BioC 2.12: CHECK report for GeneRegionScan on moscato2

Package: GeneRegionScan

Version: 1.16.0

Command: rm -rf GeneRegionScan.buildbin-libdir && mkdir GeneRegionScan.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.16.0.tar.gz >GeneRegionScan-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=GeneRegionScan.buildbin-libdir --install="check:GeneRegionScan-install.out" --force-multiarch --no-vignettes --timings GeneRegionScan_1.16.0.tar.gz && mv GeneRegionScan.buildbin-libdir/* GeneRegionScan.Rcheck/ && rmdir GeneRegionScan.buildbin-libdir

StartedAt: 2013-10-09 02:15:47 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:25:02 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 554.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GeneRegionScan.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 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.16.0'
* 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 'GeneRegionScan' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.4Mb
  sub-directories of 1Mb or more:
    exec  19.7Mb
* 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
plotOnGene,ExpressionSet: warning in plot.default(1, type = "n", xlab =
  "bp", ylab = ylab, frame = FALSE, xlim = xlim, ylim = ylim, main =
  paste("Expression of probes"), cex.main = 1): partial argument match
  of 'frame' to 'frame.plot'
plotCoexpression,ExpressionSet: no visible binding for global variable
  'interval'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [176s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   75.05   6.38   81.48
plotCoexpression 55.35   0.00   55.59
plotOnGene       19.17   0.02   19.18
exonStructure    10.50   0.01   10.52
** running examples for arch 'x64' ... [204s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   84.46   0.15   84.62
plotCoexpression 69.58   6.06   75.66
plotOnGene       21.45   0.00   21.73
exonStructure    12.73   0.00   12.73
* 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/GeneRegionScan.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GeneRegionScan' ...
** R
** data
** exec
** 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 'GeneRegionScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneRegionScan' as GeneRegionScan_1.16.0.zip
* DONE (GeneRegionScan)