Package: Repitools

Version: 1.4.2

Command: rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.4.2.tar.gz >Repitools-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.4.2.tar.gz && mv Repitools.buildbin-libdir/* Repitools.Rcheck/ && rmdir Repitools.buildbin-libdir

StartedAt: 2013-03-25 02:48:48 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:58:32 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 584.2 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/Repitools.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 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.4.2'
* 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 'Repitools' can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 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' ... NOTE
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
The following files should probably not be installed:
  'analyses1.tex', 'analyses2.tex', 'datasets.tex', 'qc.tex',
  'sInfo.tex', 'utilities.tex', 'visualisations.tex'

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' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cpgDensityCalc 11.80   0.70   12.50
sequenceCalc   11.34   0.72   12.06
cpgDensityPlot  8.58   0.63    9.20
binPlots        5.63   0.22    6.15
gcContentCalc   4.66   0.25    5.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cpgDensityCalc 11.36   0.74   12.09
sequenceCalc   10.94   0.86   11.79
cpgDensityPlot  7.91   0.60   10.03
binPlots        5.95   0.22    6.57
findClusters    5.41   0.01    5.43
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'tests.R'
 OK
** running tests for arch 'x64'
  Running '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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-2.11-bioc/meat/Repitools.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Repitools' ...
** R
** data
** inst
** preparing package for lazy loading
in method for '.featureScores' with signature '"AffymetrixCelSet","GRanges"': no definition for class "AffymetrixCelSet"
in method for 'regionStats' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
in method for 'writeWig' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
in method for 'cpgBoxplots' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
in method for '.blocksStats' with signature '"AffymetrixCelSet","GRanges"': no definition for class "AffymetrixCelSet"
** help
*** installing help indices
** building package indices
** installing vignettes
   'Repitools_vignette.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'Repitools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.4.2.zip

* DONE (Repitools)