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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ginmappeR_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.1.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ginmappeR’ 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 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getCARD2KEGG           1.846  0.083  12.074
getCARD2UniProt        0.575  0.075   6.134
getNCBINucleotide2KEGG 0.458  0.065   7.333
getNCBIGene2KEGG       0.381  0.065   7.058
getNCBIProtein2KEGG    0.369  0.040  10.866
getKEGG2NCBINucleotide 0.332  0.027   5.952
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  ginmappeR RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in /tmp/RtmpnlyHOV/RLIBS_364e2b6f657e30/ginmappeR/unitTests/test_UniProt.R: Error while sourcing  /tmp/RtmpnlyHOV/RLIBS_364e2b6f657e30/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5",  : 
    Test not TRUE
  
  
  Test files with failing tests
  
     test_UniProt.R 
       /tmp/RtmpnlyHOV/RLIBS_364e2b6f657e30/ginmappeR/unitTests/test_UniProt.R 
  
  
  Error in BiocGenerics:::testPackage("ginmappeR") : 
    unit tests failed for package ginmappeR
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ginmappeR
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ginmappeR’ ...
** 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 (ginmappeR)

R version 4.4.0 RC (2024-04-16 r86468) -- "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("ginmappeR")
Loading required package: BiocGenerics

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

Loading required package: RSQLite
Testing getKEGG2UniProt
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene
Testing getKEGG2CARD
Updating CARD database data...
CARD database downloaded successfully!
Located at /tmp/RtmpPDGkzE/card-data
Using a CARD database version downloaded on Fri 05/31/2024 04:23:43, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/31/2024 04:23:43, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/31/2024 04:23:43, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/31/2024 04:23:43, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/31/2024 04:23:43, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/31/2024 04:23:43, please consider updating it with updateCARDDataBase() function.
Testing getUniProtSimilarGenes
Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5",  : 
  Test not TRUE



RUNIT TEST PROTOCOL -- Fri May 31 04:24:07 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
ginmappeR RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /tmp/RtmpnlyHOV/RLIBS_364e2b6f657e30/ginmappeR/unitTests/test_UniProt.R: Error while sourcing  /tmp/RtmpnlyHOV/RLIBS_364e2b6f657e30/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5",  : 
  Test not TRUE


Test files with failing tests

   test_UniProt.R 
     /tmp/RtmpnlyHOV/RLIBS_364e2b6f657e30/ginmappeR/unitTests/test_UniProt.R 


Error in BiocGenerics:::testPackage("ginmappeR") : 
  unit tests failed for package ginmappeR
Execution halted