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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RforProteomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RforProteomics_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/RforProteomics.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘RforProteomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RforProteomics’ version ‘1.48.0’
* 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 ‘RforProteomics’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
See ‘/home/biocbuild/bbs-3.22-data-experiment/meat/RforProteomics.Rcheck/00install.out’ for details.
* 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  qnt.Rd: MSnSet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RforProteomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: proteomicsPackages
> ### Title: Proteomics and MS biocView packages
> ### Aliases: proteomicsPackages massSpectrometryPackages
> ###   massSpectrometryDataPackages
> 
> ### ** Examples
> 
> head(pp <- proteomicsPackages("3.0"))
Warning in download.file(url = paste(reposURL, "VIEWS", sep = "/"), destfile = tmpf,  :
  URL 'https://bioconductor.org/packages/3.0/bioc/VIEWS': status was 'SSL connect error'
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': cannot open URL 'http://bioconductor.org/packages/3.0/bioc/VIEWS'
Calls: head ... getPacksAndViews -> download.file -> .handleSimpleError -> h
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
    user system elapsed
id 8.182  0.418   8.604
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘RProtVis.Rmd’ using rmarkdown

Quitting from RProtVis.Rmd:95-99 [packs]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'http://bioconductor.org/packages/3.22/bioc/VIEWS'
---
Backtrace:
    ▆
 1. └─RforProteomics::massSpectrometryPackages()
 2.   ├─RforProteomics:::packageDF(...)
 3.   │ └─base::sapply(x@packageList, function(x) x@Package)
 4.   │   └─base::lapply(X = X, FUN = FUN, ...)
 5.   └─RforProteomics:::getPackagesInBiocView("MassSpectrometry", biocVersion = biocv)
 6.     └─biocViews::getBiocViews(rep, biocViewsVocab, "NoViewProvided")
 7.       └─biocViews:::getPacksAndViews(reposUrl, vocab, defaultView, local)
 8.         └─utils::download.file(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
cannot open URL 'http://bioconductor.org/packages/3.22/bioc/VIEWS'
--- failed re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown
starting worker pid=3507452 on localhost:11682 at 13:05:45.771
starting worker pid=3507451 on localhost:11682 at 13:05:45.776
Loading required package: mzID
Loading required package: mzID
loaded mzID and set parent environment
loaded mzID and set parent environment
reading 55merge_omssa.mzid...
reading 55merge_tandem.mzid...
55merge_omssa.mzid DONE!
55merge_tandem.mzid DONE!
trying URL 'http://www.uniprot.org/uniprot/P00924.fasta'
Content type 'text/plain;format=fasta' length 562 bytes
==================================================
downloaded 562 bytes


Quitting from RforProteomics.Rmd:1105-1110 [annot1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─ExperimentHub (local) hpaSubcellularLoc()
 2.   └─ExperimentHub:::.get_ExperimentHub()
 3.     └─ExperimentHub::ExperimentHub()
 4.       └─AnnotationHub::.Hub(...)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.               └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘RforProteomics.Rmd’

SUMMARY: processing the following files failed:
  ‘RProtVis.Rmd’ ‘RforProteomics.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/RforProteomics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RforProteomics
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘RforProteomics’ ...
** this is package ‘RforProteomics’ version ‘1.48.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
** testing if installed package keeps a record of temporary installation path
* DONE (RforProteomics)