BioC 2.12: CHECK report for pathview on moscato2

Package: pathview

Version: 1.1.4

Command: rm -rf pathview.buildbin-libdir && mkdir pathview.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathview.buildbin-libdir pathview_1.1.4.tar.gz >pathview-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=pathview.buildbin-libdir --install="check:pathview-install.out" --force-multiarch --no-vignettes --timings pathview_1.1.4.tar.gz && mv pathview.buildbin-libdir/* pathview.Rcheck/ && rmdir pathview.buildbin-libdir

StartedAt: 2013-10-09 03:27:27 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:33:25 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 357.7 seconds

RetCode: 0

Status: OK

CheckDir: pathview.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/pathview.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 'pathview/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathview' version '1.1.4'
* 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 'pathview' 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
File 'pathview/R/zzz.R':
  .onLoad calls:
    installed.packages()
    packageStartupMessage(wordwrap(disclaimer, 80))

Package startup functions should not call 'installed.packages'.
See section 'Good practice' in '?.onAttach'.

col.key: no visible binding for global variable 'node.sizes'
cpd2kegg: no visible binding for global variable 'rn.list'
cpdidmap: no visible binding for global variable 'cpd.accs'
cpdkegg2name: no visible binding for global variable 'kegg.met'
cpdname2kegg: no visible binding for global variable 'cpd.names'
eg2id: no visible global function definition for 'biocLite'
id2eg: no visible global function definition for 'biocLite'
kegg.species.code: no visible binding for global variable 'korg'
keggview.graph: no visible binding for global variable
  'KEGGEdgeSubtype'
keggview.graph: no visible binding for global variable 'nplot'
keggview.graph: no visible binding for global variable 'sci.gene'
keggview.native: no visible binding for global variable 'nplot'
pathview: no visible binding for global variable 'bods'
pathview: no visible binding for global variable 'rn.list'
sim.mol.data: no visible binding for global variable 'cpd.accs'
sim.mol.data: no visible binding for global variable 'rn.list'
sim.mol.data: no visible binding for global variable 'ko.ids'
* 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' ... [46s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
pathview 13.46   1.27   16.19
eg2id     9.16   0.09   12.15
** running examples for arch 'x64' ... [52s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
pathview 15.77   1.45   18.58
eg2id    10.94   0.11   11.27
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [23s]
 [23s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [25s]
 [25s] 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/pathview.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'pathview' ...
** 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 'pathview' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathview' as pathview_1.1.4.zip
* DONE (pathview)

BioC 2.12: CHECK report for pathview on moscato2

Summary

Command output