BioC 2.12: CHECK report for RpsiXML on moscato2

Package: RpsiXML

Version: 2.2.0

Command: rm -rf RpsiXML.buildbin-libdir && mkdir RpsiXML.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RpsiXML.buildbin-libdir RpsiXML_2.2.0.tar.gz >RpsiXML-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=RpsiXML.buildbin-libdir --install="check:RpsiXML-install.out" --force-multiarch --no-vignettes --timings RpsiXML_2.2.0.tar.gz && mv RpsiXML.buildbin-libdir/* RpsiXML.Rcheck/ && rmdir RpsiXML.buildbin-libdir

StartedAt: 2013-10-09 04:01:06 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:08:07 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 420.9 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/RpsiXML.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 'RpsiXML/DESCRIPTION' ... OK
* this is package 'RpsiXML' version '2.2.0'
* 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 'RpsiXML' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 33.8Mb
  sub-directories of 1Mb or more:
    extdata  32.7Mb
* 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 ... 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'underscore.sty'

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' ... [46s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
translateID 8.86   0.03    8.89
** running examples for arch 'x64' ... [58s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
translateID             7.79   0.05    7.91
graphSpeciesConverter   5.70   0.14    6.18
parsePsimi25Interaction 4.96   0.06    5.03
complexes               4.73   0.02    6.26
complexName             4.11   0.01    6.74
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'psimi25Source_test.R' [48s]
 [49s] OK
** running tests for arch 'x64'
  Running 'psimi25Source_test.R' [44s]
 [44s] 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 were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/RpsiXML.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RpsiXML' ...
** R
** 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 'RpsiXML' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RpsiXML' as RpsiXML_2.2.0.zip
* DONE (RpsiXML)