BioC 3.3: CHECK report for PSICQUIC on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PSICQUIC_1.9.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.3’
* 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 ... [8s/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’
.loadRegistry : <anonymous>: no visible global function definition for
  ‘str’
.retrieveData: no visible global function definition for ‘read.table’
.retrieveData : <anonymous>: no visible global function definition for
  ‘str’
.translate.uniprotkb: no visible binding for global variable ‘id’
detectionMethods: no visible global function definition for ‘browseURL’
interactionTypes: no visible global function definition for ‘browseURL’
speciesIDs: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  DataFrame browseURL id read.table str
Consider adding
  importFrom("utils", "browseURL", "read.table", "str")
to your NAMESPACE file.
* 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 ... [11s/490s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
PSICQUIC-class 5.305  0.077 184.520
IDMapper-class 0.686  0.022 287.047
interactions   0.562  0.034  11.482
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [0m/18m]
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  PSICQUIC RUnit Tests - 31 test functions, 1 error, 0 failures
  ERROR in test_addGeneInfoMinimalTable: Error : 1: Extra content at the end of the document
  
  
  Test files with failing tests
  
     test_IDMapper.R 
       test_addGeneInfoMinimalTable 
  
  
  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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.


R version 3.3.0 beta (2016-04-06 r70435) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

> 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, 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, unsplit


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


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


checking for biomart access...
   does 'http://www.ensembl.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.ensembl.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.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
Extra content at the end of the document
Timing stopped at: 0.188 0.012 282.925 
Error : 1: Extra content at the end of the document

[1] "--- test_addStandardNames"
[1] "--- test_ctor"
checking for biomart access...
   does 'http://www.ensembl.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"
[1] "--- test_.restrictBySpecies"
[1] "--- test_.retrieveData"
List of 2
 $ message: chr "Could not resolve host: intentionally.bogus"
 $ call   : language function (type, msg, asError = TRUE)  { ...
 - attr(*, "class")= chr [1:4] "COULDNT_RESOLVE_HOST" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://intentionally.bogus"
[1] "--- test_ctor"
[1] test providers: Interoporc,Spike,BioGrid
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: bhf-ucl,EBI-GOA-nonIntAct,MPIDB
[1] "--- test_initialConditions"
[1] "--- test_interactions"
[1] "--- test_interactionsFourGenes"
About to execute 18 PSICQUIC queries (6 gene pairings x 3 provider/s)
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_interactionsTwoGenes"
[1] "--- test_rawQuery"
[1] test providers: I2D,HPIDb,MBInfo
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: MPIDB,VirHostNet,MBInfo
[1] "--- test_retrieveByOmimId"
[1] test providers: MBInfo,UniProt,HPIDb
[1] "--- test_retrieveByPubmedID"
[1] test providers: InnateDB-All,Reactome-FIs,MolCon
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: VirHostNet,MatrixDB,HPIDb
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: bhf-ucl,VirHostNet,MolCon
[1] "--- test_smallMoleculeWithoutSpeciesDesignation"
[1] retrieving from ChEMBL
[1] PSICQUIC:::.runQuery: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] final query.url: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] --- http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib result: 141 15


RUNIT TEST PROTOCOL -- Thu Apr 21 06:45:29 2016 
*********************************************** 
Number of test functions: 31 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
PSICQUIC RUnit Tests - 31 test functions, 1 error, 0 failures
ERROR in test_addGeneInfoMinimalTable: Error : 1: Extra content at the end of the document


Test files with failing tests

   test_IDMapper.R 
     test_addGeneInfoMinimalTable 


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

BioC 3.3: CHECK report for PSICQUIC on morelia

Summary

Command output

name	user	system	elapsed
IDMapper-class	0.686	0.022	287.047
PSICQUIC-class	5.305	0.077	184.520
interactions	0.562	0.034	11.482
providers	0.400	0.002	1.576
rawQuery	0.037	0.003	2.082
webBrowser-functions	0.000	0.000	0.001