a4Base 1.19.0
Tobias Verbeke , Willem Ligtenberg
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/a4Base | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings a4Base_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/a4Base.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.19.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘a4Base’ can be installed ... [11s/11s] 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
* 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: no visible global function definition for
‘topTableF’
topTable,MArrayLM: no visible binding for global variable ‘number’
topTable,MArrayLM: no visible global function definition for ‘toptable’
topTable,limma: no visible global function definition for ‘topTableF’
topTable,limma: no visible binding for global variable ‘number’
topTable,limma: no visible global function definition for ‘toptable’
Undefined global functions or variables:
CairoPNG JavaGD aafSymbol addGeneInfo colorpanel convertHeight
convertUnit current.viewport dataViewport editGrob filterfun gEdit
gEditList gList gPath gTree genefilter getText glmnet gpar grid.draw
grid.garnish grid.hyperlink grid.layout grid.lines grid.newpage
grid.points grid.pretty grid.rect grid.script grid.segments grid.text
grid.xaxis grid.yaxis gridToSVG grobWidth mt.rawp2adjp number pOverA
plotViewport popViewport pushViewport rectGrob rowFtests rowttests
textGrob topTableF toptable unit unit.c viewport xaxisGrob
* 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 ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
spectralMap 10.177 0.072 10.274
plotLogRatio 7.566 0.024 7.652
computeLogRatio 6.980 0.041 7.111
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/a4Base.Rcheck/00check.log’
for details.