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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UniProt.ws_2.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/UniProt.ws.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘UniProt.ws/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘UniProt.ws’ version ‘2.48.0’
* 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 ‘UniProt.ws’ 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 ‘UniProt.ws-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UniProt.ws-class
> ### Title: UniProt.ws objects and their related methods and functions
> ### Aliases: UniProt.ws-class .UniProt.ws taxId taxId<- UniProt.ws
> ###   show,UniProt.ws-method taxId,UniProt.ws-method
> ###   availableUniprotSpecies lookupUniprotSpeciesFromTaxId
> ###   taxId<-,UniProt.ws-method species,UniProt.ws-method
> 
> ### ** Examples
> 
> 
> ## Make a UniProt.ws object
> up <- UniProt.ws(taxId=9606)
> 
> ## look at the object
> up
UniProt.ws interface object:
Taxonomy ID: 9606
Species name: Homo sapiens (Human)
List species with 'availableUniprotSpecies()'
> 
> ## get the current species
> species(up)
[1] "Homo sapiens (Human)"
> 
> ## look up available species with their tax ids
> availableUniprotSpecies("musculus")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]:
Connection timed out after 10003 milliseconds
Calls: availableUniprotSpecies ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_mapUniProt.R.............    3 tests OK 
  test_mapUniProt.R.............    3 tests OK 
  test_mapUniProt.R.............    3 tests OK 
  test_mapUniProt.R.............    4 tests OK 
  test_mapUniProt.R.............    5 tests OK 
  test_mapUniProt.R.............    6 tests OK 
  test_mapUniProt.R.............    6 tests OK 
  test_mapUniProt.R.............    7 tests OK 
  test_mapUniProt.R.............    8 tests OK 1.6s
  
  test_select.R.................    0 tests    Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached [ftp.uniprot.org]:
  Connection timed out after 10004 milliseconds
  Calls: <Anonymous> ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
  Execution halted
* 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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/UniProt.ws.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL UniProt.ws
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘UniProt.ws’ ...
** this is package ‘UniProt.ws’ version ‘2.48.0’
** 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 (UniProt.ws)

R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("UniProt.ws")

test_mapUniProt.R.............    0 tests    
test_mapUniProt.R.............    0 tests    
test_mapUniProt.R.............    1 tests OK 
test_mapUniProt.R.............    2 tests OK 
test_mapUniProt.R.............    3 tests OK 
test_mapUniProt.R.............    3 tests OK 
test_mapUniProt.R.............    3 tests OK 
test_mapUniProt.R.............    4 tests OK 
test_mapUniProt.R.............    5 tests OK 
test_mapUniProt.R.............    6 tests OK 
test_mapUniProt.R.............    6 tests OK 
test_mapUniProt.R.............    7 tests OK 
test_mapUniProt.R.............    8 tests OK 1.6s

test_select.R.................    0 tests    Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]:
Connection timed out after 10004 milliseconds
Calls: <Anonymous> ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted