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CHECK report for attract on tokay1

This page was generated on 2020-08-12 11:39:00 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE attract PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 95/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.41.0
Samuel Zimmerman
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/attract
Branch: master
Last Commit: 5d1da58
Last Changed Date: 2020-04-27 14:22:21 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: attract
Version: 1.41.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:attract.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings attract_1.41.0.tar.gz
StartedAt: 2020-08-12 00:25:40 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 00:34:38 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 537.4 seconds
RetCode: 0
Status:  OK  
CheckDir: attract.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:attract.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings attract_1.41.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/attract.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.41.0'
* 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 'attract' 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
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
* 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
calcFuncSynexprs 78.82   4.18   84.52
findAttractors   50.30   1.85   55.47
findCorrPartners  7.64   0.09    8.72
findSynexprs      6.89   0.01    7.73
plotsynexprs      5.27   0.01    6.09
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
calcFuncSynexprs 80.83   2.99   85.26
findAttractors   49.63   2.07   52.67
findCorrPartners  7.06   0.04    7.92
findSynexprs      5.98   0.02    6.81
plotsynexprs      5.09   0.02    5.93
* 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-3.12-bioc/meat/attract.Rcheck/00check.log'
for details.



Installation output

attract.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/attract_1.41.0.tar.gz && rm -rf attract.buildbin-libdir && mkdir attract.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=attract.buildbin-libdir attract_1.41.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL attract_1.41.0.zip && rm attract_1.41.0.tar.gz attract_1.41.0.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
100 4204k  100 4204k    0     0  39.4M      0 --:--:-- --:--:-- --:--:-- 41.0M

install for i386

* installing *source* package 'attract' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'attract'
    finding HTML links ... done
    AttractorModuleSet-class                html  
    SynExpressionSet-class                  html  
    attract-package                         html  
    buildCorMatrix                          html  
    buildCustomIncidenceMatrix              html  
    buildKeggIncidenceMatrix                html  
    calcFuncSynexprs                        html  
    calcInform                              html  
    calcModfstat                            html  
    calcRss                                 html  
    exprs.dat                               html  
    filterDataSet                           html  
    findAttractors                          html  
    findCorrPartners                        html  
    findOnepwaySynexprs                     html  
    findSynexprs                            html  
    flagPwayExists                          html  
    getCustomGenes                          html  
    getPwayGenes                            html  
    loring.eset                             html  
    plotsynexprs                            html  
    removeFlatGenes                         html  
    samp.info                               html  
    subset.loring.eset                      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 'attract' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'attract' as attract_1.41.0.zip
* DONE (attract)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'attract' successfully unpacked and MD5 sums checked

Tests output


Example timings

attract.Rcheck/examples_i386/attract-Ex.timings

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class000
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix000
calcFuncSynexprs78.82 4.1884.52
calcInform000
calcModfstat000
calcRss000
exprs.dat0.210.000.21
filterDataSet0.460.010.48
findAttractors50.30 1.8555.47
findCorrPartners7.640.098.72
findOnepwaySynexprs000
findSynexprs6.890.017.73
flagPwayExists000
getCustomGenes000
getPwayGenes000
loring.eset0.170.040.21
plotsynexprs5.270.016.09
removeFlatGenes0.200.020.22
samp.info000
subset.loring.eset0.100.010.11

attract.Rcheck/examples_x64/attract-Ex.timings

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class000
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix000
calcFuncSynexprs80.83 2.9985.26
calcInform000
calcModfstat000
calcRss000
exprs.dat0.140.010.16
filterDataSet0.30.00.3
findAttractors49.63 2.0752.67
findCorrPartners7.060.047.92
findOnepwaySynexprs000
findSynexprs5.980.026.81
flagPwayExists000
getCustomGenes000
getPwayGenes000
loring.eset0.130.010.14
plotsynexprs5.090.025.93
removeFlatGenes0.110.020.12
samp.info0.020.000.02
subset.loring.eset0.060.010.08