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BioC 3.0: CHECK report for pathview on oaxaca

This page was generated on 2015-04-10 10:07:01 -0700 (Fri, 10 Apr 2015).

Package 644/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.6.0
Weijun Luo
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/pathview
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: pathview
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pathview_1.6.0.tar.gz
StartedAt: 2015-04-10 02:02:55 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:07:14 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 259.1 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 --no-multiarch pathview_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/pathview.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [17s/22s] 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.
* 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'.

KEGGpathway2Graph2: no visible global function definition for
  ‘splitKEGGgroup’
KEGGpathway2Graph2: no visible global function definition for
  ‘expandKEGGPathway’
KEGGpathway2Graph2: no visible global function definition for ‘nodes’
KEGGpathway2Graph2: no visible global function definition for ‘edges’
KEGGpathway2Graph2: no visible global function definition for
  ‘getEntryID’
KEGGpathway2Graph2 : <anonymous>: no visible global function definition
  for ‘getEntryID’
KEGGpathway2Graph2: no visible global function definition for
  ‘subGraphByNodeType’
col.key: no visible binding for global variable ‘node.sizes’
combineKEGGnodes: no visible global function definition for
  ‘getKEGGnodeData’
combineKEGGnodes: no visible global function definition for
  ‘getKEGGedgeData’
combineKEGGnodes: no visible binding for global variable ‘getName’
combineKEGGnodes: no visible binding for global variable ‘getType’
combineKEGGnodes: no visible binding for global variable ‘getComponent’
combineKEGGnodes: no visible global function definition for
  ‘combineNodes’
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’
eg2id: no visible global function definition for ‘mappedkeys’
id2eg: no visible global function definition for ‘biocLite’
id2eg: no visible global function definition for ‘revmap’
id2eg: no visible global function definition for ‘mappedkeys’
kegg.species.code: no visible binding for global variable ‘korg’
keggview.graph: no visible global function definition for ‘subGraph’
keggview.graph: no visible global function definition for ‘nodes’
keggview.graph: no visible global function definition for ‘degree’
keggview.graph: no visible global function definition for
  ‘subKEGGgraph’
keggview.graph: no visible global function definition for
  ‘subtypeDisplay’
keggview.graph: no visible binding for global variable
  ‘KEGGEdgeSubtype’
keggview.graph: no visible global function definition for
  ‘edgeRenderInfo<-’
keggview.graph: no visible global function definition for
  ‘nodeRenderInfo’
keggview.graph: no visible global function definition for
  ‘graphRenderInfo’
node.info: no visible global function definition for ‘nodes’
node.info: no visible global function definition for ‘getKEGGnodeData’
node.info: no visible binding for global variable ‘getName’
node.info: no visible binding for global variable ‘getType’
node.info: no visible binding for global variable ‘getComponent’
parseKGML2: no visible global function definition for ‘xmlTreeParse’
parseKGML2: no visible global function definition for ‘xmlRoot’
parseKGML2: no visible global function definition for ‘xmlChildren’
parseKGML2: no visible binding for global variable ‘xmlName’
parseKGML2: no visible global function definition for
  ‘parsePathwayInfo’
parseKGML2: no visible binding for global variable ‘parseEntry’
parseKGML2: no visible binding for global variable ‘parseRelation’
parseKGML2: no visible binding for global variable ‘getEntryID’
parseReaction2: no visible global function definition for ‘xmlAttrs’
parseReaction2: no visible global function definition for ‘xmlChildren’
pathview: no visible binding for global variable ‘bods’
pathview: no visible binding for global variable ‘rn.list’
reaction2edge: no visible global function definition for ‘nodes’
reaction2edge: no visible global function definition for ‘edges’
reaction2edge: no visible global function definition for ‘removeEdge’
reaction2edge: no visible global function definition for ‘addEdge’
sim.mol.data: no visible global function definition for ‘revmap’
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’
subtypeDisplay.kedge : .local: no visible global function definition
  for ‘getSubtype’
subtypeDisplay.kedge : .local: no visible global function definition
  for ‘subtypeDisplay’
subtypeDisplay.kedge : .local: no visible binding for global variable
  ‘subtypeDisplay’
subtypeDisplay.kedge : .local: no visible global function definition
  for ‘getType’
subtypeDisplay,KEGGEdge : .local: no visible global function definition
  for ‘getSubtype’
subtypeDisplay,KEGGEdge : .local: no visible global function definition
  for ‘subtypeDisplay’
subtypeDisplay,KEGGEdge : .local: no visible binding for global
  variable ‘subtypeDisplay’
subtypeDisplay,KEGGEdge : .local: no visible global function definition
  for ‘getType’
* 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 ... [40s/45s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
pathview 15.648  0.992  18.223
eg2id     7.327  0.141   7.588
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [27s/28s]
 [28s/28s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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.accs0.3670.0260.394
cpdidmap0.6230.0700.694
download.kegg0.0220.0063.068
eg2id7.3270.1417.588
kegg.species.code0.0180.0010.020
korg0.0200.0010.020
mol.sum3.1120.0373.168
node.color0.5250.0130.539
node.info0.8410.0040.862
node.map0.5400.0160.558
pathview15.648 0.99218.223
sim.mol.data0.3560.0700.426
wordwrap0.0020.0000.002