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CHECK report for divergence on tokay2

This page was generated on 2019-04-09 12:44:00 -0400 (Tue, 09 Apr 2019).

Package 436/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
divergence 0.99.07
Wikum Dinalankara , Luigi Marchionni
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/divergence
Branch: master
Last Commit: e7c789c
Last Changed Date: 2019-02-15 13:13:00 -0400 (Fri, 15 Feb 2019)
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: divergence
Version: 0.99.07
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings divergence_0.99.07.tar.gz
StartedAt: 2019-04-09 02:21:33 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:26:35 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 302.8 seconds
RetCode: 0
Status:  OK  
CheckDir: divergence.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:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings divergence_0.99.07.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/divergence.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 'divergence/DESCRIPTION' ... OK
* this is package 'divergence' version '0.99.07'
* package encoding: UTF-8
* 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 'divergence' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
check_SE: no visible binding for global variable 'data'
computeSingleFeaturesetBinaryVector: no visible global function
  definition for 'dist'
computeSingleFeaturesetSupport: no visible global function definition
  for 'dist'
computeSingleFeaturesetSupport: no visible global function definition
  for 'quantile'
computeSingleRange: no visible global function definition for
  'quantile'
getRangesBySections: no visible global function definition for
  'detectCores'
rowChiSq: no visible global function definition for 'chisq.test'
rowChiSq: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  chisq.test data detectCores dist quantile xtabs
Consider adding
  importFrom("stats", "chisq.test", "dist", "quantile", "xtabs")
  importFrom("utils", "data")
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
computeUnivariateDigitization   19.00   0.08   19.08
findUnivariateGammaWithSupport  19.00   0.00   19.00
computeChiSquaredTest           17.28   0.25   17.53
computeMultivariateDigitization  7.04   0.15    7.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
computeChiSquaredTest          17.81   0.03   17.84
computeUnivariateDigitization  16.96   0.05   17.02
findUnivariateGammaWithSupport 13.19   0.00   13.19
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/divergence.Rcheck/00check.log'
for details.



Installation output

divergence.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/divergence_0.99.07.tar.gz && rm -rf divergence.buildbin-libdir && mkdir divergence.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=divergence.buildbin-libdir divergence_0.99.07.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL divergence_0.99.07.zip && rm divergence_0.99.07.tar.gz divergence_0.99.07.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 1919k  100 1919k    0     0  30.6M      0 --:--:-- --:--:-- --:--:-- 32.8M

install for i386

* installing *source* package 'divergence' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'divergence'
    finding HTML links ... done
    breastTCGA_ER                           html  
    breastTCGA_Group                        html  
    breastTCGA_Mat                          html  
    computeChiSquaredTest                   html  
    computeMultivariateBinaryMatrix         html  
    computeMultivariateDigitization         html  
    computeMultivariateSupport              html  
    computeQuantileMatrix                   html  
    computeUnivariateDigitization           html  
    computeUnivariateSupport                html  
    computeUnivariateTernaryMatrix          html  
    findMultivariateGammaWithSupport        html  
    findUnivariateGammaWithSupport          html  
    msigdb_Hallmarks                        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 'divergence' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'divergence' as divergence_0.99.07.zip
* DONE (divergence)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'divergence' successfully unpacked and MD5 sums checked

Tests output


Example timings

divergence.Rcheck/examples_i386/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest17.28 0.2517.53
computeMultivariateBinaryMatrix2.470.242.70
computeMultivariateDigitization7.040.157.20
computeMultivariateSupport1.030.001.03
computeQuantileMatrix0.070.000.06
computeUnivariateDigitization19.00 0.0819.08
computeUnivariateSupport202
computeUnivariateTernaryMatrix2.190.002.18
findMultivariateGammaWithSupport0.910.111.02
findUnivariateGammaWithSupport19 019

divergence.Rcheck/examples_x64/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest17.81 0.0317.84
computeMultivariateBinaryMatrix1.700.241.93
computeMultivariateDigitization4.650.254.90
computeMultivariateSupport0.280.010.30
computeQuantileMatrix0.070.000.06
computeUnivariateDigitization16.96 0.0517.02
computeUnivariateSupport1.320.001.31
computeUnivariateTernaryMatrix1.560.021.58
findMultivariateGammaWithSupport0.580.010.59
findUnivariateGammaWithSupport13.19 0.0013.19