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CHECK report for rTRM on tokay1

This page was generated on 2021-01-19 11:56:21 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE rTRM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1600/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTRM 1.28.0
Diego Diez
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/rTRM
Branch: RELEASE_3_12
Last Commit: 2908ebc
Last Changed Date: 2020-10-27 10:51:24 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 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: rTRM
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rTRM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rTRM_1.28.0.tar.gz
StartedAt: 2021-01-19 06:48:43 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 06:51:03 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 140.1 seconds
RetCode: 0
Status:  OK  
CheckDir: rTRM.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:rTRM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rTRM_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/rTRM.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 'rTRM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rTRM' version '1.28.0'
* 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 'rTRM' 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 ... OK
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: OK


Installation output

rTRM.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/rTRM_1.28.0.tar.gz && rm -rf rTRM.buildbin-libdir && mkdir rTRM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rTRM.buildbin-libdir rTRM_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL rTRM_1.28.0.zip && rm rTRM_1.28.0.tar.gz rTRM_1.28.0.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 2779k  100 2779k    0     0  38.0M      0 --:--:-- --:--:-- --:--:-- 40.5M

install for i386

* installing *source* package 'rTRM' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

*** installing help indices
  converting help for package 'rTRM'
    finding HTML links ... done
    annotateFreq                            html  
    annotateModule                          html  
    annotateTRM                             html  
    biogrid_hs                              html  
    biogrid_mm                              html  
    findTRM                                 html  
    getAnnotations                          html  
    getBiogridData                          html  
    getConcentricList                       html  
    getLargestComp                          html  
    getMaps                                 html  
    getMatrices                             html  
    getMotifsFromEntrezgene                 html  
    getMotifsFromSymbol                     html  
    getOrthologFromMatrix                   html  
    getOrthologs                            html  
    getOrthologsFromBiomart                 html  
    getSequencesFromGenome                  html  
    getSimilarityMatrix                     html  
    getTFclass                              html  
    getTFclassFromEntrezgene                html  
    getTFterms                              html  
    initBiomart                             html  
    layout.arc                              html  
    layout.concentric                       html  
    plotDegree                              html  
    plotGraph                               html  
    plotTRM                                 html  
    plotTRMlegend                           html  
    processBiogrid                          html  
    rTRM-package                            html  
    removeVertices                          html  
    writeTRMreport                          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 'rTRM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rTRM' as rTRM_1.28.0.zip
* DONE (rTRM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'rTRM' successfully unpacked and MD5 sums checked

Tests output

rTRM.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("rTRM")

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

removing: 4 nodes out of 8 [keeping 4 nodes]


RUNIT TEST PROTOCOL -- Tue Jan 19 06:50:52 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rTRM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.28    0.12    4.39 

rTRM.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("rTRM")

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

removing: 4 nodes out of 8 [keeping 4 nodes]


RUNIT TEST PROTOCOL -- Tue Jan 19 06:50:56 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rTRM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.95    0.18    3.12 

Example timings

rTRM.Rcheck/examples_i386/rTRM-Ex.timings

nameusersystemelapsed
findTRM0.140.020.30
getAnnotations0.000.000.06
getMaps0.020.020.03
getMatrices0.670.011.06
getOrthologs0.000.020.01
rTRM-package0.050.000.05

rTRM.Rcheck/examples_x64/rTRM-Ex.timings

nameusersystemelapsed
findTRM0.130.000.12
getAnnotations0.010.000.02
getMaps0.020.010.03
getMatrices0.650.000.66
getOrthologs0.030.000.03
rTRM-package0.040.000.03