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BioC 3.2: CHECK report for MLP on oaxaca

This page was generated on 2016-04-23 10:24:54 -0700 (Sat, 23 Apr 2016).

Package 659/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLP 1.18.1
Tobias Verbeke
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MLP
Last Changed Rev: 115649 / Revision: 116712
Last Changed Date: 2016-04-01 12:33:18 -0700 (Fri, 01 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: MLP
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLP_1.18.1.tar.gz
StartedAt: 2016-04-23 02:13:45 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:17:58 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 252.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MLP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLP_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MLP.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLP’ version ‘1.18.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘AnnotationDbi’ ‘affy’ ‘plotrix’ ‘gplots’ ‘gmodels’ ‘gdata’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘MLP’ can be installed ... [9s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' calls to packages already attached by Depends:
  ‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘GO.db’ ‘GOstats’ ‘KEGG.db’ ‘Rgraphviz’ ‘annotate’ ‘org.Cf.eg.db’
  ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘reactome.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘affy’ ‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’ ‘plotrix’
  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
addGeneSetDescription: no visible binding for global variable ‘GOTERM’
addGeneSetDescription: no visible binding for global variable
  ‘KEGGPATHID2NAME’
addGeneSetDescription: no visible binding for global variable
  ‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
  ‘org.Mm.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
  ‘org.Hs.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
  ‘org.Rn.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
  ‘org.Cf.egGO2ALLEGS’
getGeneSets: no visible binding for global variable ‘GOBPANCESTOR’
getGeneSets: no visible binding for global variable ‘GOMFANCESTOR’
getGeneSets: no visible binding for global variable ‘GOCCANCESTOR’
getGeneSets: no visible binding for global variable ‘GOTERM’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2EXTID’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2NAME’
getGeneSets: no visible binding for global variable
  ‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
  ‘reactomePATHID2EXTID’
plotGOgraph: no visible global function definition for ‘GOGraph’
plotGOgraph: no visible global function definition for ‘removeNode’
plotGOgraph: no visible global function definition for ‘nodes’
plotGOgraph: no visible global function definition for ‘layoutGraph’
plotGOgraph: no visible global function definition for ‘colorpanel’
plotGOgraph: no visible global function definition for
  ‘nodeRenderInfo<-’
plotGOgraph: no visible global function definition for ‘getGOTerm’
plotGOgraph: no visible global function definition for ‘edgeRenderInfo’
plotGOgraph: no visible global function definition for
  ‘edgeRenderInfo<-’
plotGOgraph: no visible global function definition for
  ‘graphRenderInfo’
plotGOgraph: no visible global function definition for
  ‘graphRenderInfo<-’
plotGOgraph: no visible global function definition for ‘renderGraph’
plotGeneSetSignificance: no visible global function definition for
  ‘lookUp’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [76s/81s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
MLP         38.151  3.564  41.751
getGeneSets 20.872  2.151  27.824
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.MLP.R’ [83s/84s]
 [84s/84s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MLP.Rcheck/00check.log’
for details.


MLP.Rcheck/00install.out:

* installing *source* package ‘MLP’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MLP)

MLP.Rcheck/MLP-Ex.timings:

nameusersystemelapsed
MLP38.151 3.56441.751
getGeneSets20.872 2.15127.824
mlpBarplot0.0210.0010.022
plot.MLP4.4670.1844.809
plotGOgraph0.9510.0110.965
plotGeneSetSignificance1.0430.0241.455