BioC 2.12: CHECK report for KEGGprofile on moscato2

Package: KEGGprofile

Version: 1.2.0

Command: rm -rf KEGGprofile.buildbin-libdir && mkdir KEGGprofile.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGprofile.buildbin-libdir KEGGprofile_1.2.0.tar.gz >KEGGprofile-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=KEGGprofile.buildbin-libdir --install="check:KEGGprofile-install.out" --force-multiarch --no-vignettes --timings KEGGprofile_1.2.0.tar.gz && mv KEGGprofile.buildbin-libdir/* KEGGprofile.Rcheck/ && rmdir KEGGprofile.buildbin-libdir

StartedAt: 2013-10-09 02:47:50 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:51:05 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 195.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: KEGGprofile.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/KEGGprofile.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 'KEGGprofile/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGprofile' version '1.2.0'
* 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 'KEGGprofile' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See 'E:/biocbld/bbs-2.12-bioc/meat/KEGGprofile.Rcheck/00install.out' for details.
* 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
parse_XMLfile: warning in xmlTreeParse(paste(database_dir, "/", specis,
  pathway_id, ".xml", sep = ""), useInternal = TRUE): partial argument
  match of 'useInternal' to 'useInternalNodes'
plot_profile: no visible binding for global variable 'x'
plot_profile: no visible binding for global variable 'y'
* 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' ... [25s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plot_pathway          9.28   0.36    9.64
find_enriched_pathway 5.95   0.11    6.05
** running examples for arch 'x64' ... [22s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_pathway 8.99    0.3    9.28
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/KEGGprofile.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'KEGGprofile' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0

install for x64

* installing *source* package 'KEGGprofile' ...
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
* MD5 sums
packaged installation of 'KEGGprofile' as KEGGprofile_1.2.0.zip
* DONE (KEGGprofile)

BioC 2.12: CHECK report for KEGGprofile on moscato2

Summary

Command output