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###
### Running command:
###
###   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.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL UniProt.ws
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'UniProt.ws' ...
** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> BiocGenerics:::testPackage("UniProt.ws")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Timing stopped at: 0.34 0.05 10.76
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
Timing stopped at: 0.15 0.01 10.27
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
Timing stopped at: 0.58 0.02 10.7
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
Timing stopped at: 0.2 0.04 10.61
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
In addition: Warning messages:
1: IDs not mapped: 3 
2: IDs not mapped: 3 
3: IDs not mapped: P20806 
4: IDs not mapped: 3 
Timing stopped at: 0.21 0 10.29
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
Timing stopped at: 0.18 0.07 10.36
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
Timing stopped at: 0.19 0.01 10.3
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
Timing stopped at: 0.16 0.06 10.33
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
Timing stopped at: 0.15 0.05 10.3
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout


RUNIT TEST PROTOCOL -- Fri Dec 13 06:59:22 2024 
*********************************************** 
Number of test functions: 23 
Number of errors: 9 
Number of failures: 0 

 
1 Test Suite : 
UniProt.ws RUnit Tests - 23 test functions, 9 errors, 0 failures
ERROR in test_availableUniprotSpecies: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_lookupUniprotSpeciesFromTaxId: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_replaceTaxIdMethod: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_taxname2domain: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_taxname2domain_vec: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_taxname2species: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_taxname2species_vec: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_taxname2taxid: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout
ERROR in test_taxname2taxid_vec: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [ftp.uniprot.org]: SSL/TLS connection timeout

Test files with failing tests

   test_select.R 
     test_availableUniprotSpecies 
     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