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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rpx.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rpx_2.14.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/rpx.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rpx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rpx' version '2.14.0'
* 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 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 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 BFC87 in cache in C:\Users\biocbuild\AppData\Local/R/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-archive/2012/03/PXD000001/generated"
> 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:23692960"
> 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-archive/2012/03/PXD000001//F063721.dat
2                                                 ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//F063721.dat-mztab.txt
3                                    ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//PRIDE_Exp_Complete_Ac_22134.xml.gz
4                                      ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//PRIDE_Exp_mzData_Ac_22134.xml.gz
5                                                   ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//PXD000001_mztab.txt
6                                                            ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//README.txt
7   ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
8  ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
9           ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
10            ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
11                                             ftp://ftp.pride.ebi.ac.uk/pride-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 BFC87 in cache in C:\Users\biocbuild\AppData\Local/R/cache/R/rpx.
> 
> fas <- pxget(px, "erwinia_carotovora.fasta")
Error in fix_issue_17(x) : Can't access URL(s):
 ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//erwinia_carotovora.fasta
 ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001//erwinia_carotovora.fasta
Calls: pxget ... pxget -> .local -> pxget1 -> get_url -> fix_issue_17
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
  'F:/biocbuild/bbs-3.20-bioc/meat/rpx.Rcheck/00check.log'
for details.