BioC 2.14: CHECK report for a4Base on moscato2
This page was generated on 2014-10-08 08:53:56 -0700 (Wed, 08 Oct 2014).
a4Base 1.12.0 Tobias Verbeke , Willem Ligtenberg
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/a4Base | Last Changed Rev: 88838 / Revision: 95116 | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
Summary
Package: a4Base
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Version: 1.12.0
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Command: rm -rf a4Base.buildbin-libdir && mkdir a4Base.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Base.buildbin-libdir a4Base_1.12.0.tar.gz >a4Base-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=a4Base.buildbin-libdir --install="check:a4Base-install.out" --force-multiarch --no-vignettes --timings a4Base_1.12.0.tar.gz
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StartedAt: 2014-10-07 22:20:53 -0700 (Tue, 07 Oct 2014)
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EndedAt: 2014-10-07 22:27:24 -0700 (Tue, 07 Oct 2014)
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EllapsedTime: 391.7 seconds
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RetCode: 0
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Status: OK
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CheckDir: a4Base.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf a4Base.buildbin-libdir && mkdir a4Base.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Base.buildbin-libdir a4Base_1.12.0.tar.gz >a4Base-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=a4Base.buildbin-libdir --install="check:a4Base-install.out" --force-multiarch --no-vignettes --timings a4Base_1.12.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/a4Base.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 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'JavaGD'
Depends: includes the non-default packages:
'grid' 'Biobase' 'AnnotationDbi' 'annaffy' 'mpm' 'genefilter' 'limma'
'multtest' 'glmnet' 'a4Preproc' 'a4Core' 'gplots'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'a4Base' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'Biobase' 'grid'
Please remove these calls from your code.
Packages in Depends field not imported from:
'AnnotationDbi' 'a4Preproc' 'annaffy' 'genefilter' 'glmnet' 'gplots'
'mpm' 'multtest'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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 ... NOTE
plotLogRatio: no visible global function definition for 'JavaGD'
plotLogRatio: no visible global function definition for 'grid.garnish'
plotLogRatio: no visible global function definition for
'grid.hyperlink'
plotLogRatio: no visible global function definition for 'grid.script'
plotLogRatio: no visible global function definition for 'gridToSVG'
* 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 examples ...
** running examples for arch 'i386' ... [94s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
spectralMap 14.89 1.11 16.07
computeLogRatio 11.34 0.10 11.43
plotLogRatio 9.13 0.05 9.18
** running examples for arch 'x64' ... [96s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
spectralMap 18.91 1.14 20.09
computeLogRatio 11.44 0.14 11.73
plotLogRatio 10.21 0.08 10.30
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
'E:/biocbld/bbs-2.14-bioc/meat/a4Base.Rcheck/00check.log'
for details.
a4Base.Rcheck/00install.out:
install for i386
* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
install for x64
* installing *source* package 'a4Base' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Base' as a4Base_1.12.0.zip
* DONE (a4Base)
a4Base.Rcheck/examples_i386/a4Base-Ex.timings:
name | user | system | elapsed
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a4palette | 0.01 | 0.00 | 0.01 |
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addQuantilesColors | 3.28 | 0.06 | 3.34 |
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boxPlot | 3.42 | 0.11 | 3.54 |
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combineTwoExpressionSet | 0 | 0 | 0 |
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computeLogRatio | 11.34 | 0.10 | 11.43 |
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createExpressionSet | 0.11 | 0.00 | 0.11 |
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filterVarInt | 2.71 | 0.04 | 2.76 |
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heatmap.expressionSet | 0.02 | 0.00 | 0.01 |
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histPvalue | 2.85 | 0.05 | 2.91 |
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histpvalueplotter | 3.15 | 0.03 | 4.77 |
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lassoReg | 2.67 | 0.05 | 2.98 |
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logReg | 0 | 0 | 0 |
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nlcvTT | 0 | 0 | 0 |
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plot1gene | 2.69 | 0.04 | 2.73 |
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plotComb2Samples | 3.27 | 0.27 | 3.54 |
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plotCombMultSamples | 2.76 | 0.45 | 3.21 |
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plotCombination2genes | 2.50 | 0.03 | 2.53 |
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plotLogRatio | 9.13 | 0.05 | 9.18 |
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probabilitiesPlot | 0 | 0 | 0 |
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probe2gene | 2.70 | 0.06 | 2.76 |
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profilesPlot | 2.40 | 0.03 | 2.45 |
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propdegenescalculation | 2.62 | 0.11 | 2.73 |
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replicates | 0 | 0 | 0 |
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spectralMap | 14.89 | 1.11 | 16.07 |
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tTest | 3.07 | 0.23 | 3.31 |
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volcanoPlot | 3.17 | 0.29 | 3.44 |
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a4Base.Rcheck/examples_x64/a4Base-Ex.timings:
name | user | system | elapsed
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a4palette | 0.02 | 0.00 | 0.02 |
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addQuantilesColors | 3.43 | 0.05 | 3.48 |
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boxPlot | 2.96 | 0.12 | 3.09 |
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combineTwoExpressionSet | 0 | 0 | 0 |
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computeLogRatio | 11.44 | 0.14 | 11.73 |
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createExpressionSet | 0.11 | 0.00 | 0.11 |
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filterVarInt | 2.65 | 0.07 | 2.71 |
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heatmap.expressionSet | 0.02 | 0.00 | 0.02 |
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histPvalue | 2.53 | 0.07 | 2.60 |
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histpvalueplotter | 2.57 | 0.10 | 2.68 |
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lassoReg | 2.64 | 0.04 | 2.83 |
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logReg | 0 | 0 | 0 |
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nlcvTT | 0 | 0 | 0 |
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plot1gene | 2.65 | 0.09 | 2.75 |
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plotComb2Samples | 2.42 | 0.25 | 2.67 |
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plotCombMultSamples | 2.85 | 0.52 | 3.37 |
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plotCombination2genes | 2.34 | 0.03 | 2.37 |
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plotLogRatio | 10.21 | 0.08 | 10.30 |
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probabilitiesPlot | 0 | 0 | 0 |
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probe2gene | 2.98 | 0.02 | 2.99 |
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profilesPlot | 2.28 | 0.06 | 2.34 |
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propdegenescalculation | 2.65 | 0.06 | 2.72 |
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replicates | 0 | 0 | 0 |
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spectralMap | 18.91 | 1.14 | 20.09 |
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tTest | 3.52 | 0.30 | 3.95 |
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volcanoPlot | 3.32 | 0.28 | 3.60 |
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