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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ginmappeR_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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              3.993  0.169  15.371
getUniProt2CARD           1.590  0.070  11.308
getCARD2UniProt           1.566  0.086  29.401
getKEGG2NCBINucleotide    1.432  0.116  35.577
getNCBINucleotide2KEGG    0.789  0.088 205.561
getNCBINucleotide2UniProt 0.410  0.034  22.045
getNCBIProtein2UniProt    0.397  0.034  22.045
getNCBIGene2UniProt       0.389  0.032  20.980
getUniProt2NCBINucleotide 0.323  0.033   9.184
getNCBIGene2CARD          0.093  0.005   5.086
* 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 /private/tmp/RtmpUcXTtk/RLIBS_ca26424775a0/ginmappeR/unitTests/test_UniProt.R: Error while sourcing  /private/tmp/RtmpUcXTtk/RLIBS_ca26424775a0/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G9JVE6", clusterIdentity = "1.0",  : 
    Test not TRUE
  
  
  Test files with failing tests
  
     test_UniProt.R 
       /private/tmp/RtmpUcXTtk/RLIBS_ca26424775a0/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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ginmappeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.

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

Loading required package: RSQLite
Testing getKEGG2UniProt

                                                                                  

  |=.............................| Step   1: Translating from KEGG to UniProt

                                                                                  

  |==............................| Step   2: Connecting to KEGG web services

                                                                                  

  |===...........................| Step   3: Connecting to KEGG API and translating id aag:5579347 to Uniprot

                                                                                  
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene

                                                                                  

  |=.............................| Step   1: Translating from KEGG to NCBI Protein

                                                                                  

  |==............................| Step   2: Trying to get a direct translation for KEGG id bha:BH0380 to NCBI

                                                                                  

                                                                                  

  |=.............................| Step   1: Translating from KEGG to NCBI Gene

                                                                                  

  |==............................| Step   2: Trying to get a direct translation for KEGG id aag:5579347 to NCBI

                                                                                  
Testing getKEGG2CARD

                                                                                  

  |=.............................| Step   1: Translating from KEGG to CARD
Updating CARD database data...
Deleting previous versions of CARD if any.

Downloading latest version

Extracting database

CARD database downloaded successfully!
Located at /tmp/Rtmpy6CiDt/card-data
CARD database version 3.3.0 (2024-08-26)

                                                                                  

  |==............................| Step   2: Searching CARD database and translating to KEGG

                                                                                  

  |===...........................| Step   3: Trying to get a direct translation for KEGG id ag:ACC85616 to CARD

                                                                                  
Testing getUniProtSimilarGenes

                                                                                  

  |=.............................| Step   1: Accessing UniProt similar genes database

                                                                                  

  |==............................| Step   2: Connecting to UniProt API and retrieving cluster of id G9JVE6

                                                                                  

  |===...........................| Step   3: Retrieving and parsing genes of cluster UniRef100_G9JVE6

                                                                                  
Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G9JVE6", clusterIdentity = "1.0",  : 
  Test not TRUE



RUNIT TEST PROTOCOL -- Tue Nov 19 22:49:54 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 /private/tmp/RtmpUcXTtk/RLIBS_ca26424775a0/ginmappeR/unitTests/test_UniProt.R: Error while sourcing  /private/tmp/RtmpUcXTtk/RLIBS_ca26424775a0/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G9JVE6", clusterIdentity = "1.0",  : 
  Test not TRUE


Test files with failing tests

   test_UniProt.R 
     /private/tmp/RtmpUcXTtk/RLIBS_ca26424775a0/ginmappeR/unitTests/test_UniProt.R 


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