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CHECK report for pcaGoPromoter on tokay2

This page was generated on 2019-04-09 12:00:10 -0400 (Tue, 09 Apr 2019).

Package 1161/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaGoPromoter 1.27.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

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

Command output

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### Running 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
###
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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.



Installation output

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

Tests output


Example timings

pcaGoPromoter.Rcheck/examples_i386/pcaGoPromoter-Ex.timings

nameusersystemelapsed
GOtree70.6710.0981.31
pca1.940.001.94
pcaGoPromoter-package000
primo19.87 0.6225.99
primoData000

pcaGoPromoter.Rcheck/examples_x64/pcaGoPromoter-Ex.timings

nameusersystemelapsed
GOtree87.61 2.1592.35
pca1.620.021.64
pcaGoPromoter-package000
primo17.45 0.4817.94
primoData000