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Package 393/472HostnameOS / ArchBUILDCHECKBUILD BIN
rnaSeqMap 2.7.7
Michal Okoniewski
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rnaSeqMap
Last Changed Rev: 56090 / Revision: 56351
Last Changed Date: 2011-06-09 17:02:42 -0700 (Thu, 09 Jun 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  ERROR  skipped  skipped 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: rnaSeqMap
Version: 2.7.7
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rnaSeqMap_2.7.7.tar.gz
StartedAt: 2011-06-22 05:05:54 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 05:09:48 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 234.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rnaSeqMap.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/rnaSeqMap.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaSeqMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rnaSeqMap’ version ‘2.7.7’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘rnaSeqMap’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata  25.5Mb
    scripts   1.9Mb
* 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... 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 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 sizes of PDF files under ‘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

rnaSeqMap.Rcheck/00install.out:

* installing *source* package ‘rnaSeqMap’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Rinit.c -o Rinit.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c gcoverage.c -o gcoverage.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c splicingind.c -o splicingind.o
gcc-4.2 -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-2.9-bioc/meat/rnaSeqMap.Rcheck/rnaSeqMap/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:base’:

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union


Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object(s) are masked from ‘package:IRanges’:

    updateObject

Loading required package: GenomicRanges
Loading required package: Biostrings
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘rnaSeqMap.Rnw’ 
** testing if installed package can be loaded

* DONE (rnaSeqMap)

rnaSeqMap.Rcheck/rnaSeqMap-Ex.timings:

nameusersystemelapsed
NDplots0.1350.0060.140
RleList2matrix0.0010.0000.001
addBamData0.0010.0000.001
addDataToReadset0.1540.0010.156
addExperimentsToReadset0.0000.0000.001
averageND0.0020.0000.002
buildDESeq0.0010.0010.001
buildDGEList0.0010.0000.001
findRegionsAsIR0.0010.0000.002
findRegionsAsND0.0010.0000.001
geneInChromosome0.0000.0000.001
getBamData0.0000.0010.001
getCoverageFromRS0.0010.0000.002
getFCFromND0.0020.0000.002
getSIFromND0.0010.0000.001
getSumsExp000
normalizeBySum0.0010.0000.002
plotGeneCoverage0.0010.0000.001
readsInRange0.0010.0010.001
regionBasedCoverage0.0020.0000.002
regionCoverage0.0010.0000.001
rs.list0.1110.0040.122
setSpecies0.0000.0000.001
spaceInChromosome0.0010.0000.001