BioC 2.12: CHECK report for GSEAlm on moscato2

Package: GSEAlm

Version: 1.20.0

Command: rm -rf GSEAlm.buildbin-libdir && mkdir GSEAlm.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSEAlm.buildbin-libdir GSEAlm_1.20.0.tar.gz >GSEAlm-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=GSEAlm.buildbin-libdir --install="check:GSEAlm-install.out" --force-multiarch --no-vignettes --timings GSEAlm_1.20.0.tar.gz && mv GSEAlm.buildbin-libdir/* GSEAlm.Rcheck/ && rmdir GSEAlm.buildbin-libdir

StartedAt: 2013-10-09 02:30:59 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:32:30 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 91.0 seconds

RetCode: 0

Status: OK

CheckDir: GSEAlm.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GSEAlm.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSEAlm/DESCRIPTION' ... OK
* this is package 'GSEAlm' version '1.20.0'
* 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 'GSEAlm' 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
* 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 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 ... NOTE
pvalFromPermMat: warning in matrix(as.double(NA), nr = nrow(perms),
  ncol = 2): partial argument match of 'nr' to 'nrow'
* checking Rd files ... NOTE
prepare_Rd: gsealmPerm.Rd:62: Dropping empty section \references
* 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' ... NOTE
The following files contain a license that requires
distribution of original sources:
  'crop.sty'
Please ensure that you have complied with it.
The following files should probably not be installed:
  'alltt.sty', 'array.sty', 'chngpage.sty', 'color.sty', 'crop.sty',
  'float.sty', 'flushend.sty', 'graphicx.sty', 'landscap.sty',
  'natbib.bst', 'natbib.sty', 'rmgreek.sty', 'stfloats.sty',
  'times.sty', 'url.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
gsealmPerm  7.1      0     7.1
** running examples for arch 'x64' ... [8s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
gsealmPerm 5.02   0.01    5.04
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'graph' 'lattice'
* 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

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/GSEAlm.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'GSEAlm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GSEAlm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSEAlm' as GSEAlm_1.20.0.zip
* DONE (GSEAlm)

BioC 2.12: CHECK report for GSEAlm on moscato2

Summary

Command output