BioC 2.12: CHECK report for MSnbase on moscato2

Package: MSnbase

Version: 1.7.25

Command: rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.7.25.tar.gz >MSnbase-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.7.25.tar.gz && mv MSnbase.buildbin-libdir/* MSnbase.Rcheck/ && rmdir MSnbase.buildbin-libdir

StartedAt: 2013-03-25 03:45:51 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:52:48 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 416.8 seconds

RetCode: 0

Status: OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/MSnbase.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnbase/DESCRIPTION' ... OK
* this is package 'MSnbase' version '1.7.25'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'MSnbase' 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... [77s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotMzDelta-methods 12.73   0.58   13.31
writeMzTabData       7.27   0.17   14.96
readMgfData          5.77   0.00    5.81
** running examples for arch 'x64' ... [93s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotMzDelta-methods 16.58   0.58   17.21
writeMzTabData       7.75   0.10   15.13
readMgfData          6.20   0.02    6.23
plotNA-methods       5.04   0.02    5.06
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'test-all.R' [30s]
 [31s] OK
** running tests for arch 'x64'
  Running 'test-all.R' [36s]
 [37s] 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
  'E:/biocbld/bbs-2.12-bioc/meat/MSnbase.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'MSnbase' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'scale' from package 'base' in package 'MSnbase'
** help
*** installing help indices
** building package indices
** installing vignettes
   'MSnbase-demo.Rnw' 
   'MSnbase-development.Rnw' 
   'MSnbase-io.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'MSnbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_1.7.25.zip
* DONE (MSnbase)

Summary

Command output