BioC 3.5: CHECK report for rpx on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rpx_1.12.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/rpx.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rpx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rpx’ version ‘1.12.3’
* 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 ‘rpx’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rpx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PXDataset-class
> ### Title: Class '"PXDataset"'
> ### Aliases: PXDataset-class class:PXDataset PXDataset
> ###   pxfiles,PXDataset-method pxfiles pxget,PXDataset-method pxget
> ###   pxid,PXDataset-method pxid pxref,PXDataset-method pxref
> ###   pxtax,PXDataset-method pxtax pxurl,PXDataset-method pxurl
> ###   show,PXDataset-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> px <- PXDataset("PXD000001")
Warning in file(con, "r") :
  URL 'http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000001&outputMode=XML&test=no': status was 'Failure when receiving data from the peer'
Error in file(con, "r") : 
  cannot open the connection to 'http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000001&outputMode=XML&test=no'
Calls: PXDataset -> readLines -> file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         invokeRestart("muffleWarning")
     })
  4: PXDataset("1")
  5: readLines(url)
  6: file(con, "r")
  
  testthat results ================================================================
  OK: 7 SKIPPED: 0 FAILED: 4
  1. Error: PXD000001 (@test_px.R#3) 
  2. Error: pxget uses destdir (@test_px.R#38) 
  3. Error: PXD version (@test_px.R#45) 
  4. Error: PX identifiers (@test_px.R#62) 
  
  Error: testthat unit tests failed
  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-3.5-bioc/meat/rpx.Rcheck/00check.log’
for details.


R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(rpx)
> 
> test_check("rpx")
1. Error: PXD000001 (@test_px.R#3) ---------------------------------------------
cannot open the connection to 'http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000001&outputMode=XML&test=no'
1: PXDataset(id) at testthat/test_px.R:3
2: readLines(url)
3: file(con, "r")

2. Error: pxget uses destdir (@test_px.R#38) -----------------------------------
cannot open the connection to 'http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000001&outputMode=XML&test=no'
1: PXDataset("PXD000001") at testthat/test_px.R:38
2: readLines(url)
3: file(con, "r")

3. Error: PXD version (@test_px.R#45) ------------------------------------------
cannot open the connection to 'http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000001&outputMode=XML&test=no'
1: PXDataset("PXD000001") at testthat/test_px.R:45
2: readLines(url)
3: file(con, "r")

4. Error: PX identifiers (@test_px.R#62) ---------------------------------------
cannot open the connection to 'http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=1&outputMode=XML&test=no'
1: expect_warning(px1 <- PXDataset("1")) at testthat/test_px.R:62
2: capture_warnings(object)
3: withCallingHandlers(code, warning = function(condition) {
       out$push(condition)
       invokeRestart("muffleWarning")
   })
4: PXDataset("1")
5: readLines(url)
6: file(con, "r")

testthat results ================================================================
OK: 7 SKIPPED: 0 FAILED: 4
1. Error: PXD000001 (@test_px.R#3) 
2. Error: pxget uses destdir (@test_px.R#38) 
3. Error: PXD version (@test_px.R#45) 
4. Error: PX identifiers (@test_px.R#62) 

Error: testthat unit tests failed
Execution halted

BioC 3.5: CHECK report for rpx on veracruz2

Summary

Command output