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CHECK results for GSEABase on riesling1

This page was generated on 2021-06-12 12:05:05 -0400 (Sat, 12 Jun 2021).

Package 797/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSEABase 1.55.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-06-11 14:50:09 -0400 (Fri, 11 Jun 2021)
URL: https://git.bioconductor.org/packages/GSEABase
Branch: master
Last Commit: ef54e5c
Last Changed Date: 2021-05-19 11:39:15 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
To the developers/maintainers of the GSEABase package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSEABase.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

Summary

Package: GSEABase
Version: 1.55.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABase.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GSEABase_1.55.0.tar.gz
StartedAt: 2021-06-12 00:29:43 -0400 (Sat, 12 Jun 2021)
EndedAt: 2021-06-12 00:33:04 -0400 (Sat, 12 Jun 2021)
EllapsedTime: 201.4 seconds
RetCode: 0
Status:   OK   
CheckDir: GSEABase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABase.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GSEABase_1.55.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/GSEABase.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.55.0'
* 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


Installation output

GSEABase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GSEABase_1.55.0.tar.gz && rm -rf GSEABase.buildbin-libdir && mkdir GSEABase.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSEABase.buildbin-libdir GSEABase_1.55.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GSEABase_1.55.0.zip && rm GSEABase_1.55.0.tar.gz GSEABase_1.55.0.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 72823  100 72823    0     0   733k      0 --:--:-- --:--:-- --:--:--  733k

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  
REDIRECT:topic	 |,CollectionType,CollectionType-method -> CollectionType-class.html [ FAIL ]
REDIRECT:topic	 |,CollectionIdType,CollectionIdType-method -> CollectionType-class.html [ FAIL ]
    CollectionType-constructors             html  
    GSEABase-package                        html  
    GeneColorSet-class                      html  
REDIRECT:topic	 |,GeneColorSet,GeneColorSet-method -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 |,GeneColorSet,character-method -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 coloring<-,GeneColorSet,data.frame-method -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 geneColor<-,GeneColorSet,factor-method -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 phenotypeColor<-,GeneColorSet,factor-method -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 phenotype<-,GeneColorSet,character-method -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 coloring<- -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 geneColor<- -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 phenotype<- -> GeneColorSet-class.html [ FAIL ]
REDIRECT:topic	 phenotypeColor<- -> GeneColorSet-class.html [ FAIL ]
    GeneColorSet-methods                    html  
    GeneIdentifierType-class                html  
REDIRECT:topic	 annotation<-,GeneIdentifierType,character-method -> GeneIdentifierType-class.html [ FAIL ]
    GeneIdentifierType-constructors         html  
    GeneSet-class                           html  
REDIRECT:topic	 |,GeneSet,GeneSet-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 |,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 collectionType<-,GeneSet,CollectionType-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 contributor<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 creationDate<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 description<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 geneIds<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 longDescription<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 organism<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 pubMedIds<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 setIdentifier<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 setName<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 geneIdType<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 geneIdType<-,GeneSet,GeneIdentifierType-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 setVersion<-,GeneSet,Versions-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 urls<-,GeneSet,character-method -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 collectionType<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/GSEABase.buildbin-libdir/00LOCK-GSEABase/00new/GSEABase/help/collectionType.html
REDIRECT:topic	 contributor<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 creationDate<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 geneIds<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 geneIdType<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 longDescription<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 organism<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 setIdentifier<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 setName<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 setVersion<- -> GeneSet-class.html [ FAIL ]
REDIRECT:topic	 urls<- -> GeneSet-class.html [ FAIL ]
    GeneSet-methods                         html  
    GeneSetCollection-class                 html  
REDIRECT:topic	 geneIds<-,GeneSetCollection,list-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 |,GeneSetCollection,GeneSetCollection-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 |,GeneSetCollection,ANY-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 |,ANY,GeneSetCollection-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 [<-,GeneSetCollection,ANY,ANY,ANY-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 [<-,GeneSetCollection,ANY,ANY,GeneSet-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 [<-,GeneSetCollection,character,ANY,GeneSet-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 [[<-,GeneSetCollection,ANY,ANY,ANY-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 [[<-,GeneSetCollection,numeric,ANY,GeneSet-method -> GeneSetCollection-class.html [ FAIL ]
REDIRECT:topic	 [[<-,GeneSetCollection,character,ANY,GeneSet-method -> GeneSetCollection-class.html [ FAIL ]
    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_1.55.0.zip
* DONE (GSEABase)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'GSEABase' successfully unpacked and MD5 sums checked

Tests output

GSEABase.Rcheck/tests_i386/unitTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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.

> 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


RUNIT TEST PROTOCOL -- Sat Jun 12 00:31:49 2021 
*********************************************** 
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 
  11.40    1.09   14.37 

GSEABase.Rcheck/tests_x64/unitTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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.

> 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


RUNIT TEST PROTOCOL -- Sat Jun 12 00:32:08 2021 
*********************************************** 
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 
  14.10    1.35   19.17 

Example timings

GSEABase.Rcheck/examples_i386/GSEABase-Ex.timings

nameusersystemelapsed
CollectionType-class0.370.060.44
CollectionType-constructors0.130.020.14
GSEABase-package0.080.010.11
GeneColorSet-class0.100.020.13
GeneIdentifierType-class0.070.000.14
GeneIdentifierType-constructors0.160.000.23
GeneSet-class0.090.010.13
GeneSet-methods0.070.020.07
GeneSetCollection-class000
GeneSetCollection-methods2.290.232.72
OBOCollection-class0.050.000.05
getOBOCollection0.030.000.03
getObjects0.020.000.03
goSlim-methods0.330.020.35
incidence-methods000

GSEABase.Rcheck/examples_x64/GSEABase-Ex.timings

nameusersystemelapsed
CollectionType-class0.370.080.45
CollectionType-constructors0.070.000.06
GSEABase-package0.080.020.09
GeneColorSet-class0.050.010.06
GeneIdentifierType-class0.050.000.05
GeneIdentifierType-constructors0.050.000.04
GeneSet-class0.090.000.10
GeneSet-methods0.060.000.06
GeneSetCollection-class000
GeneSetCollection-methods2.470.523.17
OBOCollection-class0.130.000.14
getOBOCollection0.030.000.03
getObjects0.010.000.05
goSlim-methods0.420.050.47
incidence-methods0.020.000.01