Package: cn.farms

Version: 1.7.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.7.1.tar.gz

StartedAt: 2013-01-16 01:41:02 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:44:30 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 207.9 seconds

RetCode: 0

Status:  OK

CheckDir: cn.farms.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.7.1’
* 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.farms’ can be installed ... 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 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mlSummarization 5.085  0.132   5.216
* 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.farms’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c laplace.cpp -o laplace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/usr/local/lib64 -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘cn.farms.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (cn.farms)

name	user	system	elapsed
combineData	1.816	0.024	1.841
createAnnotation	0.008	0.000	0.010
distributionDistance	0.528	0.004	0.531
dnaCopySf	0.164	0.004	0.168
fragLengCorr	3.920	0.008	3.934
mlSummarization	5.085	0.132	5.216
normalizeAverage	0.008	0.000	0.009
normalizeCels	0.004	0.004	0.008
normalizeNpData	0.008	0.004	0.012
plotDendrogram	0.504	0.004	0.511
plotDensity	0.604	0.008	0.611
plotEvalIc	0.728	0.016	0.781
plotRegions	0.18	0.00	0.18
plotSmoothScatter	0.356	0.020	0.374
plotViolines	0.184	0.000	0.185
slSummarization	4.524	0.032	4.558
sparseFarmsC	0.008	0.000	0.007
summarizeFarmsExact	0.012	0.000	0.014
summarizeFarmsExact2	0.012	0.004	0.014
summarizeFarmsExact3	0.020	0.000	0.019
summarizeFarmsGaussian	0.016	0.000	0.016
summarizeFarmsMethods	0.008	0.000	0.006
summarizeFarmsVariational	0.016	0.000	0.013
summarizeWindowBps	0.024	0.000	0.025
summarizeWindowMethods	0.016	0.000	0.017
summarizeWindowStd	0.016	0.000	0.016