a4Base 1.16.0
Tobias Verbeke , Willem Ligtenberg
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/a4Base | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 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 | |
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### Running command:
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### rm -rf a4Base.buildbin-libdir a4Base.Rcheck && mkdir a4Base.buildbin-libdir a4Base.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Base.buildbin-libdir a4Base_1.16.0.tar.gz >a4Base.Rcheck\00install.out 2>&1 && cp a4Base.Rcheck\00install.out a4Base-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=a4Base.buildbin-libdir --install="check:a4Base-install.out" --force-multiarch --no-vignettes --timings a4Base_1.16.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/a4Base.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-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 '1.16.0'
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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.
'library' or 'require' calls in package code:
'Cairo' 'gridSVG'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'AnnotationDbi' 'a4Preproc' 'annaffy' 'genefilter' 'glmnet' 'gplots'
'grid' 'mpm' 'multtest'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fTest: no visible global function definition for 'rowFtests'
fTest: no visible global function definition for 'mt.rawp2adjp'
filterVarInt: no visible global function definition for 'pOverA'
filterVarInt: no visible global function definition for 'filterfun'
filterVarInt: no visible global function definition for 'genefilter'
grid.imageGrob: no visible global function definition for 'grid.draw'
heatmap.expressionSet: no visible global function definition for 'unit'
heatmap.expressionSet: no visible global function definition for 'gpar'
heatmap.expressionSet : <anonymous>: no visible global function
definition for 'colorpanel'
heatmap.expressionSet: no visible global function definition for
'textGrob'
heatmap.expressionSet: no visible global function definition for
'grid.layout'
heatmap.expressionSet: no visible global function definition for
'grid.newpage'
heatmap.expressionSet: no visible global function definition for
'convertUnit'
heatmap.expressionSet: no visible global function definition for
'viewport'
heatmap.expressionSet: no visible global function definition for
'pushViewport'
heatmap.expressionSet: no visible global function definition for
'grid.text'
heatmap.expressionSet: no visible global function definition for
'grid.rect'
heatmap.expressionSet: no visible global function definition for
'popViewport'
heatmap.expressionSet: no visible global function definition for
'unit.c'
heatmap.expressionSet: no visible global function definition for
'grid.lines'
heatmap.expressionSet: no visible global function definition for
'grid.xaxis'
imageGrob: no visible global function definition for 'gTree'
imageGrob: no visible global function definition for 'gList'
lassoReg: no visible global function definition for 'glmnet'
makeImageRect: no visible global function definition for 'rectGrob'
makeImageRect: no visible global function definition for 'gpar'
plotLogRatio: no visible global function definition for 'addGeneInfo'
plotLogRatio: no visible global function definition for 'JavaGD'
plotLogRatio: no visible global function definition for 'CairoPNG'
plotLogRatio: no visible global function definition for 'viewport'
plotLogRatio: no visible global function definition for 'grid.layout'
plotLogRatio: no visible global function definition for 'pushViewport'
plotLogRatio: no visible global function definition for 'grid.rect'
plotLogRatio: no visible global function definition for 'gpar'
plotLogRatio: no visible global function definition for 'grid.text'
plotLogRatio: no visible global function definition for 'grid.garnish'
plotLogRatio: no visible global function definition for 'popViewport'
plotLogRatio: no visible global function definition for 'grid.lines'
plotLogRatio : <anonymous>: no visible global function definition for
'grid.lines'
plotLogRatio : <anonymous>: no visible global function definition for
'gpar'
plotLogRatio: no visible global function definition for 'grid.segments'
plotLogRatio: no visible global function definition for
'grid.hyperlink'
plotLogRatio: no visible global function definition for 'gPath'
plotLogRatio: no visible global function definition for 'grid.script'
plotLogRatio: no visible global function definition for 'gridToSVG'
probe2gene: no visible global function definition for 'aafSymbol'
probe2gene: no visible global function definition for 'getText'
tTest: no visible global function definition for 'rowttests'
tTest: no visible global function definition for 'mt.rawp2adjp'
tTest2: no visible global function definition for 'rowttests'
tTest2: no visible global function definition for 'mt.rawp2adjp'
volcanoplotter: no visible global function definition for
'grid.newpage'
volcanoplotter: no visible global function definition for
'plotViewport'
volcanoplotter: no visible global function definition for
'pushViewport'
volcanoplotter: no visible global function definition for 'textGrob'
volcanoplotter: no visible global function definition for 'unit'
volcanoplotter: no visible global function definition for 'gpar'
volcanoplotter: no visible global function definition for 'grobWidth'
volcanoplotter: no visible global function definition for
'convertHeight'
volcanoplotter: no visible global function definition for
'dataViewport'
volcanoplotter: no visible global function definition for 'grid.pretty'
volcanoplotter: no visible global function definition for
'current.viewport'
volcanoplotter: no visible global function definition for 'xaxisGrob'
volcanoplotter: no visible global function definition for 'grid.yaxis'
volcanoplotter: no visible global function definition for 'editGrob'
volcanoplotter: no visible global function definition for 'gEditList'
volcanoplotter: no visible global function definition for 'gEdit'
volcanoplotter: no visible global function definition for 'grid.draw'
volcanoplotter: no visible global function definition for 'grid.points'
volcanoplotter: no visible global function definition for 'grid.text'
topTable,MArrayLM : .local: no visible global function definition for
'topTableF'
topTable,MArrayLM : .local: no visible binding for global variable
'number'
topTable,MArrayLM : .local: no visible global function definition for
'toptable'
topTable,limma : .local: no visible global function definition for
'topTableF'
topTable,limma : .local: no visible binding for global variable
'number'
topTable,limma : .local: no visible global function definition for
'toptable'
* 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' ... [88s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
spectralMap 15.62 1.25 16.89
computeLogRatio 8.61 0.08 8.70
plotLogRatio 8.24 0.03 8.27
** running examples for arch 'x64' ... [91s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
spectralMap 16.49 0.73 17.22
computeLogRatio 11.48 0.11 12.21
plotLogRatio 8.64 0.06 8.70
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/a4Base.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'a4Base' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'a4Base' as a4Base_1.16.0.zip
* DONE (a4Base)