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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rpx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rpx_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rpx.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rpx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rpx’ version ‘2.8.0’
* 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 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 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:
  ── Failure ('test_px2.R:34:5'): Object content is valid (v2) ───────────────────
  length(pxf) not identical to 11L.
  1/1 mismatches
  [1] 2 - 11 == -9
  ── Error ('test_px2.R:38:5'): Object content is valid (v2) ─────────────────────
  Error in `.local(object, ...)`: No files to download.
  Backtrace:
      ▆
   1. ├─rpx::pxget(px1, "erwinia_carotovora.fasta") at test_px2.R:38:4
   2. └─rpx::pxget(px1, "erwinia_carotovora.fasta")
   3.   └─rpx (local) .local(object, ...)
  
  [ FAIL 3 | WARN 3 | SKIP 1 | PASS 11 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘rpx.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpx.Rmd’ using rmarkdown

Quitting from lines 100-102 [pxget] (rpx.Rmd)
Error: processing vignette 'rpx.Rmd' failed with diagnostics:
No files to download.
--- failed re-building ‘rpx.Rmd’

SUMMARY: processing the following file failed:
  ‘rpx.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/rpx.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rpx
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘rpx’ ...
** 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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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")
Project PXD000001 with 2 files
  'PRIDE_Exp_Complete_Ac_22134.pride.mgf.gz', 'PRIDE_Exp_Complete_Ac_22134.pride.mztab.gz' 
[ FAIL 3 | WARN 3 | SKIP 1 | PASS 11 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_px2.R:42:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_px2.R:33:5'): Object content is valid (v2) ───────────────────
sort(pxf) not identical to `fls`.
Lengths differ: 2 is not 11
── Failure ('test_px2.R:34:5'): Object content is valid (v2) ───────────────────
length(pxf) not identical to 11L.
1/1 mismatches
[1] 2 - 11 == -9
── Error ('test_px2.R:38:5'): Object content is valid (v2) ─────────────────────
Error in `.local(object, ...)`: No files to download.
Backtrace:
    ▆
 1. ├─rpx::pxget(px1, "erwinia_carotovora.fasta") at test_px2.R:38:4
 2. └─rpx::pxget(px1, "erwinia_carotovora.fasta")
 3.   └─rpx (local) .local(object, ...)

[ FAIL 3 | WARN 3 | SKIP 1 | PASS 11 ]
Error: Test failures
Execution halted