Package: cn.mops

Version: 1.5.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.mops_1.5.16.tar.gz

StartedAt: 2013-03-25 01:52:56 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:56:45 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 228.2 seconds

RetCode: 0

Status:  OK

CheckDir: cn.mops.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cn.mops.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 'cn.mops/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.mops' version '1.5.16'
* 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 'cn.mops' can be installed ... [20s/20s] 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
cn.mops      16.646  0.433  17.097
exomecn.mops  8.440  0.145   8.593
* 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 'cn.mops' ...
** 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 R_init_cnmops.c -o R_init_cnmops.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c cnmops.cpp -o cnmops.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
segment.cpp:65: warning: unused variable 'Rf_beta'
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck/cn.mops/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'cn.mops'
** help
*** installing help indices
** building package indices
** installing vignettes
   'cn.mops.Rnw' 
** testing if installed package can be loaded
* DONE (cn.mops)

name	user	system	elapsed
CNVDetectionResult	0.012	0.010	0.021
calcIntegerCopyNumbers	1.152	0.035	1.188
cn.mops	16.646	0.433	17.097
cnvr	0.593	0.018	0.610
cnvs	0.589	0.020	0.610
exomecn.mops	8.440	0.145	8.593
getReadCountsFromBAM	0.281	0.045	0.331
getSegmentReadCountsFromBAM	0.087	0.011	0.098
gr	0.587	0.017	0.604
haplocn.mops	2.662	0.032	2.694
individualCall	0.640	0.021	0.663
iniCall	0.626	0.020	0.647
integerCopyNumber	0.617	0.019	0.637
localAssessments	0.598	0.017	0.615
makeRobustCNVR	0.747	0.015	0.763
normalizeChromosomes	0.797	0.055	0.853
normalizeGenome	0.585	0.055	0.640
normalizedData	0.405	0.013	0.417
params	0.369	0.019	0.388
posteriorProbs	0.366	0.014	0.380
referencecn.mops	1.706	0.023	1.730
sampleNames	0.528	0.017	0.547
segment	0.059	0.007	0.066
segmentation	0.528	0.015	0.544
segplot	2.389	0.029	2.420