piano 1.12.1
Leif Varemo
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/piano | | Last Changed Rev: 120128 / Revision: 122332 | | Last Changed Date: 2016-08-15 02:43:08 -0700 (Mon, 15 Aug 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf piano.buildbin-libdir piano.Rcheck && mkdir piano.buildbin-libdir piano.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=piano.buildbin-libdir piano_1.12.1.tar.gz >piano.Rcheck\00install.out 2>&1 && cp piano.Rcheck\00install.out piano-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=piano.buildbin-libdir --install="check:piano-install.out" --force-multiarch --no-vignettes --timings piano_1.12.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/piano.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 'piano/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'piano' version '1.12.1'
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'BiocGenerics::union' by 'igraph::union' when loading 'piano'
Warning: replacing previous import 'BiocGenerics::normalize' by 'igraph::normalize' when loading 'piano'
See 'E:/biocbld/bbs-3.3-bioc/meat/piano.Rcheck/00install.out' for details.
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSAsummaryTable: no visible global function definition for
'write.table'
GSCsignificanceBatch: no visible global function definition for
'capture.output'
calcGeneSetStat: no visible global function definition for 'qnorm'
calcGeneSetStat: no visible global function definition for
'wilcox.test'
calcGeneSetStat: no visible global function definition for 'median'
calcGeneSetStat: no visible global function definition for 'sd'
checkLoadArg: no visible global function definition for 'sd'
consensusHeatmap: no visible binding for global variable 'median'
consensusHeatmap: no visible global function definition for 'rnorm'
consensusHeatmap: no visible global function definition for
'colorRampPalette'
consensusScores: no visible global function definition for 'median'
consensusScores: no visible global function definition for 'layout'
consensusScores: no visible global function definition for 'points'
consensusScores: no visible global function definition for 'rainbow'
consensusScores: no visible global function definition for 'par'
consensusScores: no visible global function definition for 'legend'
diffExp: no visible global function definition for 'model.matrix'
diffExp: no visible global function definition for 'dev.new'
diffExp: no visible global function definition for 'plot.new'
diffExp: no visible global function definition for 'title'
diffExp: no visible global function definition for 'text'
diffExp: no visible global function definition for 'pdf'
diffExp: no visible global function definition for 'dev.off'
diffExp: no visible global function definition for 'write.table'
diffExp: no visible global function definition for 'points'
diffExp: no visible global function definition for 'abline'
loadGSC: no visible global function definition for 'read.delim'
loadMAdata: no visible global function definition for 'read.delim'
loadMAdata: no visible global function definition for 'capture.output'
networkPlot: no visible global function definition for
'colorRampPalette'
networkPlot: no visible global function definition for 'layout'
networkPlot: no visible global function definition for 'par'
networkPlot: no visible global function definition for 'plot'
networkPlot: no visible global function definition for 'plot.new'
networkPlot: no visible global function definition for 'text'
polarPlot: no visible global function definition for 'read.delim'
polarPlot: no visible global function definition for 'pdf'
polarPlot: no visible global function definition for 'dev.new'
polarPlot: no visible global function definition for 'dev.off'
polarPlot: no visible global function definition for 'plot.new'
polarPlot: no visible global function definition for 'title'
polarPlot: no visible global function definition for 'legend'
pvalFromDistribution: no visible global function definition for
'pchisq'
pvalFromDistribution: no visible global function definition for 'pnorm'
pvalFromDistribution: no visible global function definition for 'sd'
runGSA: no visible binding for global variable 'p.adjust'
runGSAhyper: no visible global function definition for 'fisher.test'
runGSAhyper: no visible global function definition for 'p.adjust'
runQC : .runRnaDeg: no visible global function definition for 'dev.new'
runQC : .runRnaDeg: no visible global function definition for 'pdf'
runQC : .runRnaDeg: no visible global function definition for 'dev.off'
runQC : .runNuseRle: no visible global function definition for
'dev.new'
runQC : .runNuseRle: no visible global function definition for 'par'
runQC : .runNuseRle: no visible global function definition for 'pdf'
runQC : .runNuseRle: no visible global function definition for
'dev.off'
runQC : .runHist: no visible global function definition for 'dev.new'
runQC : .runHist: no visible global function definition for 'plot'
runQC : .runHist: no visible global function definition for 'lines'
runQC : .runHist: no visible global function definition for 'pdf'
runQC : .runHist: no visible global function definition for 'dev.off'
runQC : .runBoxplot: no visible global function definition for
'dev.new'
runQC : .runBoxplot: no visible global function definition for 'par'
runQC : .runBoxplot: no visible global function definition for 'pdf'
runQC : .runBoxplot: no visible global function definition for
'dev.off'
runQC : .runPca: no visible global function definition for 'prcomp'
runQC : .runPca: no visible global function definition for 'dev.new'
runQC : .runPca: no visible global function definition for 'barplot'
runQC : .runPca: no visible global function definition for 'text'
runQC : .runPca: no visible global function definition for 'plot'
runQC : .runPca: no visible global function definition for 'mtext'
runQC : .runPca: no visible global function definition for 'plot.new'
runQC : .runPca: no visible global function definition for 'title'
runQC : .runPca: no visible global function definition for 'legend'
runQC : .runPca: no visible global function definition for 'pdf'
runQC : .runPca: no visible global function definition for 'dev.off'
writeFilesForKiwi: no visible global function definition for
'write.table'
Undefined global functions or variables:
abline barplot capture.output colorRampPalette dev.new dev.off
fisher.test layout legend lines median model.matrix mtext p.adjust
par pchisq pdf plot plot.new pnorm points prcomp qnorm rainbow
read.delim rnorm sd text title wilcox.test write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
"pdf", "rainbow")
importFrom("graphics", "abline", "barplot", "layout", "legend",
"lines", "mtext", "par", "plot", "plot.new", "points",
"text", "title")
importFrom("stats", "fisher.test", "median", "model.matrix",
"p.adjust", "pchisq", "pnorm", "prcomp", "qnorm", "rnorm",
"sd", "wilcox.test")
importFrom("utils", "capture.output", "read.delim", "write.table")
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
GSAheatmap 6.47 0.04 6.52
networkPlot 5.97 0.01 6.26
runGSA 5.67 0.00 5.67
geneSetSummary 5.40 0.02 5.41
GSAsummaryTable 5.07 0.02 5.08
diffExp 4.17 0.30 7.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneSetSummary 7.55 0.00 7.55
GSAheatmap 7.23 0.10 7.32
networkPlot 6.68 0.03 6.71
runGSA 6.66 0.00 6.68
GSAsummaryTable 5.70 0.01 5.73
diffExp 5.30 0.34 5.69
* 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: 1 WARNING, 1 NOTE
See
'E:/biocbld/bbs-3.3-bioc/meat/piano.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'piano' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::union' by 'igraph::union' when loading 'piano'
Warning: replacing previous import 'BiocGenerics::normalize' by 'igraph::normalize' when loading 'piano'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::union' by 'igraph::union' when loading 'piano'
Warning: replacing previous import 'BiocGenerics::normalize' by 'igraph::normalize' when loading 'piano'
install for x64
* installing *source* package 'piano' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::union' by 'igraph::union' when loading 'piano'
Warning: replacing previous import 'BiocGenerics::normalize' by 'igraph::normalize' when loading 'piano'
* MD5 sums
packaged installation of 'piano' as piano_1.12.1.zip
* DONE (piano)