BioC 3.3: CHECK report for UniProt.ws on zin2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings UniProt.ws_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/UniProt.ws.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘UniProt.ws/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘UniProt.ws’ version ‘2.12.0’
* 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 ‘UniProt.ws’ 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
* 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 ... NOTE
.getSomeUniprotGoodies: no visible global function definition for
  ‘head’
.tryReadResult: no visible global function definition for ‘read.delim’
.tryReadResult: no visible global function definition for ‘URLencode’
availableUniprotSpecies: no visible global function definition for
  ‘read.delim’
availableUniprotSpecies: no visible global function definition for
  ‘head’
lookupUniprotSpeciesFromTaxId: no visible global function definition
  for ‘read.delim’
Undefined global functions or variables:
  URLencode head read.delim
Consider adding
  importFrom("utils", "URLencode", "head", "read.delim")
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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
UniProtWS-class 0.963  0.016  44.500
colsAndKeytypes 0.213  0.008  27.616
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘UniProt.ws_unit_tests.R’
 ERROR
Running the tests in ‘tests/UniProt.ws_unit_tests.R’ failed.
Last 13 lines of output:
  UniProt.ws RUnit Tests - 14 test functions, 0 errors, 1 failure
  FAILURE in test_mapUniprot: Error in checkTrue(res[1, 1] == "P13368") : Test not TRUE
  
  
  Test files with failing tests
  
     test_serviceAccessors.R 
       test_mapUniprot 
  
  
  Error in BiocGenerics:::testPackage("UniProt.ws") : 
    unit tests failed for package UniProt.ws
  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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/UniProt.ws.Rcheck/00check.log’
for details.


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 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("UniProt.ws")

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

Getting mapping data for P31946 ... and UNIGENE_ID
Getting mapping data for P31946 ... and PDB_ID
Getting extra data for P31946,P62258,Q04917
'select()' returned 1:many mapping between keys and columns
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217,V9HWD8,P01023,F5H5R8,P18440,Q400J6
'select()' returned 1:many mapping between keys and columns
Getting extra data for P31946,P62258,Q04917
'select()' returned 1:1 mapping between keys and columns
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217,V9HWD8,P01023,F5H5R8,P18440,Q400J6
'select()' returned 1:many mapping between keys and columns
Getting extra data for P31947,P01892,Q09160,P01889,P30461,P30466
Getting extra data for P13746,Q66LE6,P13760,Q9H2F3,P28221,P30939
Getting extra data for O00203,Q9Y2T2,P53677,Q92572,P59780,Q9UPM8
'select()' returned 1:1 mapping between keys and columns
Getting extra data for P04217,P30443
Getting extra data for P13368,P20806,Q9UM73,P97793,Q17192
Getting extra data for P13368,P20806,Q9UM73,P97793,Q17192
Getting mapping data for P13368 ... and P_REFSEQ_AC
Timing stopped at: 0.013 0 60.364 
Error in checkTrue(res[1, 1] == "P13368") : Test not TRUE



RUNIT TEST PROTOCOL -- Thu Oct 13 07:44:11 2016 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
UniProt.ws RUnit Tests - 14 test functions, 0 errors, 1 failure
FAILURE in test_mapUniprot: Error in checkTrue(res[1, 1] == "P13368") : Test not TRUE


Test files with failing tests

   test_serviceAccessors.R 
     test_mapUniprot 


Error in BiocGenerics:::testPackage("UniProt.ws") : 
  unit tests failed for package UniProt.ws
Execution halted

BioC 3.3: CHECK report for UniProt.ws on zin2

Summary

Command output

name	user	system	elapsed
UniProtWS-class	0.963	0.016	44.500
colsAndKeytypes	0.213	0.008	27.616