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BioC 2.14: CHECK report for pathview on morelia

This page was generated on 2014-10-08 09:06:14 -0700 (Wed, 08 Oct 2014).

Package 570/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.4.2
Weijun Luo
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/pathview
Last Changed Rev: 92580 / Revision: 95116
Last Changed Date: 2014-07-16 20:02:24 -0700 (Wed, 16 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: pathview
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pathview_1.4.2.tar.gz
StartedAt: 2014-10-08 00:35:19 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:39:26 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 247.2 seconds
RetCode: 0
Status:  OK 
CheckDir: pathview.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pathview_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/pathview.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathview’ version ‘1.4.2’
* 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 ... [14s/45s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘KEGGgraph’ ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'.

render.kegg.node: warning in sliced.shapes(plot.data$x + 0.5, height -
  plot.data$y, plot.data$width/2 - 0.5, plot.data$height/2 - 0.25, col
  = cols.ts, draw.border = F, shape = "rectangle"): partial argument
  match of 'col' to 'cols'
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.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 files in ‘vignettes’ ... OK
* checking examples ... [38s/44s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
pathview 15.376  0.953  18.447
eg2id     7.683  0.180   8.043
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [23s/24s]
 [24s/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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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.accs0.3390.0120.351
cpdidmap0.6130.0250.643
download.kegg0.0160.0042.897
eg2id7.6830.1808.043
kegg.species.code0.0170.0000.017
korg0.0200.0010.022
mol.sum3.0640.0393.105
node.color0.4830.0180.501
node.info0.8820.0060.889
node.map0.5760.0110.588
pathview15.376 0.95318.447
sim.mol.data0.3450.0450.390
wordwrap0.0020.0010.002