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CHECK report for divergence on tokay2

This page was generated on 2020-10-17 11:56:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE divergence PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 484/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
divergence 1.4.0
Wikum Dinalankara , Luigi Marchionni
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/divergence
Branch: RELEASE_3_11
Last Commit: f4d6c1d
Last Changed Date: 2020-04-27 15:23:05 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: divergence
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings divergence_1.4.0.tar.gz
StartedAt: 2020-10-17 03:27:07 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:32:51 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 343.7 seconds
RetCode: 0
Status:  OK  
CheckDir: divergence.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings divergence_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/divergence.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.4.0'
* 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 (user + system) or elapsed time > 5s
                                 user system elapsed
findUnivariateGammaWithSupport  18.90   0.00   18.91
computeUnivariateDigitization   18.83   0.00   18.83
computeChiSquaredTest           16.54   0.20   16.75
computeMultivariateDigitization  5.26   0.11    5.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
computeUnivariateDigitization   22.67   0.09   22.77
findUnivariateGammaWithSupport  22.61   0.02   23.54
computeChiSquaredTest           16.49   0.10   16.57
computeMultivariateDigitization  5.97   0.14    6.10
* 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-3.11-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/3.11/bioc/src/contrib/divergence_1.4.0.tar.gz && rm -rf divergence.buildbin-libdir && mkdir divergence.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=divergence.buildbin-libdir divergence_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL divergence_1.4.0.zip && rm divergence_1.4.0.tar.gz divergence_1.4.0.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
  0 1919k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1919k  100 1919k    0     0  2422k      0 --:--:-- --:--:-- --:--:-- 2438k

install for i386

* installing *source* package 'divergence' ...
** using staged installation
** 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_1.4.0.zip
* DONE (divergence)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'divergence' successfully unpacked and MD5 sums checked

Tests output


Example timings

divergence.Rcheck/examples_i386/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest16.54 0.2016.75
computeMultivariateBinaryMatrix2.330.112.44
computeMultivariateDigitization5.260.115.37
computeMultivariateSupport0.330.000.33
computeQuantileMatrix0.050.000.05
computeUnivariateDigitization18.83 0.0018.83
computeUnivariateSupport1.280.021.29
computeUnivariateTernaryMatrix1.780.001.78
findMultivariateGammaWithSupport1.110.011.13
findUnivariateGammaWithSupport18.90 0.0018.91

divergence.Rcheck/examples_x64/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest16.49 0.1016.57
computeMultivariateBinaryMatrix2.590.172.77
computeMultivariateDigitization5.970.146.10
computeMultivariateSupport0.540.000.55
computeQuantileMatrix0.080.000.08
computeUnivariateDigitization22.67 0.0922.77
computeUnivariateSupport2.140.002.14
computeUnivariateTernaryMatrix2.280.032.31
findMultivariateGammaWithSupport0.970.051.01
findUnivariateGammaWithSupport22.61 0.0223.54