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This page was generated on 2025-09-20 12:06 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 878/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ginmappeR 1.5.0  (landing page)
Fernando Sola
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/ginmappeR
git_branch: devel
git_last_commit: 1ea1ef8
git_last_commit_date: 2025-04-15 13:30:43 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ginmappeR on kjohnson3

To the developers/maintainers of the ginmappeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ginmappeR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ginmappeR
Version: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2025-09-19 19:42:04 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 19:48:30 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 385.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ginmappeR.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ginmappeR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.5.0’
* 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 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              2.570  0.076  25.904
getUniProt2NCBINucleotide 1.177  0.059 125.298
getNCBINucleotide2KEGG    0.391  0.022  64.270
getCARD2UniProt           0.295  0.019  13.089
getKEGG2NCBINucleotide    0.124  0.007  10.292
getNCBIProtein2UniProt    0.114  0.008  11.210
getNCBINucleotide2UniProt 0.114  0.007  11.107
getNCBIGene2UniProt       0.112  0.007  11.253
getNCBIGene2KEGG          0.007  0.001  13.302
* 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-3.22-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.


Installation output

ginmappeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ginmappeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ginmappeR’ ...
** this is package ‘ginmappeR’ version ‘1.5.0’
** 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)

Tests output

ginmappeR.Rcheck/tests/runTests.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr1F1Vr/card-data
CARD database version 4.0.1 (2025-05-29)

                                                                                  

  |==............................| 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   1: 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 Fri 09/19/2025 19:48:10, 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 -- Fri Sep 19 19:48:25 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 
  4.404   0.177  19.916 

Example timings

ginmappeR.Rcheck/ginmappeR-Ex.timings

nameusersystemelapsed
getCARD2KEGG 2.570 0.07625.904
getCARD2NCBIGene0.0790.0051.727
getCARD2NCBINucleotide0.1080.0050.555
getCARD2NCBIProtein0.0020.0010.442
getCARD2UniProt 0.295 0.01913.089
getKEGG2CARD0.0600.0020.847
getKEGG2NCBIGene0.0250.0011.714
getKEGG2NCBINucleotide 0.124 0.00710.292
getKEGG2NCBIProtein0.0200.0011.216
getKEGG2UniProt0.0010.0000.111
getNCBIGene2CARD0.0560.0044.906
getNCBIGene2KEGG 0.007 0.00113.302
getNCBIGene2NCBINucleotide0.0130.0022.862
getNCBIGene2NCBIProtein0.0160.0023.268
getNCBIGene2UniProt 0.112 0.00711.253
getNCBIIdenticalProteins0.0080.0021.541
getNCBINucleotide2CARD0.0250.0010.623
getNCBINucleotide2KEGG 0.391 0.02264.270
getNCBINucleotide2NCBIGene0.0090.0013.514
getNCBINucleotide2NCBIProtein0.0280.0021.044
getNCBINucleotide2UniProt 0.114 0.00711.107
getNCBIProtein2CARD0.0340.0020.605
getNCBIProtein2KEGG0.0070.0011.932
getNCBIProtein2NCBIGene0.0090.0011.375
getNCBIProtein2NCBINucleotide0.0280.0020.723
getNCBIProtein2UniProt 0.114 0.00811.210
getUniProt2CARD0.0890.0044.025
getUniProt2KEGG0.0080.0010.738
getUniProt2NCBIGene000
getUniProt2NCBINucleotide 1.177 0.059125.298
getUniProt2NCBIProtein000
getUniProtSimilarGenes0.0140.0021.026