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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:rpx.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings rpx_2.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/rpx.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rpx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rpx’ version ‘2.19.0’
* 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 ... OK
* 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:
  ── Error ('test_px2.R:59:5'): PXD022816: valid URLs and files (v2) ─────────────
  Error in `open.connection(con, open = mode)`: cannot open the connection
  Backtrace:
      ▆
   1. └─rpx::PXDataset2("PXD022816") at test_px2.R:59:5
   2.   └─rpx:::list_files(ftp_url)
   3.     └─curl::curl(url = ftp_url, "r", handle = list_files)
   4.       └─curl:::curl_connection(url, open, handle)
   5.         ├─base::withCallingHandlers(...)
   6.         ├─base::open(con, open = mode)
   7.         └─base::open.connection(con, open = mode)
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 9 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/rpx.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL rpx
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘rpx’ ...
** this is package ‘rpx’ version ‘2.19.0’
** 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 1 | WARN 1 | SKIP 1 | PASS 9 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_px2.R:59:5'): PXD022816: valid URLs and files (v2) ─────────────
Error in `open.connection(con, open = mode)`: cannot open the connection
Backtrace:
    ▆
 1. └─rpx::PXDataset2("PXD022816") at test_px2.R:59:5
 2.   └─rpx:::list_files(ftp_url)
 3.     └─curl::curl(url = ftp_url, "r", handle = list_files)
 4.       └─curl:::curl_connection(url, open, handle)
 5.         ├─base::withCallingHandlers(...)
 6.         ├─base::open(con, open = mode)
 7.         └─base::open.connection(con, open = mode)

[ FAIL 1 | WARN 1 | SKIP 1 | PASS 9 ]
Error: Test failures
Execution halted