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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:UniProt.ws.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings UniProt.ws_2.46.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/UniProt.ws.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 'UniProt.ws/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'UniProt.ws' version '2.46.1'
* 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 '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 ... NOTE
checkRd: (-1) mapUniprot.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapUniprot.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapUniprot.Rd:109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapUniprot.Rd:110-111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) utilities.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utilities.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utilities.Rd:55-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utilities.Rd:63-69: Lost braces in \itemize; meant \describe ?
* 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-objects
> ### Title: UniProt.ws objects and their related methods and functions
> ### Aliases: UniProt.ws class:UniProt.ws UniProt.ws-class
> ###   show,UniProt.ws-method species species,UniProt.ws-method taxId
> ###   taxId,UniProt.ws-method taxId<- taxId<-,UniProt.ws-method columns
> ###   columns,UniProt.ws-method keytypes keytypes,UniProt.ws-method keys
> ###   keys,UniProt.ws-method select select,UniProt.ws-method
> ###   availableUniprotSpecies lookupUniprotSpeciesFromTaxId
> ### Keywords: classes methods
> 
> ### ** 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]: SSL/TLS connection timeout
Calls: availableUniprotSpecies ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'UniProt.ws_unit_tests.R'
 ERROR
Running the tests in 'tests/UniProt.ws_unit_tests.R' failed.
Last 13 lines of output:
       test_lookupUniprotSpeciesFromTaxId 
       test_replaceTaxIdMethod 
  
     test_utilities.R 
       test_taxname2domain 
       test_taxname2domain_vec 
       test_taxname2species 
       test_taxname2species_vec 
       test_taxname2taxid 
       test_taxname2taxid_vec 
  
  
  Error in BiocGenerics:::testPackage("UniProt.ws") : 
    unit tests failed for package UniProt.ws
  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, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/UniProt.ws.Rcheck/00check.log'
for details.