BioC 2.12: CHECK report for rols on moscato2

Package: rols

Version: 1.1.6

Command: rm -rf rols.buildbin-libdir && mkdir rols.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rols.buildbin-libdir rols_1.1.6.tar.gz >rols-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=rols.buildbin-libdir --install="check:rols-install.out" --force-multiarch --no-vignettes --timings rols_1.1.6.tar.gz && mv rols.buildbin-libdir/* rols.Rcheck/ && rmdir rols.buildbin-libdir

StartedAt: 2013-03-25 04:40:09 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:44:36 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 266.4 seconds

RetCode: 0

Status: OK

CheckDir: rols.Rcheck

Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/rols.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 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '1.1.6'
* 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 'rols' 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 ... NOTE
Found the following possibly unsafe calls:
File 'rols/R/queries.R':
  unlockBinding("ontologies", .rolsEnv)
* 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... [91s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
allIds        59.77   0.03   68.21
CVParam-class  1.77   0.03    9.47
** running examples for arch 'x64' ... [90s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
allIds        61.09   0.06   69.33
CVParam-class  1.33   0.07    7.33
* 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/rols.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'rols' ...
** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
   'rols.Rnw' 
processing file: rols.Rnw
output file: E:\biocbld\bbs-2.12-bioc\meat\rols.buildbin-libdir\rols\doc\rols.R
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class

install for x64

* installing *source* package 'rols' ...
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
* MD5 sums
packaged installation of 'rols' as rols_1.1.6.zip
* DONE (rols)

Summary

Command output