BioC 2.12: CHECK report for BiSeq on moscato2

Package: BiSeq

Version: 1.0.3

Command: rm -rf BiSeq.buildbin-libdir && mkdir BiSeq.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiSeq.buildbin-libdir BiSeq_1.0.3.tar.gz >BiSeq-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=BiSeq.buildbin-libdir --install="check:BiSeq-install.out" --force-multiarch --no-vignettes --timings BiSeq_1.0.3.tar.gz && mv BiSeq.buildbin-libdir/* BiSeq.Rcheck/ && rmdir BiSeq.buildbin-libdir

StartedAt: 2013-10-09 01:14:29 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:23:35 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 545.2 seconds

RetCode: 0

Status: OK

CheckDir: BiSeq.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/BiSeq.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 'BiSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiSeq' version '1.0.3'
* 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 'BiSeq' 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 ... 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 should probably not be installed:
  'unsrturl.bst'

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' ... [103s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
estLocCor        19.03   0.01   19.05
makeVariogram    17.86   0.00   17.89
betaRegression   16.94   0.03   16.98
summarizeRegions  6.43   0.14    6.57
plotBindingSites  6.06   0.02    6.18
** running examples for arch 'x64' ... [129s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
estLocCor         30.92   0.07   30.99
makeVariogram     26.75   0.00   26.76
betaRegression    18.62   0.01   18.75
summarizeRegions   6.10   0.11    6.21
compareTwoSamples  6.06   0.00    6.07
plotBindingSites   5.97   0.01    5.99
* 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
  'E:/biocbld/bbs-2.12-bioc/meat/BiSeq.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'BiSeq' ...
** R
** data
** 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 'BiSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiSeq' as BiSeq_1.0.3.zip
* DONE (BiSeq)

BioC 2.12: CHECK report for BiSeq on moscato2

Summary

Command output