BioC 2.13: CHECK report for cnvGSA on moscato1

Package: cnvGSA

Version: 1.6.0

Command: rm -rf cnvGSA.buildbin-libdir && mkdir cnvGSA.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cnvGSA.buildbin-libdir cnvGSA_1.6.0.tar.gz >cnvGSA-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=cnvGSA.buildbin-libdir --install="check:cnvGSA-install.out" --force-multiarch --no-vignettes --timings cnvGSA_1.6.0.tar.gz && mv cnvGSA.buildbin-libdir/* cnvGSA.Rcheck/ && rmdir cnvGSA.buildbin-libdir

StartedAt: 2014-04-05 03:13:37 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:16:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 165.5 seconds

RetCode: 0

Status:  OK

CheckDir: cnvGSA.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/cnvGSA.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cnvGSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cnvGSA' version '1.6.0'
* 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 whether package 'cnvGSA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'brglm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
f.add_binned_bhfdr: no visible binding for global variable 'GsSize'
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'cnvGSA-vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [62s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
cnvGSAFisher 44.06   0.38   44.52
getCnvGenes   5.85   0.08    7.36
** running examples for arch 'x64' ... [66s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
cnvGSAFisher 53.12   0.63   53.74
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/cnvGSA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'cnvGSA' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'cnvGSA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cnvGSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cnvGSA' as cnvGSA_1.6.0.zip
* DONE (cnvGSA)

name	user	system	elapsed
CnvGSAInput-class	0	0	0
CnvGSAOutput-class	2.14	0.11	2.36
cnvGSAFisher	44.06	0.38	44.52
cnvGSAexportBurdenStats	1.48	0.06	1.56
getCnvGenes	5.85	0.08	7.36
readGMT	1.42	0.00	1.55
readGVF	1.41	0.00	1.40
readParamsRFile	0.05	0.00	0.04
summary-methods	1.95	0.04	2.00

name	user	system	elapsed
CnvGSAInput-class	0.02	0.00	0.02
CnvGSAOutput-class	1.63	0.00	1.64
cnvGSAFisher	53.12	0.63	53.74
cnvGSAexportBurdenStats	1.26	0.08	1.41
getCnvGenes	4.49	0.09	4.58
readGMT	1.05	0.00	1.05
readGVF	1.15	0.00	1.15
readParamsRFile	0	0	0
summary-methods	1.16	0.06	1.22