Package: pathview

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pathview_0.99.9.tar.gz

StartedAt: 2013-03-25 03:57:16 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:01:18 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 242.3 seconds

RetCode: 0

Status:  OK

CheckDir: pathview.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pathview.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pathview/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathview' version '0.99.9'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'pathview' can be installed ... [19s/19s] 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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [46s/51s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
pathview 14.973  3.961  20.386
eg2id    11.655  0.363  12.037
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [16s/20s]
 [16s/21s] 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/pathview.Rcheck/00check.log'
for details.

* installing *source* package 'pathview' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'pathview.Rnw' 
** testing if installed package can be loaded
* DONE (pathview)

name	user	system	elapsed
cpd.accs	0.513	0.026	0.539
cpdidmap	0.535	0.047	0.583
download.kegg	0.050	0.017	3.100
eg2id	11.655	0.363	12.037
kegg.species.code	0.041	0.008	0.049
korg	0.040	0.008	0.048
mol.sum	3.272	0.095	3.367
node.color	0.549	0.036	0.585
node.info	1.041	0.014	1.055
node.map	0.511	0.035	0.555
pathview	14.973	3.961	20.386
sim.mol.data	0.640	0.050	0.696
wordwrap	0.004	0.008	0.012