Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 156/658HostnameOS / ArchBUILDCHECKBUILD BIN
CSAR 1.11.0
Jose M Muino
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CSAR
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: CSAR
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CSAR_1.11.0.tar.gz
StartedAt: 2013-03-25 01:58:57 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:01:45 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 168.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CSAR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CSAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CSAR' version '1.11.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'CSAR' can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package 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 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getThreshold           9.062  0.122   9.193
CSAR-package           8.159  0.135   8.301
getPermutatedWinScores 7.639  0.112   7.966
permutatedWinScores    7.446  0.103   7.550
* 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

CSAR.Rcheck/00install.out:

* installing *source* package 'CSAR' ...
** 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 CSAR.c -o CSAR.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 CSAR.so CSAR.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CSAR.Rcheck/CSAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: unique
** help
*** installing help indices
** building package indices
** installing vignettes
   'CSAR.Rnw' 
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: unique
* DONE (CSAR)

CSAR.Rcheck/CSAR-Ex.timings:

nameusersystemelapsed
CSAR-package8.1590.1358.301
ChIPseqScore2.1650.0192.185
distance2Genes2.9490.0252.974
genesWithPeaks2.9780.0263.007
getPermutatedWinScores7.6390.1127.966
getThreshold9.0620.1229.193
loadMappedReads0.0060.0070.012
mappedReads2Nhits0.8320.0130.845
permutatedWinScores7.4460.1037.550
sampleSEP3_test0.0110.0080.020
score2wig2.3540.0282.382
sigWin2.8870.0272.914