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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:rpx.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rpx_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/rpx.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rpx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rpx’ version ‘2.16.0’
* package encoding: UTF-8
* 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 code 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 loading without being on the library search path ... 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 ‘rpx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PXDataset2
> ### Title: New PXDataset (v2) to find and download proteomics data
> ### Aliases: PXDataset2 class:PXDataset2 PXDataset pxtitle
> ###   pxfiles,PXDataset2-method pxfiles pxget,PXDataset2-method pxget
> ###   pxid,PXDataset2-method pxid pxref,PXDataset2-method pxref
> ###   pxtax,PXDataset2-method pxtax pxurl,PXDataset2-method pxurl
> ###   show,PXDataset2-method pxCacheInfo,PXdataset-method pxCacheInfo
> ###   pxinstruments pxSubmissionDate pxPublicationDate pxptms pxprotocols
> ###   pxCacheInfo,PXDataset2-method
> 
> ### ** Examples
> 
> 
> px <- PXDataset("PXD000001")
Loading PXD000001 from cache.
> px
Project PXD000001 with 11 files
 Resource ID BFC30 in cache in /home/biocbuild/.cache/R/rpx.
 [1] 'F063721.dat' ... [11] 'erwinia_carotovora.fasta'
 Use 'pxfiles(.)' to see all files.
> pxtax(px)
[1] "Erwinia carotovora"
> pxurl(px)
[1] "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001"
> pxref(px)
[1] "Gatto L, Christoforou A; Using R and Bioconductor for proteomics data analysis., Biochim Biophys Acta, 2013 May 18, doi:10.1016/j.bbapap.2013.04.032 PMID:NA"
> pxfiles(px)
Project PXD000001 files (11):
 [remote] F063721.dat
 [local]  F063721.dat-mztab.txt
 [remote] PRIDE_Exp_Complete_Ac_22134.xml.gz
 [remote] PRIDE_Exp_mzData_Ac_22134.xml.gz
 [remote] PXD000001_mztab.txt
 [remote] README.txt
 [local]  TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
 [remote] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
 [remote] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
 [remote] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
 ...
> pxfiles(px, as.vector = FALSE)
   ID                                                                 NAME
1   1                                                          F063721.dat
2   2                                                F063721.dat-mztab.txt
3   3                                   PRIDE_Exp_Complete_Ac_22134.xml.gz
4   4                                     PRIDE_Exp_mzData_Ac_22134.xml.gz
5   5                                                  PXD000001_mztab.txt
6   6                                                           README.txt
7   7  TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
8   8 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
9   9          TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
10 10            TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
11 11                                             erwinia_carotovora.fasta
                                                                                                                                   URI
1                                                           ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/F063721.dat
2                                                 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/F063721.dat-mztab.txt
3                                    ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PRIDE_Exp_Complete_Ac_22134.xml.gz
4                                      ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PRIDE_Exp_mzData_Ac_22134.xml.gz
5                                                   ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PXD000001_mztab.txt
6                                                            ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/README.txt
7   ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
8  ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
9           ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
10            ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
11                                             ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta
     TYPE MAPPINGS        PX
1      id        - PXD000001
2   mztab        - PXD000001
3     xml        - PXD000001
4     xml        - PXD000001
5   mztab        - PXD000001
6     doc        - PXD000001
7     raw        - PXD000001
8     raw        - PXD000001
9     raw        - PXD000001
10 rawbin        - PXD000001
11    fas        - PXD000001
> 
> pxCacheInfo(px)
Resource ID BFC30 in cache in /home/biocbuild/.cache/R/rpx.
> 
> fas <- pxget(px, "erwinia_carotovora.fasta")
Downloading erwinia_carotovora.fasta file.
Warning: download failed
  web resource path: ‘ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/erwinia_carotovora.fasta’
  local file path: ‘/home/biocbuild/.cache/R/rpx/20be60663c7a84_erwinia_carotovora.fasta’
  reason: Failure when receiving data from the peer [ftp.pride.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC32
  fpath: ‘ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/erwinia_carotovora.fasta’
  reason: download failed
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
Calls: pxget ... .local -> pxget1 -> bfcadd -> bfcadd -> .util_download
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.21-bioc/meat/rpx.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL rpx
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘rpx’ ...
** this is package ‘rpx’ version ‘2.16.0’
** 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 (rpx)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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")
Project PXD000001 with 11 files
  [1] 'F063721.dat' ... [11] 'erwinia_carotovora.fasta'
 Use 'pxfiles(.)' to see all files.
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 11 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_px2.R:44:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  7.545   0.381  21.096