Package: RefNet

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RefNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RefNet_1.18.0.tar.gz

StartedAt: 2019-04-16 02:16:24 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:20:41 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 256.5 seconds

RetCode: 0

Status:  OK

CheckDir: RefNet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RefNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RefNet_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RefNet.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RefNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RefNet’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
RefNet-class    20.334  1.136  25.033
providers       19.163  0.800  22.966
interactions    18.775  0.785  20.953
providerClasses 18.556  0.795  20.825
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/RefNet.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RefNet
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RefNet’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’
* DONE (RefNet)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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':

    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, colMeans, colSums, colnames,
    dirname, 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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

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: RCurl
Loading required package: bitops
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...
snapshotDate(): 2018-10-24
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/10364'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/10365'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/12810'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/12814'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27766'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27767'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27768'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27769'
[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...
snapshotDate(): 2018-10-24
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/10364'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/10365'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/12810'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/12814'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27766'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27767'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27768'
downloading 0 resources
loading from cache 
    '/Users/biocbuild//.AnnotationHub/27769'
[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 -- Tue Apr 16 02:20:36 2019 
*********************************************** 
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 
Warning messages:
1: In is.na(psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(refnet@psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
3: In is.na(refnet@psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
> 
> proc.time()
   user  system elapsed 
 48.329   2.201  65.650 

name	user	system	elapsed
RefNet-class	20.334	1.136	25.033
detectDuplicateInteractions	0.023	0.001	0.024
interactions	18.775	0.785	20.953
pickBestFromDupGroup	0.021	0.001	0.022
providerClasses	18.556	0.795	20.825
providers	19.163	0.800	22.966
pubmedAbstract	0.016	0.002	0.399