Package: exomeCopy

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch exomeCopy_1.6.0.tar.gz

StartedAt: 2013-05-01 05:05:52 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:09:20 -0700 (Wed, 01 May 2013)

EllapsedTime: 208.2 seconds

RetCode: 0

Status:  OK

CheckDir: exomeCopy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/exomeCopy.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [17s/17s] 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/38s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compileCopyCountSegments 5.940  0.108   6.126
plotCompiledCNV          5.232  0.076   5.399
exomeCopy                5.159  0.065   5.308
copyCountSegments        5.110  0.078   5.269
plot.exomeCopyObject     5.119  0.062   5.221
* 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

* installing *source* package 'exomeCopy' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c exomeCopy.c -o exomeCopy.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o exomeCopy.so exomeCopy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)

name	user	system	elapsed
ExomeCopy-class	0.013	0.006	0.018
compileCopyCountSegments	5.940	0.108	6.126
copyCountSegments	5.110	0.078	5.269
countBamInGRanges	0.693	0.013	0.716
exomeCopy	5.159	0.065	5.308
generateBackground	0.345	0.004	0.355
getGCcontent	0.050	0.005	0.075
negLogLike	0.033	0.005	0.038
plot.exomeCopyObject	5.119	0.062	5.221
plotCompiledCNV	5.232	0.076	5.399
subdivideGRanges	0.186	0.004	0.190