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CHECK report for CompGO on tokay2

This page was generated on 2019-04-09 12:18:24 -0400 (Tue, 09 Apr 2019).

Package 325/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompGO 1.19.0
Ashley J. Waardenberg
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CompGO
Branch: master
Last Commit: 5355e9c
Last Changed Date: 2018-10-30 11:54:32 -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: CompGO
Version: 1.19.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CompGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CompGO_1.19.0.tar.gz
StartedAt: 2019-04-09 01:57:36 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:04:39 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 423.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CompGO.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:CompGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CompGO_1.19.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CompGO.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 'CompGO/DESCRIPTION' ... OK
* this is package 'CompGO' version '1.19.0'
* 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 'CompGO' 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
PCAplot: no visible global function definition for 'par'
PCAplot: no visible global function definition for 'text'
compareZscores: no visible global function definition for 'pnorm'
compareZscores: no visible global function definition for 'p.adjust'
compareZscores: no visible global function definition for 'setNames'
doZtrans.single: no visible binding for global variable 'Term'
doZtrans.single: no visible binding for global variable 'Z'
plotDendrogram: no visible global function definition for 'cor'
plotDendrogram: no visible global function definition for 'hclust'
plotDendrogram: no visible global function definition for 'dist'
plotInteractive: no visible global function definition for 'cor'
plotInteractive: no visible global function definition for 'hclust'
plotInteractive: no visible global function definition for 'dist'
plotInteractive: no visible global function definition for 'png'
plotInteractive: no visible global function definition for 'par'
plotInteractive: no visible global function definition for 'dev.off'
plotInteractive: no visible global function definition for 'text'
plotInteractive: no visible binding for global variable 'Var1'
plotInteractive: no visible binding for global variable 'Var2'
plotInteractive: no visible binding for global variable 'value'
plotPairwise: no visible global function definition for
  'complete.cases'
plotPairwise: no visible global function definition for 'setNames'
plotPairwise: no visible global function definition for 'cor'
plotTwoGODags: no visible global function definition for 'goDag'
plotTwoGODags: no visible global function definition for 'nodes'
plotTwoGODags: no visible global function definition for
  'nodeRenderInfo<-'
plotZRankedDAG: no visible global function definition for 'goDag'
plotZRankedDAG: no visible global function definition for 'nodes'
plotZRankedDAG: no visible global function definition for
  'nodeRenderInfo<-'
plotZScores: no visible global function definition for 'complete.cases'
plotZScores: no visible global function definition for 'setNames'
plotZScores: no visible global function definition for 'cor'
slidingJaccard: no visible binding for global variable 'useRawPvals'
zTransformDirectory: no visible global function definition for
  'read.table'
zTransformDirectory: no visible global function definition for
  'complete.cases'
zTransformDirectory: no visible binding for global variable 'var'
Undefined global functions or variables:
  Term Var1 Var2 Z complete.cases cor dev.off dist goDag hclust
  nodeRenderInfo<- nodes p.adjust par png pnorm read.table setNames
  text useRawPvals value var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "complete.cases", "cor", "dist", "hclust",
             "p.adjust", "pnorm", "setNames", "var")
  importFrom("utils", "read.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plotTwoGODags 5.03   0.58    5.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plotTwoGODags 5.76   0.22    5.98
* 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-3.9-bioc/meat/CompGO.Rcheck/00check.log'
for details.



Installation output

CompGO.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/CompGO_1.19.0.tar.gz && rm -rf CompGO.buildbin-libdir && mkdir CompGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CompGO.buildbin-libdir CompGO_1.19.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CompGO_1.19.0.zip && rm CompGO_1.19.0.tar.gz CompGO_1.19.0.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 99676  100 99676    0     0  1432k      0 --:--:-- --:--:-- --:--:-- 1595k

install for i386

* installing *source* package 'CompGO' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CompGO'
    finding HTML links ... done
    PCAplot                                 html  
    annotateBedFromDb                       html  
    bed.sample                              html  
    compareZscores                          html  
    doZtrans.single                         html  
    gata4                                   html  
    getFnAnot_genome                        html  
    mef2a                                   html  
    nkx25                                   html  
    p300                                    html  
    plotDendrogram                          html  
    plotInteractive                         html  
    plotPairwise                            html  
    plotTwoGODags                           html  
    plotZRankedDAG                          html  
    plotZScores                             html  
    slidingJaccard                          html  
    srf                                     html  
    tbx5                                    html  
    viewKegg                                html  
    zTransformDirectory                     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 'CompGO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CompGO' as CompGO_1.19.0.zip
* DONE (CompGO)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CompGO' successfully unpacked and MD5 sums checked

Tests output


Example timings

CompGO.Rcheck/examples_i386/CompGO-Ex.timings

nameusersystemelapsed
annotateBedFromDb0.80.00.8
compareZscores0.080.020.17
doZtrans.single0.020.010.03
getFnAnot_genome000
plotPairwise0.560.060.63
plotTwoGODags5.030.585.61
plotZRankedDAG000
plotZScores0.960.010.97
slidingJaccard0.090.050.14
viewKegg000
zTransformDirectory000

CompGO.Rcheck/examples_x64/CompGO-Ex.timings

nameusersystemelapsed
annotateBedFromDb0.720.090.81
compareZscores0.070.040.09
doZtrans.single0.020.000.02
getFnAnot_genome000
plotPairwise0.640.010.67
plotTwoGODags5.760.225.98
plotZRankedDAG000
plotZScores1.110.031.14
slidingJaccard0.060.010.08
viewKegg000
zTransformDirectory000