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BioC experimental data: CHECK report for DeSousa2013 on moscato2

This page was generated on 2014-10-04 17:42:05 -0700 (Sat, 04 Oct 2014).

Package 52/197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeSousa2013 1.0.0
Xin Wang
Snapshot Date: 2014-10-04 07:15:22 -0700 (Sat, 04 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs/DeSousa2013
Last Changed Rev: 2799 / Revision: 3055
Last Changed Date: 2014-04-11 14:27:08 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: DeSousa2013
Version: 1.0.0
Command: rm -rf DeSousa2013.buildbin-libdir && mkdir DeSousa2013.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DeSousa2013.buildbin-libdir DeSousa2013_1.0.0.tar.gz >DeSousa2013-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DeSousa2013.buildbin-libdir --install="check:DeSousa2013-install.out" --force-multiarch --no-vignettes --timings DeSousa2013_1.0.0.tar.gz
StartedAt: 2014-10-04 09:38:11 -0700 (Sat, 04 Oct 2014)
EndedAt: 2014-10-04 09:51:03 -0700 (Sat, 04 Oct 2014)
EllapsedTime: 772.0 seconds
RetCode: 0
Status:  OK  
CheckDir: DeSousa2013.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf DeSousa2013.buildbin-libdir && mkdir DeSousa2013.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DeSousa2013.buildbin-libdir DeSousa2013_1.0.0.tar.gz >DeSousa2013-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DeSousa2013.buildbin-libdir --install="check:DeSousa2013-install.out" --force-multiarch --no-vignettes --timings DeSousa2013_1.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-data-experiment/meat/DeSousa2013.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeSousa2013/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeSousa2013' version '1.0.0'
* 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 whether package 'DeSousa2013' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [92s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
compGapStats   19.93   0.28   20.20
selTopVarGenes  7.86   0.02    7.90
pbs2unigenes    4.60   0.06   42.68
** running examples for arch 'x64' ... [89s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
compGapStats    24.23   0.30   27.86
selTopVarGenes  10.20   0.02   10.22
buildClassifier  6.47   0.06    9.07
pbs2unigenes     5.19   0.14    5.33
conClust         1.21   0.01    5.49
findDiffGenes    1.14   0.06    6.91
* 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-data-experiment/meat/DeSousa2013.Rcheck/00check.log'
for details.

DeSousa2013.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'DeSousa2013' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeSousa2013' as DeSousa2013_1.0.0.zip
* DONE (DeSousa2013)

DeSousa2013.Rcheck/examples_i386/DeSousa2013-Ex.timings:

nameusersystemelapsed
CRCPipeLine000
buildClassifier4.660.084.75
compGapStats19.93 0.2820.20
conClust1.100.034.51
data-AMC000
filterDiffGenes1.840.041.87
filterSamples0.190.010.20
findDiffGenes1.170.002.79
geneExpPre0.020.000.02
pamClassify0.20.00.2
pbs2unigenes 4.60 0.0642.68
progAMC0.110.000.11
selTopVarGenes7.860.027.90

DeSousa2013.Rcheck/examples_x64/DeSousa2013-Ex.timings:

nameusersystemelapsed
CRCPipeLine000
buildClassifier6.470.069.07
compGapStats24.23 0.3027.86
conClust1.210.015.49
data-AMC000
filterDiffGenes2.450.042.48
filterSamples0.170.000.74
findDiffGenes1.140.066.91
geneExpPre000
pamClassify0.190.010.20
pbs2unigenes5.190.145.33
progAMC0.130.000.97
selTopVarGenes10.20 0.0210.22