GeneExpressionSignature 1.19.0
Yang Cao , Fei Li ,Lu Han
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneExpressionSignature | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -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 | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && mkdir GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneExpressionSignature.buildbin-libdir GeneExpressionSignature_1.19.0.tar.gz >GeneExpressionSignature.Rcheck\00install.out 2>&1 && cp GeneExpressionSignature.Rcheck\00install.out GeneExpressionSignature-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GeneExpressionSignature.buildbin-libdir --install="check:GeneExpressionSignature-install.out" --force-multiarch --no-vignettes --timings GeneExpressionSignature_1.19.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/GeneExpressionSignature.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' version '1.19.0'
* 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 'GeneExpressionSignature' can be installed ... OK
* checking installed package size ... OK
* 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
Packages in Depends field not imported from:
'Biobase' 'PGSEA'
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
RankMerging: no visible global function definition for 'exprs'
RankMerging: no visible global function definition for 'as'
RankMerging: no visible global function definition for 'phenoData'
RankMerging: no visible global function definition for 'new'
ScoreGSEA : PRL.Distance: no visible global function definition for
'exprs'
ScoreGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'new'
ScorePGSEA: no visible global function definition for 'PGSEA'
ScorePGSEA: no visible global function definition for 'pnorm'
getRLs : Check.Log: no visible global function definition for 'median'
integratePRL: no visible global function definition for 'phenoData'
integratePRL: no visible global function definition for 'exprs'
integratePRL: no visible global function definition for 'new'
integratePRL: no visible global function definition for 'as'
Undefined global functions or variables:
PGSEA as exprs median new phenoData pnorm
Consider adding
importFrom("methods", "as", "new")
importFrom("stats", "median", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
SignatureDistance 10.05 0.03 10.08
ScoreGSEA 10.02 0.05 10.07
ScorePGSEA 6.58 0.12 6.70
RankMerging 5.15 0.02 5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ScoreGSEA 9.35 0.02 9.36
SignatureDistance 9.22 0.03 9.25
ScorePGSEA 5.60 0.03 5.64
* 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: 2 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/GeneExpressionSignature.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GeneExpressionSignature' ...
** 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 'GeneExpressionSignature' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneExpressionSignature' as GeneExpressionSignature_1.19.0.zip
* DONE (GeneExpressionSignature)