BioC 3.2: CHECK report for PSICQUIC on linux1.bioconductor.org

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### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PSICQUIC_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSICQUIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PSICQUIC’ version ‘1.8.1’
* 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 ‘PSICQUIC’ can be installed ... [7s/8s] 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
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘httr’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.loadRegistry: no visible global function definition for ‘DataFrame’
.translate.uniprotkb: no visible binding for global variable ‘id’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PSICQUIC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PSICQUIC-class
> ### Title: PSICQUIC
> ### Aliases: class:PSICQUIC PSICQUIC-class PSICQUIC show,PSICQUIC-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>    psicquic <- PSICQUIC()
Warning in .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
>      # obtain the list of two dozen (or so) currently live
>      # PSICQUIC-compliant data providers
>    providers(psicquic)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘providers’ for signature ‘"logical"’
Calls: providers -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/16s]
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
       test_rawQuery 
       test_retrieveByDetectionMethod 
       test_retrieveByInteractionType 
       test_retrieveByOmimId 
       test_retrieveByPubmedID 
       test_retrieveByPubmedIdOnly 
       test_retrieveBySpeciesId 
       test_smallMoleculeWithoutSpeciesDesignation 
  
  
  Error in BiocGenerics:::testPackage("PSICQUIC") : 
    unit tests failed for package PSICQUIC
  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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.


R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("PSICQUIC")

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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit


Attaching package: 'plyr'

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

    desc

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

    rename

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:httr':

    content

Loading required package: DBI

checking for biomart access...
   does 'http://www.biomart.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.categorize"
[1] "--- test_.translate.ensemblGene"
checking for biomart access...
   does 'http://www.biomart.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.translate.ensemblProt"
[1] "--- test_.translate.locuslink"
[1] "--- test_.translate.refseq"
[1] "--- test_.translate.string"
[1] "--- test_.translate.uniprotkb"
[1] "--- test_translateAll"
[1] "--- test_addGeneInfo"
[1] "--- test_addGeneInfoMinimalTable"
checking for biomart access...
   does 'http://www.biomart.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_addStandardNames"
[1] "--- test_ctor"
checking for biomart access...
   does 'http://www.biomart.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_preserveKnownGeneIdentifiers"
Loading required package: bitops
[1] "--- test_.enumerateSearchPairs"
[1] "--- test_.loadRegistry"
Timing stopped at: 0.004 0 0.161 
Error in checkEquals(colnames(tbl), c("url")) : 
  target is NULL, current is character
In addition: Warning message:
In PSICQUIC:::.loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_.restrictBySpecies"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.003 0.004 0.164 
Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_.retrieveData"
Timing stopped at: 0.003 0 0.162 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_ctor"
Timing stopped at: 0.003 0 0.159 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_handleEmbeddedSingleQuote"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0 0.165 
Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_initialConditions"
[1] "--- test_interactions"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0 0.163 
Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_interactionsFourGenes"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.007 0 0.174 
Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_interactionsTwoGenes"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0 0.174 
Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_rawQuery"
Timing stopped at: 0.003 0 0.159 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0 0.162 
Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_retrieveByInteractionType"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.007 0 0.174 
Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_retrieveByOmimId"
Timing stopped at: 0.003 0 0.162 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'interactions' for signature '"logical"'
In addition: Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
[1] "--- test_retrieveByPubmedID"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.007 0 0.165 
Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_retrieveByPubmedIdOnly"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0 0.165 
Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_retrieveBySpeciesId"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.006 0 0.163 
Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

[1] "--- test_smallMoleculeWithoutSpeciesDesignation"
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
Timing stopped at: 0.007 0 0.165 
Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>



RUNIT TEST PROTOCOL -- Sun Oct 25 06:56:31 2015 
*********************************************** 
Number of test functions: 31 
Number of errors: 15 
Number of failures: 1 

 
1 Test Suite : 
PSICQUIC RUnit Tests - 31 test functions, 15 errors, 1 failure
FAILURE in test_.loadRegistry: Error in checkEquals(colnames(tbl), c("url")) : 
  target is NULL, current is character
ERROR in test_.restrictBySpecies: Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_.retrieveData: Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
ERROR in test_ctor: Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
ERROR in test_handleEmbeddedSingleQuotes: Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_interactions: Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_interactionsFourGenes: Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_interactionsTwoGenes: Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_rawQuery: Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
ERROR in test_retrieveByDetectionMethod: Error in providers %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_retrieveByInteractionType: Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_retrieveByOmimId: Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'interactions' for signature '"logical"'
ERROR in test_retrieveByPubmedID: Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_retrieveByPubmedIdOnly: Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_retrieveBySpeciesId: Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>

ERROR in test_smallMoleculeWithoutSpeciesDesignation: Error in provider %in% providers(psicquic) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'providers' for signature '"logical"'
Calls: providers -> <Anonymous>


Test files with failing tests

   test_PSICQUIC.R 
     test_.loadRegistry 
     test_.restrictBySpecies 
     test_.retrieveData 
     test_ctor 
     test_handleEmbeddedSingleQuotes 
     test_interactions 
     test_interactionsFourGenes 
     test_interactionsTwoGenes 
     test_rawQuery 
     test_retrieveByDetectionMethod 
     test_retrieveByInteractionType 
     test_retrieveByOmimId 
     test_retrieveByPubmedID 
     test_retrieveByPubmedIdOnly 
     test_retrieveBySpeciesId 
     test_smallMoleculeWithoutSpeciesDesignation 


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

name	user	system	elapsed
IDMapper-class	0.219	0.008	0.900

BioC 3.2: CHECK report for PSICQUIC on linux1.bioconductor.org

Summary

Command output