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Package 469/671HostnameOS / ArchBUILDCHECKBUILD BIN
pathview 1.1.2
Weijun Luo
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/pathview
Last Changed Rev: 76120 / Revision: 76155
Last Changed Date: 2013-04-29 08:16:58 -0700 (Mon, 29 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: pathview
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pathview_1.1.2.tar.gz
StartedAt: 2013-05-01 09:06:38 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 09:11:33 -0700 (Wed, 01 May 2013)
EllapsedTime: 295.3 seconds
RetCode: 0
Status:  OK 
CheckDir: pathview.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pathview.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pathview/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathview' version '1.1.2'
* 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 ... [18s/40s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [58s/64s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
pathview 20.469  1.827  24.578
eg2id    14.927  0.359  15.471
mol.sum   5.132  0.151   5.313
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [23s/23s]
 [23s/24s] 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.

pathview.Rcheck/00install.out:

* 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
* DONE (pathview)

pathview.Rcheck/pathview-Ex.timings:

nameusersystemelapsed
cpd.accs0.5860.0310.617
cpdidmap0.9160.0820.997
download.kegg0.0530.0163.030
eg2id14.927 0.35915.471
kegg.species.code0.0390.0080.047
korg0.0610.0130.074
mol.sum5.1320.1515.313
node.color0.7270.0380.804
node.info1.1750.0091.195
node.map0.7490.0330.785
pathview20.469 1.82724.578
sim.mol.data0.4300.0560.488
wordwrap0.0270.0090.036