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Package 92/514HostnameOS / ArchBUILDCHECKBUILD BIN
ChIPseqR 1.8.0
Peter Humburg
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/ChIPseqR
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: ChIPseqR
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPseqR_1.8.0.tar.gz
StartedAt: 2012-03-24 00:11:55 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:19:12 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 437.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ChIPseqR.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.8.0'
* 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 'ChIPseqR' can be installed ... OK
* 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 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: startScore.Rd:38: Dropping empty section \references
* 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 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 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

ChIPseqR.Rcheck/00install.out:

* installing *source* package 'ChIPseqR' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66: warning: unused variable 'tmp_stat'
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ChIPseqR.so startScore.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/ChIPseqR.Rcheck/ChIPseqR/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Introduction.Rnw' 
** testing if installed package can be loaded

* DONE (ChIPseqR)

ChIPseqR.Rcheck/ChIPseqR-Ex.timings:

nameusersystemelapsed
BindScore28.342 1.68730.290
ChIPseqR-package0.0000.0000.001
RLEBindScore-class17.878 1.75319.860
RLEReadCounts-class0.0260.0000.027
ReadCounts0.0280.0000.029
alignFeature20.33211.24133.444
callBindingSites21.968 1.76424.239
pos2gff0.0080.0000.009
simpleNucCall20.454 1.78122.989
strandPileup0.0160.0000.016
windowCounts0.0660.0010.067