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BioC 2.12: CHECK report for exomeCopy on george2

This page was generated on 2013-10-09 09:37:49 -0700 (Wed, 09 Oct 2013).

Package 209/671HostnameOS / ArchBUILDCHECKBUILD BIN
exomeCopy 1.6.0
Michael Love
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/exomeCopy
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: exomeCopy
Version: 1.6.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings exomeCopy_1.6.0.tar.gz
StartedAt: 2013-10-09 01:37:13 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:41:18 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 244.4 seconds
RetCode: 0
Status:  OK 
CheckDir: exomeCopy.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/exomeCopy.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomeCopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomeCopy’ version ‘1.6.0’
* 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 ‘exomeCopy’ can be installed ... [22s/22s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compileCopyCountSegments 5.604  0.040   5.647
plotCompiledCNV          5.549  0.004   5.575
plot.exomeCopyObject     5.348  0.004   5.358
copyCountSegments        5.273  0.016   5.291
* 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

exomeCopy.Rcheck/00install.out:

* installing *source* package ‘exomeCopy’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c exomeCopy.c -o exomeCopy.o
gcc -std=gnu99 -shared -L/usr/local/lib -o exomeCopy.so exomeCopy.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/exomeCopy.Rcheck/exomeCopy/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (exomeCopy)

exomeCopy.Rcheck/exomeCopy-Ex.timings:

nameusersystemelapsed
ExomeCopy-class0.0080.0000.009
compileCopyCountSegments5.6040.0405.647
copyCountSegments5.2730.0165.291
countBamInGRanges0.5880.0200.607
exomeCopy4.8640.0044.868
generateBackground0.3520.0040.354
getGCcontent0.0720.0040.072
negLogLike0.0360.0000.040
plot.exomeCopyObject5.3480.0045.358
plotCompiledCNV5.5490.0045.575
subdivideGRanges0.1520.0000.149