BioC 3.5: CHECK report for RefNet on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RefNet_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.12.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
RefNet-class    16.130  0.623  19.023
providerClasses 15.394  0.567  17.443
providers       14.040  0.549  15.858
interactions    12.603  0.496  14.393
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  RefNet RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in /Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck/RefNet/unitTests/test_RefNet.R: Error while sourcing  /Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck/RefNet/unitTests/test_RefNet.R : Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
    Unexpected format to the list of available marts.
  Please check the following URL manually, and try ?listMarts for advice.
  http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
  
  Test files with failing tests
  
     test_RefNet.R 
       /Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck/RefNet/unitTests/test_RefNet.R 
  
  
  Error in BiocGenerics:::testPackage("RefNet") : 
    unit tests failed for package RefNet
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck/00check.log’
for details.


R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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, 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

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
> 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(): 2017-04-25
loading from cache '/Users/biocbuild//.AnnotationHub/10364'
loading from cache '/Users/biocbuild//.AnnotationHub/10365'
loading from cache '/Users/biocbuild//.AnnotationHub/12810'
loading from cache '/Users/biocbuild//.AnnotationHub/12814'
loading from cache '/Users/biocbuild//.AnnotationHub/27766'
loading from cache '/Users/biocbuild//.AnnotationHub/27767'
loading from cache '/Users/biocbuild//.AnnotationHub/27768'
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...
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
  Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt


RUNIT TEST PROTOCOL -- Wed Oct 18 08:06:50 2017 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck/RefNet/unitTests/test_RefNet.R: Error while sourcing  /Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck/RefNet/unitTests/test_RefNet.R : Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
  Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

Test files with failing tests

   test_RefNet.R 
     /Users/biocbuild/bbs-3.5-bioc/meat/RefNet.Rcheck/RefNet/unitTests/test_RefNet.R 


Error in BiocGenerics:::testPackage("RefNet") : 
  unit tests failed for package RefNet
Execution halted

BioC 3.5: CHECK report for RefNet on veracruz2

Summary

Command output

name	user	system	elapsed
RefNet-class	16.130	0.623	19.023
detectDuplicateInteractions	0.046	0.001	0.048
interactions	12.603	0.496	14.393
pickBestFromDupGroup	0.039	0.001	0.044
providerClasses	15.394	0.567	17.443
providers	14.040	0.549	15.858
pubmedAbstract	0.010	0.002	0.374