piano 1.6.2
Leif Varemo
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/piano | | Last Changed Rev: 96647 / Revision: 102249 | | Last Changed Date: 2014-11-10 02:16:23 -0800 (Mon, 10 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | 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 piano.buildbin-libdir piano.Rcheck && mkdir piano.buildbin-libdir piano.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=piano.buildbin-libdir piano_1.6.2.tar.gz >piano.Rcheck\00install.out 2>&1 && cp piano.Rcheck\00install.out piano-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=piano.buildbin-libdir --install="check:piano-install.out" --force-multiarch --no-vignettes --timings piano_1.6.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/piano.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'piano/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'piano' version '1.6.2'
* 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 'piano' 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
'library' or 'require' calls in package code:
'affy' 'affyPLM' 'gtools' 'limma' 'plier' 'plotrix' 'rsbml'
'snowfall' 'yeast2.db'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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
GSCsignificanceBatch: no visible global function definition for
'sfInit'
GSCsignificanceBatch: no visible global function definition for
'sfLapply'
GSCsignificanceBatch: no visible global function definition for
'sfStop'
diffExp: no visible global function definition for 'lmFit'
diffExp: no visible global function definition for 'makeContrasts'
diffExp: no visible global function definition for 'contrasts.fit'
diffExp: no visible global function definition for 'eBayes'
diffExp: no visible global function definition for 'decideTests'
diffExp: no visible global function definition for 'vennDiagram'
diffExp: no visible global function definition for 'topTable'
loadGSC: no visible global function definition for 'rsbml_read'
loadGSC: no visible global function definition for 'reactions'
loadGSC: no visible global function definition for 'model'
loadGSC: no visible global function definition for 'reactants'
loadGSC: no visible global function definition for 'products'
loadGSC: no visible global function definition for 'modifiers'
loadGSC: no visible global function definition for 'name'
loadGSC: no visible global function definition for 'species'
loadGSC: no visible global function definition for 'compartment'
loadMAdata: no visible global function definition for 'ReadAffy'
loadMAdata: no visible global function definition for
'normalize.AffyBatch.qspline'
loadMAdata: no visible global function definition for 'justPlier'
loadMAdata: no visible global function definition for 'rma'
loadMAdata: no visible global function definition for 'mas5'
loadMAdata: no visible global function definition for 'cdfName'
loadMAdata: no visible binding for global variable 'yeast2ORF'
loadMAdata: no visible global function definition for 'toTable'
loadMAdata: no visible binding for global variable 'yeast2CHRLOC'
polarPlot: no visible global function definition for 'mixedsort'
polarPlot: no visible global function definition for 'radial.plot'
runQC : .runRnaDeg: no visible global function definition for
'AffyRNAdeg'
runQC : .runRnaDeg: no visible global function definition for
'plotAffyRNAdeg'
runQC : .runNuseRle: no visible global function definition for 'fitPLM'
runQC : .runNuseRle: no visible global function definition for 'RLE'
runQC : .runNuseRle: no visible global function definition for 'NUSE'
* 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' ... [47s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
diffExp 5.71 0.46 10.12
networkPlot 5.85 0.00 5.85
GSAheatmap 5.57 0.00 5.57
geneSetSummary 5.18 0.00 5.18
** running examples for arch 'x64' ... [49s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
diffExp 8.47 0.28 9.18
networkPlot 6.93 0.03 6.96
geneSetSummary 6.10 0.00 6.10
GSAheatmap 5.73 0.00 5.73
GSAsummaryTable 5.71 0.02 5.72
runGSA 5.52 0.00 5.52
* 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/piano.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'piano' ...
** 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 'piano' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'piano' as piano_1.6.2.zip
* DONE (piano)