Multiple platform build/check report for BioC 3.9 - CHECK report for UniProt.ws on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings UniProt.ws_2.24.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/UniProt.ws.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.24.2’
* 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 sizes of PDF files under ‘inst/doc’ ... 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)
Warning in file(con, "r") :
  cannot open URL 'https://www.uniprot.org/uniprot/?query=organism:9606&format=tab&columns=id': HTTP status was '502 Bad Gateway'
Error in file(con, "r") : 
  cannot open the connection to 'https://www.uniprot.org/uniprot/?query=organism:9606&format=tab&columns=id'
Calls: UniProt.ws -> .getUniprots -> readLines -> file
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:
  
  Test files with failing tests
  
     test_select.R 
       test_newTaxId 
  
  
  Error in BiocGenerics:::testPackage("UniProt.ws") : 
    unit tests failed for package UniProt.ws
  In addition: Warning messages:
  1: In file(file, "rt") :
    URL 'https://www.uniprot.org/uniprot/?query=P04217+or+V9HWD8+or+P01023+or+F5H5R8+or+P18440+or+Q400J6+or+A4Z6T7+or+P11245&format=tab&columns=id,clusters': status was 'Failure when receiving data from the peer'
  2: In file(file, "rt") :
    URL 'https://www.uniprot.org/uniprot/?query=P04217+or+V9HWD8+or+P01023+or+F5H5R8+or+P18440+or+Q400J6+or+A4Z6T7+or+P11245&format=tab&columns=id,clusters': status was 'SSL connect error'
  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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/UniProt.ws.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL UniProt.ws
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> 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

Timing stopped at: 0.01 0.012 21.02
Error in file(con, "r") : 
  cannot open the connection to 'https://www.uniprot.org/uniprot/?query=organism:10090&format=tab&columns=id'
In addition: Warning message:
In file(con, "r") :
  URL 'https://www.uniprot.org/uniprot/?query=organism:10090&format=tab&columns=id': status was 'SSL connect error'
Getting mapping data for P31946 ... and PDB_ID
Getting mapping data for P31946 ... and HGNC_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 PDB_ID
Getting mapping data for P04217 ... and HGNC_ID
Getting extra data for P04217, V9HWD8, P01023... (8 total)
'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... (8 total)
reading url
    https://www.uniprot.org/uniprot/?query=P04217+or+V9HWD8+or+P01023+or+F5H5R8+or+P18440+or+Q400J6+or+A4Z6T7+or+P11245&format=tab&columns=id,clusters
failed on attempt 1 of 5
reading url
    https://www.uniprot.org/uniprot/?query=P04217+or+V9HWD8+or+P01023+or+F5H5R8+or+P18440+or+Q400J6+or+A4Z6T7+or+P11245&format=tab&columns=id,clusters
failed on attempt 2 of 5
'select()' returned 1:many mapping between keys and columns
Getting extra data for Q9HBI6, P33151, Q9H0W5... (100 total)
'select()' returned 1:1 mapping between keys and columns
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 -- Wed Oct 16 07:52:24 2019 
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Number of test functions: 20 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
UniProt.ws RUnit Tests - 20 test functions, 1 error, 0 failures
ERROR in test_newTaxId: Error in file(con, "r") : 
  cannot open the connection to 'https://www.uniprot.org/uniprot/?query=organism:10090&format=tab&columns=id'

Test files with failing tests

   test_select.R 
     test_newTaxId 


Error in BiocGenerics:::testPackage("UniProt.ws") : 
  unit tests failed for package UniProt.ws
In addition: Warning messages:
1: In file(file, "rt") :
  URL 'https://www.uniprot.org/uniprot/?query=P04217+or+V9HWD8+or+P01023+or+F5H5R8+or+P18440+or+Q400J6+or+A4Z6T7+or+P11245&format=tab&columns=id,clusters': status was 'Failure when receiving data from the peer'
2: In file(file, "rt") :
  URL 'https://www.uniprot.org/uniprot/?query=P04217+or+V9HWD8+or+P01023+or+F5H5R8+or+P18440+or+Q400J6+or+A4Z6T7+or+P11245&format=tab&columns=id,clusters': status was 'SSL connect error'
Execution halted

CHECK report for UniProt.ws on celaya2

Summary

Command output

Installation output

Tests output

Example timings