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CHECK report for GOstats on tokay1

This page was generated on 2021-05-06 12:31:32 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GOstats package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 767/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOstats 2.56.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GOstats
Branch: RELEASE_3_12
Last Commit: 8f988c3
Last Changed Date: 2020-10-27 10:24:14 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GOstats
Version: 2.56.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GOstats_2.56.0.tar.gz
StartedAt: 2021-05-06 03:20:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:27:11 -0400 (Thu, 06 May 2021)
EllapsedTime: 428.1 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: GOstats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GOstats_2.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GOstats.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOstats/DESCRIPTION' ... OK
* this is package 'GOstats' version '2.56.0'
* 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 'GOstats' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYxjiKK/R.INSTALL156868f16793/GOstats/man/hyperGTest.Rd:47: file link 'geneGoHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYxjiKK/R.INSTALL156868f16793/GOstats/man/hyperGTest.Rd:48: file link 'geneKeggHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GOstats.Rcheck/00install.out' for details.
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/GOstats.Rcheck/00check.log'
for details.



Installation output

GOstats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GOstats_2.56.0.tar.gz && rm -rf GOstats.buildbin-libdir && mkdir GOstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOstats.buildbin-libdir GOstats_2.56.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GOstats_2.56.0.zip && rm GOstats_2.56.0.tar.gz GOstats_2.56.0.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 1570k  100 1570k    0     0  31.3M      0 --:--:-- --:--:-- --:--:-- 31.9M

install for i386

* installing *source* package 'GOstats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GOstats'
    finding HTML links ... done
    GOHyperGResult-class                    html  
    GOstats-defunct                         html  
    GOstats-package                         html  
    Ndists                                  html  
    OBOHyperGResult-class                   html  
    compCorrGraph                           html  
    compGdist                               html  
    hyperGTest                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYxjiKK/R.INSTALL156868f16793/GOstats/man/hyperGTest.Rd:47: file link 'geneGoHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYxjiKK/R.INSTALL156868f16793/GOstats/man/hyperGTest.Rd:48: file link 'geneKeggHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic
    idx2dimnames                            html  
    makeGOGraph                             html  
    notConn                                 html  
    oneGOGraph                              html  
    probeSetSummary                         html  
    shortestPath                            html  
    simLL                                   html  
    termGraphs                              html  
    triadCensus                             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 'GOstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOstats' as GOstats_2.56.0.zip
* DONE (GOstats)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GOstats' successfully unpacked and MD5 sums checked

Tests output

GOstats.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> require("GOstats") || stop("unable to load GOstats")
Loading required package: GOstats
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: graph


Attaching package: 'GOstats'

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

    makeGOGraph

[1] TRUE
> BiocGenerics:::testPackage("GOstats", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db




RUNIT TEST PROTOCOL -- Thu May 06 03:25:23 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GOstats RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In makeValidParams(.Object) :
  converting geneIds from list to atomic vector via unlist
2: In makeValidParams(.Object) : removing duplicate IDs in geneIds
3: In makeValidParams(.Object) :
  converting univ from list to atomic vector via unlist
4: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
  81.73   43.53  125.26 

GOstats.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> require("GOstats") || stop("unable to load GOstats")
Loading required package: GOstats
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: graph


Attaching package: 'GOstats'

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

    makeGOGraph

[1] TRUE
> BiocGenerics:::testPackage("GOstats", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db




RUNIT TEST PROTOCOL -- Thu May 06 03:27:02 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GOstats RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In makeValidParams(.Object) :
  converting geneIds from list to atomic vector via unlist
2: In makeValidParams(.Object) : removing duplicate IDs in geneIds
3: In makeValidParams(.Object) :
  converting univ from list to atomic vector via unlist
4: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
  62.04   36.96   99.03 

Example timings

GOstats.Rcheck/examples_i386/GOstats-Ex.timings

nameusersystemelapsed
Ndists0.060.030.10
compCorrGraph0.810.010.83
compGdist0.320.000.31
idx2dimnames0.560.020.58
makeGOGraph1.550.161.71
notConn0.040.000.04
oneGOGraph0.300.120.47
probeSetSummary3.010.253.27
shortestPath3.300.083.37
simLL0.700.050.75
triadCensus000

GOstats.Rcheck/examples_x64/GOstats-Ex.timings

nameusersystemelapsed
Ndists0.070.000.07
compCorrGraph0.890.030.92
compGdist0.150.000.16
idx2dimnames0.440.020.45
makeGOGraph0.870.020.89
notConn0.030.000.04
oneGOGraph0.250.040.29
probeSetSummary2.030.032.07
shortestPath2.350.022.35
simLL0.750.030.79
triadCensus000