c -o regionmining.o
regionmining.c: In function 'avg':
regionmining.c:12: warning: operation on 'n' may be undefined
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c splicingind.c -o splicingind.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rnaSeqMap.so Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/rnaSeqMap.Rcheck/rnaSeqMap/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'rnaSeqMap.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (rnaSeqMap)

rnaSeqMap.Rcheck/rnaSeqMap-Ex.timings:

nameusersystemelapsed
NDplots0.1240.0110.148
RleList2matrix0.0010.0000.001
addBamData000
addDataToReadset0.1200.0040.130
addExperimentsToReadset000
averageND0.0010.0000.001
bam2sig0.0000.0000.001
buildDESeq000
buildDGEList000
findRegionsAsIR000
findRegionsAsND0.0000.0000.001
gRanges2CamelMeasures0.0000.0010.000
geneInChromosome0.0000.0000.001
generators0.0010.0000.000
getBamData0.0000.0010.001
getCoverageFromRS000
getFCFromND000
getSIFromND000
getSumsExp000
measures000
normalizations0.0010.0000.001
normalizeBySum000
parseGff30.0000.0000.001
plotGeneCoverage000
readsInRange0.0000.0010.000
regionBasedCoverage0.0000.0000.001
regionCoverage000
rs.list0.0910.0060.102
setSpecies0.0010.0000.001
spaceInChromosome000