Saskia Freytag
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RUVcorr |
| Branch: RELEASE_3_8 |
| Last Commit: a7abd8a |
| Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:25:10 -0400 (Sat, 13 Apr 2019).
| Package 1371/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RUVcorr 1.14.0 Saskia Freytag
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RUVcorr |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RUVcorr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RUVcorr_1.14.0.tar.gz |
| StartedAt: 2019-04-13 05:15:28 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:17:41 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 132.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RUVcorr.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RUVcorr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RUVcorr_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RUVcorr.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RUVcorr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RUVcorr' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'RUVcorr' 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
* 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
ECDFPlot: no visible global function definition for 'plot'
ECDFPlot: no visible global function definition for 'lines'
PCAPlot: no visible global function definition for 'prcomp'
PCAPlot: no visible global function definition for 'layout'
PCAPlot: no visible global function definition for 'par'
PCAPlot: no visible global function definition for 'plot'
PCAPlot: no visible global function definition for 'legend'
PCAPlot: no visible global function definition for 'mtext'
RLEPlot : <anonymous>: no visible global function definition for
'median'
RLEPlot: no visible global function definition for 'layout'
RLEPlot: no visible global function definition for 'par'
RLEPlot: no visible global function definition for 'plot.new'
RLEPlot: no visible global function definition for 'legend'
RLEPlot: no visible global function definition for 'mtext'
RLEPlot: no visible global function definition for 'plot'
RLEPlot: no visible global function definition for 'boxplot'
RLEPlot: no visible global function definition for 'abline'
assessQuality: no visible global function definition for 'cor'
calculateThreshold: no visible global function definition for 'loess'
compareRanks: no visible global function definition for 'cor'
correlationPlot: no visible global function definition for 'mtext'
correlationPlot: no visible global function definition for 'rect'
eigenvaluePlot: no visible global function definition for 'plot'
findWeights : <anonymous>: no visible global function definition for
'cor'
findWeights : <anonymous>: no visible global function definition for
'var'
funcThresh: no visible global function definition for 'cor'
genePlot: no visible global function definition for 'plot'
genePlot: no visible global function definition for 'points'
histogramPlot: no visible global function definition for 'density'
histogramPlot: no visible global function definition for 'hist'
histogramPlot: no visible global function definition for 'lines'
histogramPlot : <anonymous>: no visible global function definition for
'density'
mashUp: no visible global function definition for 'cor'
plot.optimizeParameters : <anonymous>: no visible global function
definition for 'xtabs'
plotDesign: no visible global function definition for 'par'
plotDesign: no visible global function definition for 'image'
plotThreshold: no visible global function definition for 'plot'
plotThreshold : <anonymous>: no visible global function definition for
'points'
prioritise: no visible global function definition for 'cor'
simulateGEdata: no visible global function definition for 'runif'
simulateGEdata: no visible global function definition for 'rnorm'
simulateGEdata: no visible global function definition for 'cor'
wcor : <anonymous>: no visible global function definition for 'cor'
Undefined global functions or variables:
abline boxplot cor density hist image layout legend lines loess
median mtext par plot plot.new points prcomp rect rnorm runif var
xtabs
Consider adding
importFrom("graphics", "abline", "boxplot", "hist", "image", "layout",
"legend", "lines", "mtext", "par", "plot", "plot.new",
"points", "rect")
importFrom("stats", "cor", "density", "loess", "median", "prcomp",
"rnorm", "runif", "var", "xtabs")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/RUVcorr.Rcheck/00check.log'
for details.
RUVcorr.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RUVcorr_1.14.0.tar.gz && rm -rf RUVcorr.buildbin-libdir && mkdir RUVcorr.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RUVcorr.buildbin-libdir RUVcorr_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RUVcorr_1.14.0.zip && rm RUVcorr_1.14.0.tar.gz RUVcorr_1.14.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1612k 100 1612k 0 0 15.8M 0 --:--:-- --:--:-- --:--:-- 16.4M
install for i386
* installing *source* package 'RUVcorr' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RUVcorr'
finding HTML links ... done
ECDFPlot html
PCAPlot html
RLEPlot html
RUVNaiveRidge html
RUVcorr html
assessQuality html
background html
calculateThreshold html
compareRanks html
correlationPlot html
eigenvaluePlot html
empNegativeControls html
findIQR html
findMinmaxSamples html
findWeights html
funcPara html
funcThresh html
genePlot html
histogramPlot html
is.optimizeParameters html
is.simulateGEdata html
makePosSemiDef html
makeRankedList html
mashUp html
optimizeParameters html
plot.optimizeParameters html
plotDesign html
plotThreshold html
print.simulateGEdata html
prioritise html
simulateGEdata html
splitByFactor html
wcor html
** building package indices
** installing vignettes
'RUVcorrVignetteNew.Rnw'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'RUVcorr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RUVcorr' as RUVcorr_1.14.0.zip
* DONE (RUVcorr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RUVcorr' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
RUVcorr.Rcheck/examples_i386/RUVcorr-Ex.timings
|
RUVcorr.Rcheck/examples_x64/RUVcorr-Ex.timings
|