BioC 3.5: CHECK report for rpx on malbec2

Package: rpx

Version: 1.12.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rpx_1.12.1.tar.gz

StartedAt: 2017-08-16 02:00:26 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:01:42 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 75.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: rpx.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rpx_1.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/rpx.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.1’
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
PXDataset-class 4.664  0.064  15.241
* 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:
  ==================================================
  2. Failure: PXD version (@test_px.R#44) ----------------------------------------
  p@formatVersion not identical to "1.2.0".
  1/1 mismatches
  x[1]: "1.3.0"
  y[1]: "1.2.0"
  
  
  testthat results ================================================================
  OK: 19 SKIPPED: 0 FAILED: 2
  1. Failure: PXD000001 (@test_px.R#26) 
  2. Failure: PXD version (@test_px.R#44) 
  
  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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/rpx.Rcheck/00check.log’
for details.

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 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.

> # 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")
Object of class "PXDataset"
 Id: PXD000001 with 12 files
 [1] 'F063721.dat' ... [12] 'generated'
 Use 'pxfiles(.)' to see all files.
1. Failure: PXD000001 (@test_px.R#26) ------------------------------------------
pxref(px1) not identical to `ref`.
1/1 mismatches
x[1]: "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\"> <html><head> <title>
x[1]: 301 Moved Permanently</title> </head><body> <h1>Moved Permanently</h1> <p>
x[1]: The document has moved <a href=\"https://eutils.ncbi.nlm.nih.gov/entrez/eu
x[1]: tils/efetch.fcgi/efetch.fcgi?db=pubmed&amp;id=23692960&amp;rettype=docsum&
x[1]: amp;retmode=text\">here</a>.</p> </body></html>"
y[1]: "Gatto L, Christoforou A. Using R and Bioconductor for proteomics data ana
y[1]: lysis. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):42-51. Review"


trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
Content type 'unknown' length 1657668 bytes (1.6 MB)
==================================================
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
Content type 'unknown' length 1657668 bytes (1.6 MB)
==================================================
2. Failure: PXD version (@test_px.R#44) ----------------------------------------
p@formatVersion not identical to "1.2.0".
1/1 mismatches
x[1]: "1.3.0"
y[1]: "1.2.0"


testthat results ================================================================
OK: 19 SKIPPED: 0 FAILED: 2
1. Failure: PXD000001 (@test_px.R#26) 
2. Failure: PXD version (@test_px.R#44) 

Error: testthat unit tests failed
Execution halted

* installing *source* package ‘rpx’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpx)

name	user	system	elapsed
PXDataset-class	4.664	0.064	15.241
pxannounced	0.140	0.012	0.665