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BioC 3.0: CHECK report for piano on zin1

This page was generated on 2015-04-10 09:40:49 -0700 (Fri, 10 Apr 2015).

Package 660/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 1.6.2
Leif Varemo
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/piano
Last Changed Rev: 96647 / Revision: 102249
Last Changed Date: 2014-11-10 02:16:23 -0800 (Mon, 10 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: piano
Version: 1.6.2
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings piano_1.6.2.tar.gz
StartedAt: 2015-04-10 02:58:35 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:00:03 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 87.9 seconds
RetCode: 0
Status:  OK 
CheckDir: piano.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings piano_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/piano.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘1.6.2’
* 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 ‘piano’ can be installed ... [4s/4s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘affy’ ‘affyPLM’ ‘gtools’ ‘limma’ ‘plier’ ‘plotrix’ ‘rsbml’
  ‘snowfall’ ‘yeast2.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
GSCsignificanceBatch: no visible global function definition for
  ‘sfInit’
GSCsignificanceBatch: no visible global function definition for
  ‘sfLapply’
GSCsignificanceBatch: no visible global function definition for
  ‘sfStop’
diffExp: no visible global function definition for ‘lmFit’
diffExp: no visible global function definition for ‘makeContrasts’
diffExp: no visible global function definition for ‘contrasts.fit’
diffExp: no visible global function definition for ‘eBayes’
diffExp: no visible global function definition for ‘decideTests’
diffExp: no visible global function definition for ‘vennDiagram’
diffExp: no visible global function definition for ‘topTable’
loadGSC: no visible global function definition for ‘rsbml_read’
loadGSC: no visible global function definition for ‘reactions’
loadGSC: no visible global function definition for ‘model’
loadGSC: no visible global function definition for ‘reactants’
loadGSC: no visible global function definition for ‘products’
loadGSC: no visible global function definition for ‘modifiers’
loadGSC: no visible global function definition for ‘name’
loadGSC: no visible global function definition for ‘species’
loadGSC: no visible global function definition for ‘compartment’
loadMAdata: no visible global function definition for ‘ReadAffy’
loadMAdata: no visible global function definition for
  ‘normalize.AffyBatch.qspline’
loadMAdata: no visible global function definition for ‘justPlier’
loadMAdata: no visible global function definition for ‘rma’
loadMAdata: no visible global function definition for ‘mas5’
loadMAdata: no visible global function definition for ‘cdfName’
loadMAdata: no visible binding for global variable ‘yeast2ORF’
loadMAdata: no visible global function definition for ‘toTable’
loadMAdata: no visible binding for global variable ‘yeast2CHRLOC’
polarPlot: no visible global function definition for ‘mixedsort’
polarPlot: no visible global function definition for ‘radial.plot’
runQC : .runRnaDeg: no visible global function definition for
  ‘AffyRNAdeg’
runQC : .runRnaDeg: no visible global function definition for
  ‘plotAffyRNAdeg’
runQC : .runNuseRle: no visible global function definition for ‘fitPLM’
runQC : .runNuseRle: no visible global function definition for ‘RLE’
runQC : .runNuseRle: no visible global function definition for ‘NUSE’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [33s/34s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
diffExp 5.02  0.084   5.619
* 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/piano.Rcheck/00check.log’
for details.

piano.Rcheck/00install.out:

* installing *source* package ‘piano’ ...
** 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 (piano)

piano.Rcheck/piano-Ex.timings:

nameusersystemelapsed
GSAheatmap4.1720.0044.215
GSAsummaryTable4.1120.0044.181
consensusHeatmap0.1840.0080.193
consensusScores0.0880.0000.087
diffExp5.0200.0845.619
extractFactors0.6600.0360.698
geneSetSummary4.3330.0004.345
loadGSC0.0240.0000.024
loadMAdata0.5120.0320.544
networkPlot4.8880.0124.954
polarPlot1.0440.0441.089
runGSA4.1120.0044.124
runGSAhyper0.2120.0000.212
runQC1.6250.0441.864
writeFilesForKiwi0.1480.0040.157