Multiple platform build/check report for BioC 3.14 - CHECK results for GSEABase on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: GSEABase

Version: 1.56.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABase.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GSEABase_1.56.0.tar.gz

StartedAt: 2022-04-12 20:51:55 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:55:26 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 211.2 seconds

RetCode: 0

Status: OK

CheckDir: GSEABase.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABase.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GSEABase_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GSEABase.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 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.56.0'
* 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 'GSEABase' 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 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 'unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'unitTests.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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GSEABase_1.56.0.tar.gz && rm -rf GSEABase.buildbin-libdir && mkdir GSEABase.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSEABase.buildbin-libdir GSEABase_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GSEABase_1.56.0.zip && rm GSEABase_1.56.0.tar.gz GSEABase_1.56.0.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 72843  100 72843    0     0   457k      0 --:--:-- --:--:-- --:--:--  458k

install for i386

* installing *source* package 'GSEABase' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSEABase'
    finding HTML links ... done
    CollectionType-class                    html  
    CollectionType-constructors             html  
    GSEABase-package                        html  
    GeneColorSet-class                      html  
    GeneColorSet-methods                    html  
    GeneIdentifierType-class                html  
    GeneIdentifierType-constructors         html  
    GeneSet-class                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GSEABase.buildbin-libdir/00LOCK-GSEABase/00new/GSEABase/help/collectionType.html
    GeneSet-methods                         html  
    GeneSetCollection-class                 html  
    GeneSetCollection-methods               html  
    OBOCollection-class                     html  
    details-methods                         html  
    getOBOCollection                        html  
    getObjects                              html  
    goSlim-methods                          html  
    incidence-methods                       html  
    mapIdentifiers-methods                  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 'GSEABase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSEABase' as GSEABase_1.56.0.zip
* DONE (GSEABase)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GSEABase' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("GSEABase")

Attaching package: 'BiocGenerics'

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")'.


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


Attaching package: 'graph'

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

    addNode




'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Tue Apr 12 20:54:56 2022 
*********************************************** 
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GSEABase RUnit Tests - 79 test functions, 0 errors, 0 failures
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  18.06    1.57   21.06


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("GSEABase")

Attaching package: 'BiocGenerics'

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")'.


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


Attaching package: 'graph'

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

    addNode




'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Tue Apr 12 20:55:16 2022 
*********************************************** 
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GSEABase RUnit Tests - 79 test functions, 0 errors, 0 failures
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  18.43    1.18   19.62

name	user	system	elapsed
CollectionType-class	0.36	0.01	0.38
CollectionType-constructors	0.18	0.00	0.22
GSEABase-package	0.07	0.01	0.08
GeneColorSet-class	0.39	0.00	0.39
GeneIdentifierType-class	0.06	0.00	0.06
GeneIdentifierType-constructors	0.05	0.00	0.05
GeneSet-class	0.08	0.02	0.09
GeneSet-methods	0.05	0.00	0.05
GeneSetCollection-class	0	0	0
GeneSetCollection-methods	2.29	0.47	2.93
OBOCollection-class	0.10	0.01	0.11
getOBOCollection	0.04	0.00	0.05
getObjects	0.02	0.00	0.01
goSlim-methods	0.68	0.14	0.89
incidence-methods	0.02	0.00	0.02

name	user	system	elapsed
CollectionType-class	0.81	0.04	0.94
CollectionType-constructors	0.09	0.00	0.09
GSEABase-package	0.11	0.00	0.10
GeneColorSet-class	0.12	0.00	0.13
GeneIdentifierType-class	0.06	0.02	0.08
GeneIdentifierType-constructors	0.05	0.01	0.06
GeneSet-class	0.5	0.0	0.5
GeneSet-methods	0.06	0.00	0.06
GeneSetCollection-class	0	0	0
GeneSetCollection-methods	3.43	0.27	3.88
OBOCollection-class	0.07	0.01	0.09
getOBOCollection	0.05	0.00	0.05
getObjects	0.03	0.00	0.03
goSlim-methods	0.78	0.04	0.95
incidence-methods	0	0	0

CHECK results for GSEABase on tokay2

Summary

Command output

Installation output

Tests output

Example timings