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BioC 2.14: CHECK report for CSAR on zin2

This page was generated on 2014-10-08 08:48:43 -0700 (Wed, 08 Oct 2014).

Package 200/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSAR 1.16.0
Jose M Muino
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CSAR
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: CSAR
Version: 1.16.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CSAR_1.16.0.tar.gz
StartedAt: 2014-10-07 22:57:43 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:59:37 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 113.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CSAR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/CSAR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSAR’ version ‘1.16.0’
* 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 ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
CSAR-package           6.940  0.028   7.035
getThreshold           6.848  0.008   6.884
permutatedWinScores    6.145  0.008   6.176
getPermutatedWinScores 6.044  0.008   6.080
* 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

CSAR.Rcheck/00install.out:

* installing *source* package ‘CSAR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CSAR.c -o CSAR.o
gcc -std=gnu99 -shared -L/usr/local/lib -o CSAR.so CSAR.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/CSAR.Rcheck/CSAR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: unique, unlist
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: unique, unlist
* DONE (CSAR)

CSAR.Rcheck/CSAR-Ex.timings:

nameusersystemelapsed
CSAR-package6.9400.0287.035
ChIPseqScore1.6680.0001.674
distance2Genes2.2960.0002.298
genesWithPeaks2.2490.0002.251
getPermutatedWinScores6.0440.0086.080
getThreshold6.8480.0086.884
loadMappedReads0.0000.0000.001
mappedReads2Nhits0.7320.0000.749
permutatedWinScores6.1450.0086.176
sampleSEP3_test0.0040.0000.002
score2wig1.7520.0001.763
sigWin2.2240.0002.244