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BioC 3.5: CHECK report for piano on veracruz2

This page was generated on 2017-08-16 13:30:58 -0400 (Wed, 16 Aug 2017).

Package 981/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 1.16.2
Leif Varemo
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/piano
Last Changed Rev: 131627 / Revision: 131943
Last Changed Date: 2017-07-28 03:33:07 -0400 (Fri, 28 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: piano
Version: 1.16.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings piano_1.16.2.tar.gz
StartedAt: 2017-08-16 06:30:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:31:40 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 95.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: piano.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings piano_1.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/piano.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.2’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘piano’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/piano.Rcheck/00install.out’ for details.
* 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
'library' or 'require' call to ‘snowfall’ in package code.
  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 ... OK
* 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
networkPlot     5.126  0.073   5.386
GSAheatmap      4.858  0.099   5.110
GSAsummaryTable 4.768  0.093   5.008
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/piano.Rcheck/00check.log’
for details.


piano.Rcheck/00install.out:

* installing *source* package ‘piano’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘piano’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘piano’
* DONE (piano)

piano.Rcheck/piano-Ex.timings:

nameusersystemelapsed
GSAheatmap4.8580.0995.110
GSAsummaryTable4.7680.0935.008
consensusHeatmap1.6450.0441.740
consensusScores0.1210.0130.136
diffExp3.4620.1263.993
extractFactors0.4260.0090.442
geneSetSummary3.9820.0714.147
loadGSC0.0130.0000.014
loadMAdata0.2490.0070.264
networkPlot5.1260.0735.386
polarPlot1.6820.0281.758
runGSA3.5460.0533.697
runGSAhyper0.3100.0050.320
runQC1.0720.0321.161
writeFilesForKiwi0.1500.0040.155