Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:28 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for divergence on tokay2


To the developers/maintainers of the divergence package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/divergence.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 521/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
divergence 1.10.0  (landing page)
Wikum Dinalankara , Luigi Marchionni
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/divergence
git_branch: RELEASE_3_14
git_last_commit: 3431649
git_last_commit_date: 2021-10-26 12:49:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: divergence
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings divergence_1.10.0.tar.gz
StartedAt: 2022-04-12 18:43:50 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:48:23 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 272.2 seconds
RetCode: 0
Status:   OK  
CheckDir: divergence.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings divergence_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/divergence.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.10.0'
* 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 LazyData ... 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
computeChiSquaredTest          14.22   0.18   14.39
computeUnivariateDigitization  13.96   0.11   14.07
findUnivariateGammaWithSupport 12.93   0.03   12.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
computeChiSquaredTest          16.14   0.06   16.20
computeUnivariateDigitization  15.39   0.05   15.44
findUnivariateGammaWithSupport 14.75   0.00   14.75
* 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-3.14-bioc/meat/divergence.Rcheck/00check.log'
for details.



Installation output

divergence.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/divergence_1.10.0.tar.gz && rm -rf divergence.buildbin-libdir && mkdir divergence.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=divergence.buildbin-libdir divergence_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL divergence_1.10.0.zip && rm divergence_1.10.0.tar.gz divergence_1.10.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 13 1917k   13  262k    0     0   735k      0  0:00:02 --:--:--  0:00:02  734k
100 1917k  100 1917k    0     0  1415k      0  0:00:01  0:00:01 --:--:-- 1415k
100 1917k  100 1917k    0     0  1415k      0  0:00:01  0:00:01 --:--:-- 1415k

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_1.10.0.zip
* DONE (divergence)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'divergence' successfully unpacked and MD5 sums checked

Tests output


Example timings

divergence.Rcheck/examples_i386/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest14.22 0.1814.39
computeMultivariateBinaryMatrix2.160.042.20
computeMultivariateDigitization4.190.144.32
computeMultivariateSupport0.330.000.33
computeQuantileMatrix0.060.000.06
computeUnivariateDigitization13.96 0.1114.07
computeUnivariateSupport1.230.001.23
computeUnivariateTernaryMatrix1.370.001.37
findMultivariateGammaWithSupport0.590.100.69
findUnivariateGammaWithSupport12.93 0.0312.95

divergence.Rcheck/examples_x64/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest16.14 0.0616.20
computeMultivariateBinaryMatrix1.810.061.87
computeMultivariateDigitization4.110.154.27
computeMultivariateSupport0.350.000.34
computeQuantileMatrix0.060.000.06
computeUnivariateDigitization15.39 0.0515.44
computeUnivariateSupport1.410.001.41
computeUnivariateTernaryMatrix1.560.021.57
findMultivariateGammaWithSupport0.670.030.71
findUnivariateGammaWithSupport14.75 0.0014.75