Package: cn.mops

Version: 1.5.16

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.5.16.tar.gz

StartedAt: 2013-03-25 00:54:31 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:59:17 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 285.8 seconds

RetCode: 0

Status:  OK

CheckDir: cn.mops.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [25s/25s] 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 ... [59s/61s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cn.mops      22.334  0.168  22.955
exomecn.mops  7.172  0.008   7.214
* 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c segment.cpp -o segment.o
segment.cpp: In function ‘SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
segment.cpp:60:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
segment.cpp:61:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:62:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:63:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable]
segment.cpp:65:9: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
g++ -shared -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** 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	0.492	0.008	0.501
calcIntegerCopyNumbers	1.428	0.052	1.481
cn.mops	22.334	0.168	22.955
cnvr	0.488	0.012	0.503
cnvs	0.452	0.000	0.452
exomecn.mops	7.172	0.008	7.214
getReadCountsFromBAM	0.352	0.000	0.351
getSegmentReadCountsFromBAM	0.104	0.004	0.109
gr	0.448	0.000	0.450
haplocn.mops	2.176	0.008	2.364
individualCall	0.580	0.012	0.674
iniCall	0.480	0.008	0.498
integerCopyNumber	0.460	0.008	0.498
localAssessments	0.496	0.000	0.559
makeRobustCNVR	0.725	0.000	0.773
normalizeChromosomes	0.816	0.004	0.874
normalizeGenome	1.284	0.004	1.317
normalizedData	0.468	0.004	0.555
params	0.436	0.012	0.478
posteriorProbs	0.456	0.008	0.525
referencecn.mops	2.716	0.020	3.020
sampleNames	0.484	0.000	0.496
segment	0.064	0.000	0.066
segmentation	0.520	0.000	0.551
segplot	2.328	0.008	2.773