BioC 2.13: CHECK report for ArrayTools on moscato1
This page was generated on 2014-04-05 09:49:45 -0700 (Sat, 05 Apr 2014).
ArrayTools 1.22.0 Arthur Li
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ArrayTools | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
Package: ArrayTools
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Version: 1.22.0
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Command: rm -rf ArrayTools.buildbin-libdir && mkdir ArrayTools.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayTools.buildbin-libdir ArrayTools_1.22.0.tar.gz >ArrayTools-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=ArrayTools.buildbin-libdir --install="check:ArrayTools-install.out" --force-multiarch --no-vignettes --timings ArrayTools_1.22.0.tar.gz && mv ArrayTools.buildbin-libdir/* ArrayTools.Rcheck/ && rmdir ArrayTools.buildbin-libdir
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StartedAt: 2014-04-05 02:16:17 -0700 (Sat, 05 Apr 2014)
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EndedAt: 2014-04-05 02:18:21 -0700 (Sat, 05 Apr 2014)
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EllapsedTime: 124.7 seconds
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RetCode: 0
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Status: OK
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CheckDir: ArrayTools.Rcheck
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Warnings: 0
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Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/ArrayTools.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ArrayTools' version '1.22.0'
* 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 'ArrayTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'affy' 'Biobase' 'methods'
A package should be listed in only one of these fields.
* 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
preProcessGeneST: no visible binding for global variable
'hugene10stCONTROL'
preProcessGeneST: no visible binding for global variable
'mogene10stCONTROL'
regress: no visible global function definition for 'permute.1'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'ArrayTools.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [13s] OK
** running examples for arch 'x64' ... [13s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
preProcess3prime 5.07 0.03 5.1
* 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 3 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/ArrayTools.Rcheck/00check.log'
for details.
ArrayTools.Rcheck/00install.out:
install for i386
* installing *source* package 'ArrayTools' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'ArrayTools'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'ArrayTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayTools' as ArrayTools_1.22.0.zip
* DONE (ArrayTools)
ArrayTools.Rcheck/examples_i386/ArrayTools-Ex.timings:
name | user | system | elapsed
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Output2HTML | 0.12 | 0.00 | 0.12 |
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QC | 0.02 | 0.00 | 0.01 |
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Sort | 0.21 | 0.00 | 0.41 |
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contrastMatrix-class | 0.05 | 0.00 | 0.04 |
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createExpressionSet | 0.07 | 0.00 | 0.08 |
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createGSEAFiles | 0 | 0 | 0 |
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createIndex | 0.29 | 0.00 | 0.30 |
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createIngenuityFile | 0.07 | 0.00 | 0.06 |
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designMatrix-class | 0.00 | 0.01 | 0.01 |
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eSetExample | 0.02 | 0.00 | 0.02 |
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exprsExample | 0 | 0 | 0 |
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geneFilter | 2.81 | 0.08 | 2.89 |
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interactionResult-class | 0.38 | 0.00 | 0.37 |
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pDataExample | 0.00 | 0.02 | 0.02 |
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postInteraction | 0.21 | 0.00 | 0.22 |
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preProcess3prime | 4.79 | 0.04 | 4.85 |
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preProcessGeneST | 0.03 | 0.00 | 0.03 |
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qa3prime | 0 | 0 | 0 |
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qaGeneST | 0.03 | 0.00 | 0.03 |
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regress | 0.09 | 0.00 | 0.09 |
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regressResult-class | 0.09 | 0.00 | 0.09 |
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selectSigGene | 0.10 | 0.00 | 0.09 |
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selectSigGeneInt | 0.26 | 0.00 | 0.26 |
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ArrayTools.Rcheck/examples_x64/ArrayTools-Ex.timings:
name | user | system | elapsed
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Output2HTML | 0.15 | 0.00 | 0.16 |
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QC | 0.06 | 0.00 | 0.06 |
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Sort | 0.10 | 0.00 | 0.09 |
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contrastMatrix-class | 0.06 | 0.00 | 0.07 |
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createExpressionSet | 0.09 | 0.00 | 0.09 |
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createGSEAFiles | 0.02 | 0.00 | 0.02 |
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createIndex | 0.33 | 0.00 | 0.32 |
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createIngenuityFile | 0.08 | 0.00 | 0.08 |
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designMatrix-class | 0.07 | 0.00 | 0.08 |
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eSetExample | 0 | 0 | 0 |
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exprsExample | 0.02 | 0.00 | 0.02 |
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geneFilter | 2.89 | 0.03 | 2.91 |
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interactionResult-class | 0.35 | 0.00 | 0.36 |
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pDataExample | 0.02 | 0.00 | 0.02 |
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postInteraction | 0.24 | 0.00 | 0.24 |
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preProcess3prime | 5.07 | 0.03 | 5.10 |
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preProcessGeneST | 0.03 | 0.00 | 0.03 |
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qa3prime | 0.02 | 0.00 | 0.01 |
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qaGeneST | 0.03 | 0.00 | 0.04 |
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regress | 0.11 | 0.00 | 0.11 |
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regressResult-class | 0.11 | 0.00 | 0.10 |
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selectSigGene | 0.12 | 0.00 | 0.13 |
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selectSigGeneInt | 0.3 | 0.0 | 0.3 |
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