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CHECK report for RefNet on tokay1

This page was generated on 2020-04-15 12:22:57 -0400 (Wed, 15 Apr 2020).

Package 1406/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RefNet 1.22.0
Paul Shannon
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/RefNet
Branch: RELEASE_3_10
Last Commit: e2997ca
Last Changed Date: 2019-10-29 13:08:57 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RefNet
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RefNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RefNet_1.22.0.tar.gz
StartedAt: 2020-04-15 05:56:49 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:09:44 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 775.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RefNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RefNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RefNet_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RefNet.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RefNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RefNet' version '1.22.0'
* 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 'RefNet' 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
Examples with CPU or elapsed time > 5s
                 user system elapsed
RefNet-class    40.63   2.35   52.27
interactions    33.60   1.11   36.58
providerClasses 32.73   1.09   35.69
providers       26.78   0.92   29.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
RefNet-class    31.90   1.63   39.52
providerClasses 32.10   1.03   34.99
providers       25.69   1.06   28.42
interactions    24.70   0.95   27.30
* 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

RefNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/RefNet_1.22.0.tar.gz && rm -rf RefNet.buildbin-libdir && mkdir RefNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RefNet.buildbin-libdir RefNet_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL RefNet_1.22.0.zip && rm RefNet_1.22.0.tar.gz RefNet_1.22.0.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 92407  100 92407    0     0   934k      0 --:--:-- --:--:-- --:--:--  970k

install for i386

* installing *source* package 'RefNet' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' 
** help
*** installing help indices
  converting help for package 'RefNet'
    finding HTML links ... done
    RefNet-class                            html  
    detectDuplicateInteractions             html  
    interactions                            html  
    pickBestFromDupGroup                    html  
    providerClasses                         html  
    providers                               html  
    pubmedAbstract                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RefNet' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
* MD5 sums
packaged installation of 'RefNet' as RefNet_1.22.0.zip
* DONE (RefNet)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'RefNet' successfully unpacked and MD5 sums checked

Tests output

RefNet.Rcheck/tests_i386/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
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, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

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

    desc

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

    rename

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: shiny
[1] TRUE
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' 
> BiocGenerics:::testPackage('RefNet')
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    cache

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

    content


[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
snapshotDate(): 2019-10-29
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
[1] RefNet ready.
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.combinations"
[1] "--- test_.filterOnColumnValue"
[1] "--- test_.findHits"
[1] "--- test_.smartRbind"
[1] "--- test_ctor"
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
snapshotDate(): 2019-10-29
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmp4UQwC7/BiocFileCache
[1] RefNet ready.
[1] "--- test_detectDuplicateInteractions"
[1] "--- test_interactions"
[1] "--- test_pickBestFromDupGroup"
[1] "--- test_providerMix_PSICQUIC_and_native"
[1] "--- test_pubmedAbstract"
[1] "--- test_recon2Interactions"


RUNIT TEST PROTOCOL -- Wed Apr 15 06:08:20 2020 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RefNet RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  54.67    2.54  261.51

RefNet.Rcheck/tests_x64/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
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':

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

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    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, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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Attaching package: 'IRanges'

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Loading required package: PSICQUIC
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Attaching package: 'plyr'

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Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: shiny
[1] TRUE
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' 
> BiocGenerics:::testPackage('RefNet')
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpctTxFL/BiocFileCache
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[1] RefNet ready.
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.combinations"
[1] "--- test_.filterOnColumnValue"
[1] "--- test_.findHits"
[1] "--- test_.smartRbind"
[1] "--- test_ctor"
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
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loading from cache
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loading from cache
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[1] RefNet ready.
[1] "--- test_detectDuplicateInteractions"
[1] "--- test_interactions"
[1] "--- test_pickBestFromDupGroup"
[1] "--- test_providerMix_PSICQUIC_and_native"
[1] "--- test_pubmedAbstract"
[1] "--- test_recon2Interactions"


RUNIT TEST PROTOCOL -- Wed Apr 15 06:09:38 2020 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RefNet RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  58.96    2.98   77.26

Example timings

RefNet.Rcheck/examples_i386/RefNet-Ex.timings

nameusersystemelapsed
RefNet-class40.63 2.3552.27
detectDuplicateInteractions0.020.000.03
interactions33.60 1.1136.58
pickBestFromDupGroup0.030.000.04
providerClasses32.73 1.0935.69
providers26.78 0.9229.85
pubmedAbstract0.470.170.98

RefNet.Rcheck/examples_x64/RefNet-Ex.timings

nameusersystemelapsed
RefNet-class31.90 1.6339.52
detectDuplicateInteractions0.010.000.01
interactions24.70 0.9527.30
pickBestFromDupGroup0.020.000.01
providerClasses32.10 1.0334.99
providers25.69 1.0628.42
pubmedAbstract0.420.050.72