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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings UniProt.ws_2.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/UniProt.ws.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘UniProt.ws/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘UniProt.ws’ version ‘2.44.0’
* 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 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 ... 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")
      kingdom Taxon Node                     Official (scientific) name
ANTMS       E     520121                            Anthocoris musculus
ANTMU       E     208057                           Anthoscopus musculus
APOMU       E     238007                                Apomys musculus
BAIMU       E     213557                               Baiomys musculus
BALMU       E       9771                          Balaenoptera musculus
BLEMU       E     197864                           Blepharisma musculus
MOUSE       E      10090                                   Mus musculus
MUSMB       E      35531                        Mus musculus bactrianus
MUSMC       E      10091                         Mus musculus castaneus
MUSMM       E      57486                        Mus musculus molossinus
MUSMS       E     186842                     Mus musculus x Mus spretus
MUSMX       E     477816 Mus musculus musculus x Mus musculus castaneus
POVM1       V    1891730                    Mus musculus polyomavirus 1
> 
> ## get the current taxId
> taxId(up)
[1] 9606
> 
> ## look up the species that goes with a tax id
> lookupUniprotSpeciesFromTaxId(9606)
[1] "Homo sapiens"
> 
> ## set the taxId to something else
> taxId(up) <- 10090
> up
UniProt.ws interface object:
Taxonomy ID: 10090
Species name: Mus musculus (Mouse)
List species with 'availableUniprotSpecies()'
> 
> ## list the possible key types
> head(keytypes(up))
[1] "Allergome"     "ArachnoServer" "Araport"       "BioCyc"       
[5] "BioGRID"       "BioMuta"      
> 
> ## list of possible columns
> head(columns(up))
[1] "absorption"              "accession"              
[3] "annotation_score"        "cc_activity_regulation" 
[5] "cc_allergen"             "cc_alternative_products"
> 
> ## list all possible keys of type entrez gene ID
> egs <- keys(up, "GeneID")
Error: 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
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_select_1 
       test_select_2 
       test_select_3 
       test_select_4 
       test_select_5 
       test_select_6 
       test_select_8 
  
     test_serviceAccessors.R 
       test_mapUniProt 
  
  
  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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘UniProt.ws.Rmd’ using rmarkdown

Quitting from lines 119-124 [select] (UniProt.ws.Rmd)
Error: processing vignette 'UniProt.ws.Rmd' failed with diagnostics:
'idmapping_run' failed:
  Internal Server Error (HTTP 500).
--- failed re-building ‘UniProt.ws.Rmd’

SUMMARY: processing the following file failed:
  ‘UniProt.ws.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/UniProt.ws.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL UniProt.ws
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Timing stopped at: 0.078 0.008 5.389
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.019 0 4.851
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.032 0 4.885
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.031 0 4.901
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.034 0 4.905
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.029 0 4.905
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.383 0.14 5.399
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.015 0.004 4.891
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
Timing stopped at: 0.005 0 4.871
Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).


RUNIT TEST PROTOCOL -- Fri May 31 09:19:30 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_mapUniProt: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_select_1: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_select_2: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_select_3: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_select_4: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_select_5: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_select_6: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_select_8: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).
ERROR in test_mapUniProt: Error : 'idmapping_run' failed:
  Internal Server Error (HTTP 500).

Test files with failing tests

   test_mapUniProt.R 
     test_mapUniProt 

   test_select.R 
     test_select_1 
     test_select_2 
     test_select_3 
     test_select_4 
     test_select_5 
     test_select_6 
     test_select_8 

   test_serviceAccessors.R 
     test_mapUniProt 


Error in BiocGenerics:::testPackage("UniProt.ws") : 
  unit tests failed for package UniProt.ws
Execution halted