Package: GeneRegionScan

Version: 1.14.0

Command: rm -rf GeneRegionScan.buildbin-libdir && mkdir GeneRegionScan.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.14.0.tar.gz >GeneRegionScan-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=GeneRegionScan.buildbin-libdir --install="check:GeneRegionScan-install.out" --force-multiarch --no-vignettes --timings GeneRegionScan_1.14.0.tar.gz && mv GeneRegionScan.buildbin-libdir/* GeneRegionScan.Rcheck/ && rmdir GeneRegionScan.buildbin-libdir

StartedAt: 2013-03-25 01:07:42 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:15:24 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 462.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/GeneRegionScan.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.14.0'
* 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 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 for portable file names ... 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
readGeneInput: warning in readFASTA(gene, strip.desc = FALSE): partial
  argument match of 'strip.desc' to 'strip.descs'
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' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   62.59   5.20   69.42
plotCoexpression 48.53   5.19   53.76
plotOnGene       17.24   0.02   17.25
exonStructure     9.22   0.00    9.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   68.47   5.19   73.73
plotCoexpression 55.83   4.93   60.80
plotOnGene       18.97   0.00   18.97
exonStructure    10.52   0.00   10.52
* 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
  'D:/biocbld/bbs-2.11-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
   'GeneRegionScan.Rnw' 
** 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_1.14.0.zip

* DONE (GeneRegionScan)