Morten Hansen
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/pcaGoPromoter |
| Branch: master |
| Last Commit: ce12953 |
| Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:00:10 -0400 (Tue, 09 Apr 2019).
| Package 1161/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pcaGoPromoter 1.27.0 Morten Hansen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: pcaGoPromoter |
| Version: 1.27.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaGoPromoter.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pcaGoPromoter_1.27.0.tar.gz |
| StartedAt: 2019-04-09 04:48:51 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:54:47 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 355.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pcaGoPromoter.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaGoPromoter.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pcaGoPromoter_1.27.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pcaGoPromoter.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pcaGoPromoter/DESCRIPTION' ... OK
* this is package 'pcaGoPromoter' version '1.27.0'
* 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 'pcaGoPromoter' 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 ... NOTE
'library' or 'require' calls in package code:
'GO.db' 'Rgraphviz' 'parallel' 'pcaGoPromoter.Hs.hg19'
'pcaGoPromoter.Mm.mm9' 'pcaGoPromoter.Rn.rn4'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
getRankedProbeIds.pca plot.GOtree plot.pca print.GOtree print.pca
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dropVarNull: no visible global function definition for 'var'
dropVarNull: no visible global function definition for 'na.omit'
getMatricesWithHits: no visible global function definition for
'fisher.test'
getMatricesWithHits: no visible global function definition for
'p.adjust'
getSigGOTermsOnce: no visible global function definition for
'fisher.test'
getSigGOTermsOnce : <anonymous>: no visible global function definition
for 'binom.test'
getSigGOTermsOnce: no visible global function definition for 'p.adjust'
leaveOutFindPvalues : <anonymous>: no visible global function
definition for 'median'
makeGOtreeRgraphviz: no visible global function definition for 'new'
makeGOtreeRgraphviz: no visible global function definition for 'rgb'
makeGOtreeRgraphviz: no visible global function definition for
'addNode'
makeGOtreeRgraphviz: no visible global function definition for
'addEdge'
makeGOtreeRgraphviz: no visible global function definition for 'nodes'
makeGOtreeRgraphviz: no visible global function definition for
'nodeRenderInfo<-'
makeGOtreeRgraphviz: no visible global function definition for
'edgeRenderInfo<-'
makeGOtreeRgraphviz: no visible global function definition for
'parRenderInfo<-'
makeGOtreeRgraphviz: no visible global function definition for 'par'
makeGOtreeRgraphviz: no visible global function definition for
'renderGraph'
makeGOtreeRgraphviz: no visible global function definition for
'layoutGraph'
makeGOtreeRgraphviz: no visible global function definition for 'legend'
newSearchGOtreeForTerms: no visible binding for global variable
'GOBPANCESTOR'
pca: no visible global function definition for 'annotation'
pca: no visible global function definition for 'exprs'
pca: no visible global function definition for 'var'
pca: no visible global function definition for 'na.omit'
pca: no visible global function definition for 'prcomp'
pcaInfoPlot: no visible global function definition for 'plot'
plot.pca: no visible global function definition for 'par'
plot.pca: no visible global function definition for 'layout'
plot.pca: no visible global function definition for 'var'
plot.pca: no visible global function definition for 'plot'
plot.pca: no visible global function definition for 'polygon'
plot.pca: no visible global function definition for 'lines'
plot.pca: no visible global function definition for 'points'
plot.pca: no visible global function definition for 'abline'
plot.pca: no visible global function definition for 'box'
plot.pca: no visible global function definition for 'text'
plot.pca: no visible global function definition for 'plot.new'
plot.pca: no visible global function definition for 'legend'
primo: no visible global function definition for 'data'
primoData.getPromoters: no visible global function definition for
'readFASTA'
primoHits: no visible global function definition for 'data'
printAnnText: no visible global function definition for 'mtext'
printAnnotation: no visible global function definition for 'mtext'
Undefined global functions or variables:
GOBPANCESTOR abline addEdge addNode annotation binom.test box data
edgeRenderInfo<- exprs fisher.test layout layoutGraph legend lines
median mtext na.omit new nodeRenderInfo<- nodes p.adjust par
parRenderInfo<- plot plot.new points polygon prcomp readFASTA
renderGraph rgb text var
Consider adding
importFrom("grDevices", "rgb")
importFrom("graphics", "abline", "box", "layout", "legend", "lines",
"mtext", "par", "plot", "plot.new", "points", "polygon",
"text")
importFrom("methods", "new")
importFrom("stats", "binom.test", "fisher.test", "median", "na.omit",
"p.adjust", "prcomp", "var")
importFrom("utils", "data")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOtree 70.67 10.09 81.31
primo 19.87 0.62 25.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOtree 87.61 2.15 92.35
primo 17.45 0.48 17.94
* 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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/pcaGoPromoter.Rcheck/00check.log'
for details.
pcaGoPromoter.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/pcaGoPromoter_1.27.0.tar.gz && rm -rf pcaGoPromoter.buildbin-libdir && mkdir pcaGoPromoter.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaGoPromoter.buildbin-libdir pcaGoPromoter_1.27.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pcaGoPromoter_1.27.0.zip && rm pcaGoPromoter_1.27.0.tar.gz pcaGoPromoter_1.27.0.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 134k 100 134k 0 0 1588k 0 --:--:-- --:--:-- --:--:-- 1730k
install for i386
* installing *source* package 'pcaGoPromoter' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pcaGoPromoter'
finding HTML links ... done
GOtree html
pca html
pcaGoPromoter-package html
primo html
primoData html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'pcaGoPromoter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaGoPromoter' as pcaGoPromoter_1.27.0.zip
* DONE (pcaGoPromoter)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'pcaGoPromoter' successfully unpacked and MD5 sums checked
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pcaGoPromoter.Rcheck/examples_i386/pcaGoPromoter-Ex.timings
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pcaGoPromoter.Rcheck/examples_x64/pcaGoPromoter-Ex.timings
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