DeSousa2013 1.9.0
Xin Wang
| Snapshot Date: 2016-05-28 09:20:19 -0700 (Sat, 28 May 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/DeSousa2013 | | Last Changed Rev: 3763 / Revision: 3781 | | Last Changed Date: 2016-05-03 14:48:02 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf DeSousa2013.buildbin-libdir DeSousa2013.Rcheck && mkdir DeSousa2013.buildbin-libdir DeSousa2013.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DeSousa2013.buildbin-libdir DeSousa2013_1.9.0.tar.gz >DeSousa2013.Rcheck\00install.out 2>&1 && cp DeSousa2013.Rcheck\00install.out DeSousa2013-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DeSousa2013.buildbin-libdir --install="check:DeSousa2013-install.out" --force-multiarch --no-vignettes --timings DeSousa2013_1.9.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-data-experiment/meat/DeSousa2013.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-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 '1.9.0'
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CRCPipeLine: no visible global function definition for 'data'
CRCPipeLine: no visible global function definition for 'pdf'
CRCPipeLine: no visible global function definition for 'graphics.off'
compGapStats: no visible binding for global variable 'mad'
compGapStats : fun: no visible global function definition for 'hclust'
compGapStats : fun: no visible global function definition for 'as.dist'
compGapStats : fun: no visible global function definition for 'cor'
compGapStats : fun: no visible global function definition for 'cutree'
compGapStats: no visible binding for global variable 'median'
figClassify: no visible global function definition for 'layout'
figClassify: no visible global function definition for 'par'
figClassify: no visible global function definition for 'image'
figClassify: no visible global function definition for 'axis'
figClassify: no visible global function definition for 'box'
figClassify: no visible global function definition for 'gray'
figClassify: no visible global function definition for 'mtext'
figClassify: no visible global function definition for 'barplot'
figClassify: no visible global function definition for 'grid'
figGAP: no visible global function definition for 'par'
figGAP: no visible global function definition for 'lines'
figGAP: no visible global function definition for 'title'
figKM: no visible global function definition for 'plot'
figKM: no visible global function definition for 'axis'
figKM: no visible global function definition for 'box'
figKM: no visible global function definition for 'text'
figKM: no visible global function definition for 'legend'
figPAMCV: no visible global function definition for 'boxplot'
figSilh: no visible global function definition for 'plot'
filterSamples: no visible global function definition for 'as.dist'
filterSamples: no visible global function definition for 'cor'
pamClassify: no visible global function definition for 'hclust'
pamClassify: no visible global function definition for 'as.dist'
pamClassify: no visible global function definition for 'cor'
pbs2unigenes: no visible global function definition for 'mappedkeys'
progAMC: no visible global function definition for 'pchisq'
selTopVarGenes: no visible binding for global variable 'mad'
selTopVarGenes: no visible binding for global variable 'median'
Undefined global functions or variables:
as.dist axis barplot box boxplot cor cutree data graphics.off gray
grid hclust image layout legend lines mad mappedkeys median mtext par
pchisq pdf plot text title
Consider adding
importFrom("grDevices", "graphics.off", "gray", "pdf")
importFrom("graphics", "axis", "barplot", "box", "boxplot", "grid",
"image", "layout", "legend", "lines", "mtext", "par",
"plot", "text", "title")
importFrom("stats", "as.dist", "cor", "cutree", "hclust", "mad",
"median", "pchisq")
importFrom("utils", "data")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compGapStats 17.99 0.16 67.67
selTopVarGenes 5.77 0.05 5.81
pbs2unigenes 4.46 0.06 153.16
conClust 1.34 0.02 7.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compGapStats 22.06 0.19 45.49
selTopVarGenes 6.93 0.01 6.94
pbs2unigenes 5.67 0.24 5.93
buildClassifier 4.16 0.04 5.38
findDiffGenes 1.00 0.01 7.55
* 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
* DONE
Status: 3 NOTEs
See
'D:/biocbld/bbs-3.4-data-experiment/meat/DeSousa2013.Rcheck/00check.log'
for details.
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_1.9.0.zip
* DONE (DeSousa2013)