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BioC experimental data: CHECK report for DeSousa2013 on zin1

This page was generated on 2015-08-22 17:43:48 -0700 (Sat, 22 Aug 2015).

Package 61/246HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeSousa2013 1.5.0
Xin Wang
Snapshot Date: 2015-08-22 06:15:25 -0700 (Sat, 22 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/DeSousa2013
Last Changed Rev: 3281 / Revision: 3391
Last Changed Date: 2015-04-16 13:20:43 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
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 

Summary

Package: DeSousa2013
Version: 1.5.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DeSousa2013_1.5.0.tar.gz
StartedAt: 2015-08-22 07:56:42 -0700 (Sat, 22 Aug 2015)
EndedAt: 2015-08-22 08:00:46 -0700 (Sat, 22 Aug 2015)
EllapsedTime: 243.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DeSousa2013.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DeSousa2013_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/DeSousa2013.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeSousa2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeSousa2013’ version ‘1.5.0’
* 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 ‘DeSousa2013’ can be installed ... [16s/18s] OK
* checking installed package size ... NOTE
  installed size is 44.7Mb
  sub-directories of 1Mb or more:
    data  43.7Mb
* 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
Namespaces in Imports field not imported from:
  ‘frmaTools’ ‘hgu133plus2frmavecs’ ‘rgl’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pbs2unigenes: no visible global function definition for ‘mappedkeys’
* 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 ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
compGapStats   18.519  0.116  18.707
selTopVarGenes  5.649  0.023   5.692
pbs2unigenes    5.304  0.040   5.598
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-data-experiment/meat/DeSousa2013.Rcheck/00check.log’
for details.


DeSousa2013.Rcheck/00install.out:

* installing *source* package ‘DeSousa2013’ ...
** 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 (DeSousa2013)

DeSousa2013.Rcheck/DeSousa2013-Ex.timings:

nameusersystemelapsed
CRCPipeLine0.0010.0000.001
buildClassifier3.8480.0843.954
compGapStats18.519 0.11618.707
conClust0.7970.0080.805
data-AMC0.0020.0000.002
filterDiffGenes1.4480.0001.451
filterSamples0.1520.0000.158
findDiffGenes0.8820.0000.925
geneExpPre0.0010.0000.000
pamClassify0.1310.0000.131
pbs2unigenes5.3040.0405.598
progAMC0.0880.0040.238
selTopVarGenes5.6490.0235.692