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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_1.2.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.2.3’
* 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 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           9.128  0.211  33.580
getCARD2UniProt        0.882  0.051   5.853
getKEGG2NCBINucleotide 0.355  0.032   8.156
getNCBINucleotide2KEGG 0.274  0.024  32.526
getNCBIGene2CARD       0.179  0.015   7.698
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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 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-arm64/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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

                                                                                  
[1] "A0A1S4G4Z1"
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

                                                                                  
[1] "BAB04099"
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/Rtmpq2sVbN/card-data
CARD database version 4.0.0 (2024-12-17)

                                                                                  

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

                                                                                  

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

                                                                                  
[1] "ARO:3002804"
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

                                                                                  
[1] "UniRef100_G9JVE6"
Testing getUniProt2KEGG

                                                                                  

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

                                                                                  

  |==............................| Step   2: Trying to get a direct translation for UniProt id A0A6I6H1L5 to KEGG

                                                                                  
[1] "fls:GLV81_10715"
Testing getUniProt2NCBIProtein, getUniProt2NCBINucleotide, getUniProt2NCBIGene

                                                                                  

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

                                                                                  

  |==............................| Step   2: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI

                                                                                  
[1] "QIB98918.1"
Testing getUniProt2CARD

                                                                                  

  |=.............................| Step   1: Translating from UniProt to CARD
Using a CARD database version downloaded on Tue 03/25/2025 21:01:02, please consider updating it with updateCARDDataBase() function.

                                                                                  

  |==............................| Step   2: Translating Uniprot id A0A1S7BGS4 to CARD

                                                                                  

  |===...........................| Step   3: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD

                                                                                  
[1] "ARO:3004185"


RUNIT TEST PROTOCOL -- Tue Mar 25 21:01:17 2025 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ginmappeR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 14.385   0.510  23.666