Package: cn.farms

Version: 1.3.5

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.3.5.tar.gz

StartedAt: 2012-03-23 23:52:26 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:54:57 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 150.7 seconds

RetCode: 0

Status:  OK

CheckDir: cn.farms.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.3.5’
* 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 whether package ‘cn.farms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 examples ... OK
* 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-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c laplace.cpp -o laplace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: /loc/home/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/00_pkg_src/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘cn.farms.Rnw’ 
** testing if installed package can be loaded
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: /loc/home/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/00_pkg_src/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================

* DONE (cn.farms)

name	user	system	elapsed
combineData	1.848	0.032	1.884
createAnnotation	0	0	0
distributionDistance	0.440	0.012	0.459
dnaCopySf	0.168	0.004	0.172
fragLengCorr	4.136	0.028	4.169
mlSummarization	4.517	0.112	4.637
normalizeAverage	0.004	0.000	0.002
normalizeCels	0.000	0.000	0.001
normalizeNpData	0	0	0
plotDendrogram	0.424	0.008	0.432
plotDensity	0.608	0.012	0.618
plotEvalIc	0.400	0.016	0.416
plotRegions	0.464	0.008	0.469
plotSmoothScatter	0.952	0.020	0.972
plotViolines	0.176	0.004	0.178
slSummarization	4.168	0.036	4.211
sparseFarmsC	0.000	0.000	0.001
summarizeFarmsExact	0.008	0.000	0.007
summarizeFarmsExact2	0.004	0.004	0.007
summarizeFarmsExact3	0.008	0.000	0.007
summarizeFarmsGaussian	0.004	0.000	0.003
summarizeFarmsMethods	0.004	0.000	0.003
summarizeFarmsVariational	0.004	0.000	0.004
summarizeWindowBps	0.008	0.000	0.008
summarizeWindowMethods	0.004	0.000	0.002
summarizeWindowStd	0.004	0.000	0.004