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CHECK report for GOstats on tokay1

This page was generated on 2018-04-12 13:17:33 -0400 (Thu, 12 Apr 2018).

Package 604/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOstats 2.44.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GOstats
Branch: RELEASE_3_6
Last Commit: fc64ca2
Last Changed Date: 2017-10-30 12:39:02 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOstats
Version: 2.44.0
Command: rm -rf GOstats.buildbin-libdir GOstats.Rcheck && mkdir GOstats.buildbin-libdir GOstats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOstats.buildbin-libdir GOstats_2.44.0.tar.gz >GOstats.Rcheck\00install.out 2>&1 && cp GOstats.Rcheck\00install.out GOstats-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOstats.buildbin-libdir --install="check:GOstats-install.out" --force-multiarch --no-vignettes --timings GOstats_2.44.0.tar.gz
StartedAt: 2018-04-12 00:29:10 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:34:07 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 297.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GOstats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOstats.buildbin-libdir GOstats.Rcheck && mkdir GOstats.buildbin-libdir GOstats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOstats.buildbin-libdir GOstats_2.44.0.tar.gz >GOstats.Rcheck\00install.out 2>&1 && cp GOstats.Rcheck\00install.out GOstats-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOstats.buildbin-libdir --install="check:GOstats-install.out" --force-multiarch --no-vignettes --timings GOstats_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOstats.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '2.44.0'
* 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-3.6-bioc/tmpdir/RtmpmoaSBX/R.INSTALL18e035802a9f/GOstats/man/hyperGTest.Rd:47: missing file link 'geneGoHyperGeoTest'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmoaSBX/R.INSTALL18e035802a9f/GOstats/man/hyperGTest.Rd:48: missing file link 'geneKeggHyperGeoTest'
See 'C:/Users/biocbuild/bbs-3.6-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 installed files from 'inst/doc' ... 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-3.6-bioc/meat/GOstats.Rcheck/00check.log'
for details.

Installation output

GOstats.Rcheck/00install.out


install for i386

* installing *source* package 'GOstats' ...
** R
** data
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpmoaSBX/R.INSTALL18e035802a9f/GOstats/man/hyperGTest.Rd:47: missing file link 'geneGoHyperGeoTest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmoaSBX/R.INSTALL18e035802a9f/GOstats/man/hyperGTest.Rd:48: missing file link 'geneKeggHyperGeoTest'
    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
In R CMD INSTALL

install for x64

* installing *source* package 'GOstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOstats' as GOstats_2.44.0.zip
* DONE (GOstats)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GOstats.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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

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 Apr 12 00:33:08 2018 
*********************************************** 
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) :
  converting univ from list to atomic vector via unlist
3: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
  37.00    1.17   38.17

GOstats.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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

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 Apr 12 00:34:02 2018 
*********************************************** 
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) :
  converting univ from list to atomic vector via unlist
3: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
  52.98    0.85   53.84

Example timings

GOstats.Rcheck/examples_i386/GOstats-Ex.timings

nameusersystemelapsed
Ndists0.070.010.08
compCorrGraph1.510.031.55
compGdist0.680.050.74
idx2dimnames0.040.000.04
makeGOGraph2.640.082.84
notConn0.030.000.03
oneGOGraph0.520.080.65
probeSetSummary2.360.132.49
shortestPath2.360.012.38
simLL0.640.020.65
triadCensus000

GOstats.Rcheck/examples_x64/GOstats-Ex.timings

nameusersystemelapsed
Ndists0.040.020.06
compCorrGraph1.300.001.29
compGdist0.550.000.55
idx2dimnames0.010.000.01
makeGOGraph1.850.051.89
notConn0.030.000.03
oneGOGraph0.360.010.38
probeSetSummary2.700.112.81
shortestPath2.700.032.74
simLL0.550.000.54
triadCensus000