Package: inSilicoMerging

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch inSilicoMerging_1.2.3.tar.gz

StartedAt: 2013-03-25 00:06:11 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:14:58 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 527.3 seconds

RetCode: 0

Status:  OK

CheckDir: inSilicoMerging.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/inSilicoMerging.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'inSilicoMerging/DESCRIPTION' ... OK
* this is package 'inSilicoMerging' version '1.2.3'
* 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 'inSilicoMerging' 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
measureGenesOverlap            159.247 19.976 186.255
plotDendrogram                  27.276  1.972  20.566
measureSamplesOverlap           22.895  3.544  29.011
measureAsymmetry                19.474  5.069  39.112
measureGenesMeanCorrCoef        17.911  3.426  23.546
plotMDS                         17.040  2.062  21.219
measureSignificantGenesOverlap  11.337  3.968  17.665
measureSamplesMeanCorrCoef      11.708  3.380  16.936
plotRLE                          9.626  3.109  14.927
plotGeneWiseDensity              5.344  1.928   9.327
plotGeneWiseBoxPlot              5.343  1.871   8.986
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'inSilicoMerging_unit_tests.R'
 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 'inSilicoMerging' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'inSilicoMerging.Rnw' 
** testing if installed package can be loaded

* DONE (inSilicoMerging)

name	user	system	elapsed
measureAsymmetry	19.474	5.069	39.112
measureGenesMeanCorrCoef	17.911	3.426	23.546
measureGenesOverlap	159.247	19.976	186.255
measureSamplesMeanCorrCoef	11.708	3.380	16.936
measureSamplesOverlap	22.895	3.544	29.011
measureSignificantGenesOverlap	11.337	3.968	17.665
merge	1.107	0.349	2.970
plotDendrogram	27.276	1.972	20.566
plotGeneWiseBoxPlot	5.343	1.871	8.986
plotGeneWiseDensity	5.344	1.928	9.327
plotMDS	17.040	2.062	21.219
plotRLE	9.626	3.109	14.927