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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings UniProt.ws_2.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/UniProt.ws.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.28.0’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘UniProt.ws-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UniProt.ws-objects
> ### Title: UniProt.ws objects and their related methods and functions
> ### Aliases: UniProt.ws class:UniProt.ws UniProt.ws-class
> ###   show,UniProt.ws-method species species,UniProt.ws-method taxId
> ###   taxId,UniProt.ws-method taxId<- taxId<-,UniProt.ws-method cols
> ###   columns columns,UniProt.ws-method keytypes keytypes,UniProt.ws-method
> ###   keys keys,UniProt.ws-method select select,UniProt.ws-method
> ###   availableUniprotSpecies lookupUniprotSpeciesFromTaxId
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> ## Make a UniProt.ws object
> up <- UniProt.ws(taxId=9606)
> 
> ## look at the object
> up
"UniProt.ws" object:
An interface object for UniProt web services
Current Taxonomy ID:
9606
Current Species name:
Homo sapiens
To change Species see: help('availableUniprotSpecies')
> 
> ## get the current species
> species(up)
[1] "Homo sapiens"
> 
> ## look up available species with their tax ids
> availableUniprotSpecies("musculus")
   taxon ID                Species name
1    520121         Anthocoris musculus
2    208057        Anthoscopus musculus
3    238007             Apomys musculus
4    213557            Baiomys musculus
5      9771       Balaenoptera musculus
6    197864        Blepharisma musculus
7     10090                Mus musculus
8     35531     Mus musculus bactrianus
9     10091      Mus musculus castaneus
10    57486     Mus musculus molossinus
11  1891730 Mus musculus polyomavirus 1
> 
> ## get the current taxId
> taxId(up)
[1] 9606
> 
> ## look up the species that goes with a tax id
> lookupUniprotSpeciesFromTaxId(9606)
[1] "Homo sapiens"
> 
> ## set the taxId to something else
> taxId(up) <- 10090
Warning in readLines(idUrl) :
  URL 'https://www.uniprot.org/uniprot/?query=organism:10090&format=tab&columns=id': Timeout of 60 seconds was reached
Error in readLines(idUrl) : cannot read from connection
Calls: taxId<- -> taxId<- -> .getUniprots -> readLines
Execution halted
* 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:
  
   
  1 Test Suite : 
  UniProt.ws RUnit Tests - 9 test functions, 1 error, 0 failures
  ERROR in /home/biocbuild/bbs-3.11-bioc/R/library/UniProt.ws/unitTests/test_select.R: Error while sourcing  /home/biocbuild/bbs-3.11-bioc/R/library/UniProt.ws/unitTests/test_select.R : Error in readLines(idUrl) : cannot read from connection
  
  Test files with failing tests
  
     test_select.R 
       /home/biocbuild/bbs-3.11-bioc/R/library/UniProt.ws/unitTests/test_select.R 
  
  
  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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/UniProt.ws.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL UniProt.ws
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘UniProt.ws’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (UniProt.ws)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Error in readLines(idUrl) : cannot read from connection
In addition: Warning message:
In readLines(idUrl) :
  URL 'https://www.uniprot.org/uniprot/?query=organism:9606&format=tab&columns=id': Timeout of 60 seconds was reached
Getting extra data for P04217, P30443
Getting extra data for P13368, P20806, Q9UM73... (5 total)
Getting extra data for P13368, P20806, Q9UM73... (5 total)
Getting mapping data for P13368 ... and P_REFSEQ_AC
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and GENENAME


RUNIT TEST PROTOCOL -- Sat Oct 17 06:24:16 2020 
*********************************************** 
Number of test functions: 9 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
UniProt.ws RUnit Tests - 9 test functions, 1 error, 0 failures
ERROR in /home/biocbuild/bbs-3.11-bioc/R/library/UniProt.ws/unitTests/test_select.R: Error while sourcing  /home/biocbuild/bbs-3.11-bioc/R/library/UniProt.ws/unitTests/test_select.R : Error in readLines(idUrl) : cannot read from connection

Test files with failing tests

   test_select.R 
     /home/biocbuild/bbs-3.11-bioc/R/library/UniProt.ws/unitTests/test_select.R 


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