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BioC 3.3: CHECK report for pathview on oaxaca

This page was generated on 2016-10-13 12:59:00 -0700 (Thu, 13 Oct 2016).

Package 835/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.12.0
Weijun Luo
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/pathview
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pathview
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pathview_1.12.0.tar.gz
StartedAt: 2016-10-13 04:53:02 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 04:55:53 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 171.1 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 pathview_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pathview.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pathview’ can be installed ... 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
Package in Depends field not imported from: ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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'.

circles: no visible global function definition for ‘polygon’
col.key: no visible binding for global variable ‘node.sizes’
col.key: no visible global function definition for ‘image’
col.key: no visible global function definition for ‘text’
colorpanel2: no visible global function definition for ‘col2rgb’
colorpanel2: no visible global function definition for ‘rgb’
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’
download.kegg: no visible global function definition for
  ‘download.file’
ellipses: no visible global function definition for ‘polygon’
geneannot.map: no visible binding for global variable ‘bods’
geneannot.map: no visible global function definition for ‘biocLite’
geneannot.map: no visible global function definition for ‘columns’
geneannot.map: no visible global function definition for ‘select’
kegg.legend: no visible global function definition for ‘par’
kegg.legend: no visible global function definition for ‘text’
kegg.legend: no visible global function definition for ‘segments’
kegg.legend: no visible global function definition for ‘polygon’
kegg.legend: no visible global function definition for ‘rect’
kegg.species.code: no visible binding for global variable ‘korg’
keggview.graph: no visible binding for global variable
  ‘KEGGEdgeSubtype’
keggview.graph: no visible global function definition for ‘pdf’
keggview.graph: no visible global function definition for ‘par’
keggview.graph: no visible global function definition for ‘layout’
keggview.graph: no visible global function definition for ‘text’
keggview.graph: no visible global function definition for ‘dev.off’
keggview.native: no visible global function definition for ‘png’
keggview.native: no visible global function definition for ‘par’
keggview.native: no visible global function definition for
  ‘rasterImage’
keggview.native: no visible global function definition for ‘dev.off’
mol.sum: no visible binding for global variable ‘IQR’
pathview: no visible binding for global variable ‘bods’
pathview: no visible binding for global variable ‘rn.list’
pathview.stamp: no visible global function definition for ‘text’
render.kegg.node: no visible global function definition for ‘text’
render.kegg.node: no visible global function definition for ‘col2rgb’
sim.mol.data: no visible binding for global variable ‘bods’
sim.mol.data: no visible global function definition for ‘biocLite’
sim.mol.data: no visible global function definition for ‘keys’
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’
sim.mol.data: no visible global function definition for ‘rnorm’
sliced.shapes: no visible global function definition for ‘polygon’
subtypeDisplay,KEGGEdge: Error while checking: only works for closures
Undefined global functions or variables:
  IQR KEGGEdgeSubtype biocLite bods col2rgb columns cpd.accs cpd.names
  dev.off download.file image kegg.met keys ko.ids korg layout
  node.sizes par pdf png polygon rasterImage rect rgb rn.list rnorm
  segments select text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "png", "rgb")
  importFrom("graphics", "image", "layout", "par", "polygon",
             "rasterImage", "rect", "segments", "text")
  importFrom("stats", "IQR", "rnorm")
  importFrom("utils", "download.file")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
pathview 11.405  1.083  13.658
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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.accs0.1130.0120.126
cpdidmap0.5750.0480.624
download.kegg0.0190.0073.149
eg2id1.7820.0421.839
kegg.species.code0.0170.0010.018
korg0.0180.0020.021
mol.sum1.0550.0241.081
node.color0.3110.0140.326
node.info0.5100.0060.516
node.map0.2960.0030.299
pathview11.405 1.08313.658
sim.mol.data1.2170.0534.326
wordwrap0.0010.0000.001