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This page was generated on 2025-11-08 23:55 -0500 (Sat, 08 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4821 |
| 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 18/27 | Hostname | OS / Arch | CHECK | |||||||
| ginmappeR 1.7.0 (landing page) Fernando Sola
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | |||||||
|
To the developers/maintainers of the ginmappeR package: - 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. |
| Package: ginmappeR |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ginmappeR_1.7.0.tar.gz |
| StartedAt: 2025-11-08 16:24:42 -0500 (Sat, 08 Nov 2025) |
| EndedAt: 2025-11-08 16:57:55 -0500 (Sat, 08 Nov 2025) |
| EllapsedTime: 1992.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ginmappeR.Rcheck |
| Warnings: NA |
ginmappeR.Rcheck/tests/test_CARD.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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.
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Type 'contributors()' for more information and
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Type 'q()' to quit R.
> library(RUnit)
> library(ginmappeR)
> library('UniProt.ws')
> library('KEGGREST')
> library('httr')
> library('rentrez')
> library('XML')
>
> utils::globalVariables('cardPath')
[1] "cardPath"
> cardPath <<- tempdir()
>
> # GitHub Actions imports
> # source('../../../R/CARDFunctions.R')
> # source('../../../R/00utils.R')
>
> # # Local execution imports
> setwd('../00_pkg_src/ginmappeR/')
> source('R/CARDFunctions.R')
> source('R/00utils.R')
>
> #########################
> # CARD database to NCBI #
> #########################
>
> ### Test getCARD2NCBIProtein
> message('Testing getCARD2NCBIProtein')
Testing getCARD2NCBIProtein
> # Positive cases
> .testEquals(getCARD2NCBIProtein('3002535'), 'CAA38525.1')
Updating CARD database data...
Deleting previous versions of CARD if any.
Downloading latest version
The download of CARD database failed, please try again.
If the error persists try using changeCARDPath() to refresh CARD folder location.
If not, consider downloading and extracting it manually. Then, use changeCARDPath() function to indicate the folder where it is located.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id 3002535 to NCBI
|===...........................| Step 3: Accessing CARD database and translating id 3002535 to NCBI
|====..........................| Step 4: Accessing CARD database and translating id 3002535 to NCBI
|=====.........................| Step 5: Accessing CARD database and translating id 3002535 to NCBI
|======........................| Step 6: Accessing CARD database and translating id 3002535 to NCBI
|=======.......................| Step 7: Accessing CARD database and translating id 3002535 to NCBI
|========......................| Step 8: Accessing CARD database and translating id 3002535 to NCBI
|=========.....................| Step 9: Accessing CARD database and translating id 3002535 to NCBI
|==========....................| Step 10: Accessing CARD database and translating id 3002535 to NCBI
|===========...................| Step 11: Accessing CARD database and translating id 3002535 to NCBI
|============..................| Step 12: Accessing CARD database and translating id 3002535 to NCBI
|=============.................| Step 13: Accessing CARD database and translating id 3002535 to NCBI
|==============................| Step 14: Accessing CARD database and translating id 3002535 to NCBI
|===============...............| Step 15: Accessing CARD database and translating id 3002535 to NCBI
|================..............| Step 16: Accessing CARD database and translating id 3002535 to NCBI
|=================.............| Step 17: Accessing CARD database and translating id 3002535 to NCBI
|==================............| Step 18: Accessing CARD database and translating id 3002535 to NCBI
|===================...........| Step 19: Accessing CARD database and translating id 3002535 to NCBI
|====================..........| Step 20: Accessing CARD database and translating id 3002535 to NCBI
|=====================.........| Step 21: Accessing CARD database and translating id 3002535 to NCBI
[1] NA
Test failed:
NA != CAA38525.1
> .testEquals(getCARD2NCBIProtein('ARO:3002535'), 'CAA38525.1')
Updating CARD database data...
Deleting previous versions of CARD if any.
Downloading latest version
The download of CARD database failed, please try again.
If the error persists try using changeCARDPath() to refresh CARD folder location.
If not, consider downloading and extracting it manually. Then, use changeCARDPath() function to indicate the folder where it is located.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id ARO:3002535 to NCBI
|===...........................| Step 3: Accessing CARD database and translating id ARO:3002535 to NCBI
|====..........................| Step 4: Accessing CARD database and translating id ARO:3002535 to NCBI
|=====.........................| Step 5: Accessing CARD database and translating id ARO:3002535 to NCBI
|======........................| Step 6: Accessing CARD database and translating id ARO:3002535 to NCBI
|=======.......................| Step 7: Accessing CARD database and translating id ARO:3002535 to NCBI
|========......................| Step 8: Accessing CARD database and translating id ARO:3002535 to NCBI
|=========.....................| Step 9: Accessing CARD database and translating id ARO:3002535 to NCBI
|==========....................| Step 10: Accessing CARD database and translating id ARO:3002535 to NCBI
|===========...................| Step 11: Accessing CARD database and translating id ARO:3002535 to NCBI
|============..................| Step 12: Accessing CARD database and translating id ARO:3002535 to NCBI
|=============.................| Step 13: Accessing CARD database and translating id ARO:3002535 to NCBI
|==============................| Step 14: Accessing CARD database and translating id ARO:3002535 to NCBI
|===============...............| Step 15: Accessing CARD database and translating id ARO:3002535 to NCBI
|================..............| Step 16: Accessing CARD database and translating id ARO:3002535 to NCBI
|=================.............| Step 17: Accessing CARD database and translating id ARO:3002535 to NCBI
|==================............| Step 18: Accessing CARD database and translating id ARO:3002535 to NCBI
|===================...........| Step 19: Accessing CARD database and translating id ARO:3002535 to NCBI
|====================..........| Step 20: Accessing CARD database and translating id ARO:3002535 to NCBI
|=====================.........| Step 21: Accessing CARD database and translating id ARO:3002535 to NCBI
[1] NA
Test failed:
NA != CAA38525.1
> .testEquals(getCARD2NCBIProtein('3003988'), 'APB03221.1')
Updating CARD database data...
Deleting previous versions of CARD if any.
Downloading latest version
The download of CARD database failed, please try again.
If the error persists try using changeCARDPath() to refresh CARD folder location.
If not, consider downloading and extracting it manually. Then, use changeCARDPath() function to indicate the folder where it is located.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id 3003988 to NCBI
|===...........................| Step 3: Accessing CARD database and translating id 3003988 to NCBI
|====..........................| Step 4: Accessing CARD database and translating id 3003988 to NCBI
|=====.........................| Step 5: Accessing CARD database and translating id 3003988 to NCBI
|======........................| Step 6: Accessing CARD database and translating id 3003988 to NCBI
|=======.......................| Step 7: Accessing CARD database and translating id 3003988 to NCBI
|========......................| Step 8: Accessing CARD database and translating id 3003988 to NCBI
|=========.....................| Step 9: Accessing CARD database and translating id 3003988 to NCBI
|==========....................| Step 10: Accessing CARD database and translating id 3003988 to NCBI
|===========...................| Step 11: Accessing CARD database and translating id 3003988 to NCBI
|============..................| Step 12: Accessing CARD database and translating id 3003988 to NCBI
|=============.................| Step 13: Accessing CARD database and translating id 3003988 to NCBI
|==============................| Step 14: Accessing CARD database and translating id 3003988 to NCBI
|===============...............| Step 15: Accessing CARD database and translating id 3003988 to NCBI
|================..............| Step 16: Accessing CARD database and translating id 3003988 to NCBI
|=================.............| Step 17: Accessing CARD database and translating id 3003988 to NCBI
|==================............| Step 18: Accessing CARD database and translating id 3003988 to NCBI
|===================...........| Step 19: Accessing CARD database and translating id 3003988 to NCBI
|====================..........| Step 20: Accessing CARD database and translating id 3003988 to NCBI
|=====================.........| Step 21: Accessing CARD database and translating id 3003988 to NCBI
[1] NA
Test failed:
NA != APB03221.1
> .testEquals(getCARD2NCBIProtein(c('3003988', 'ARO:3002535')), c('APB03221.1', 'CAA38525.1'))
Updating CARD database data...
Deleting previous versions of CARD if any.
Downloading latest version
The download of CARD database failed, please try again.
If the error persists try using changeCARDPath() to refresh CARD folder location.
If not, consider downloading and extracting it manually. Then, use changeCARDPath() function to indicate the folder where it is located.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id 3003988 to NCBI
|===...........................| Step 3: Accessing CARD database and translating id 3003988 to NCBI
|====..........................| Step 4: Accessing CARD database and translating id 3003988 to NCBI
|=====.........................| Step 5: Accessing CARD database and translating id 3003988 to NCBI
|======........................| Step 6: Accessing CARD database and translating id 3003988 to NCBI
|=======.......................| Step 7: Accessing CARD database and translating id 3003988 to NCBI
|========......................| Step 8: Accessing CARD database and translating id 3003988 to NCBI
|=========.....................| Step 9: Accessing CARD database and translating id 3003988 to NCBI
|==========....................| Step 10: Accessing CARD database and translating id 3003988 to NCBI
|===========...................| Step 11: Accessing CARD database and translating id 3003988 to NCBI
|============..................| Step 12: Accessing CARD database and translating id 3003988 to NCBI
|=============.................| Step 13: Accessing CARD database and translating id 3003988 to NCBI
|==============................| Step 14: Accessing CARD database and translating id 3003988 to NCBI
|===============...............| Step 15: Accessing CARD database and translating id 3003988 to NCBI
|================..............| Step 16: Accessing CARD database and translating id 3003988 to NCBI
|=================.............| Step 17: Accessing CARD database and translating id 3003988 to NCBI
|==================............| Step 18: Accessing CARD database and translating id 3003988 to NCBI
|===================...........| Step 19: Accessing CARD database and translating id 3003988 to NCBI
|====================..........| Step 20: Accessing CARD database and translating id 3003988 to NCBI
|=====================.........| Step 21: Accessing CARD database and translating id 3003988 to NCBI
|======================........| Step 22: Accessing CARD database and translating id ARO:3002535 to NCBI
|=======================.......| Step 23: Accessing CARD database and translating id ARO:3002535 to NCBI
|========================......| Step 24: Accessing CARD database and translating id ARO:3002535 to NCBI
|=========================.....| Step 25: Accessing CARD database and translating id ARO:3002535 to NCBI
|==========================....| Step 26: Accessing CARD database and translating id ARO:3002535 to NCBI
|===========================...| Step 27: Accessing CARD database and translating id ARO:3002535 to NCBI
|============================..| Step 28: Accessing CARD database and translating id ARO:3002535 to NCBI
|=============================.| Step 29: Accessing CARD database and translating id ARO:3002535 to NCBI
|..............................| Step 30: Accessing CARD database and translating id ARO:3002535 to NCBI
|=.............................| Step 31: Accessing CARD database and translating id ARO:3002535 to NCBI
|==............................| Step 32: Accessing CARD database and translating id ARO:3002535 to NCBI
|===...........................| Step 33: Accessing CARD database and translating id ARO:3002535 to NCBI
|====..........................| Step 34: Accessing CARD database and translating id ARO:3002535 to NCBI
|=====.........................| Step 35: Accessing CARD database and translating id ARO:3002535 to NCBI
|======........................| Step 36: Accessing CARD database and translating id ARO:3002535 to NCBI
|=======.......................| Step 37: Accessing CARD database and translating id ARO:3002535 to NCBI
|========......................| Step 38: Accessing CARD database and translating id ARO:3002535 to NCBI
|=========.....................| Step 39: Accessing CARD database and translating id ARO:3002535 to NCBI
|==========....................| Step 40: Accessing CARD database and translating id ARO:3002535 to NCBI
|===========...................| Step 41: Accessing CARD database and translating id ARO:3002535 to NCBI
[1] NA NA
Test failed:
NANA != APB03221.1CAA38525.1
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBIProtein('test'), NA)
Updating CARD database data...
Deleting previous versions of CARD if any.
Downloading latest version
The download of CARD database failed, please try again.
If the error persists try using changeCARDPath() to refresh CARD folder location.
If not, consider downloading and extracting it manually. Then, use changeCARDPath() function to indicate the folder where it is located.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id test to NCBI
|===...........................| Step 3: Accessing CARD database and translating id test to NCBI
|====..........................| Step 4: Accessing CARD database and translating id test to NCBI
|=====.........................| Step 5: Accessing CARD database and translating id test to NCBI
|======........................| Step 6: Accessing CARD database and translating id test to NCBI
|=======.......................| Step 7: Accessing CARD database and translating id test to NCBI
|========......................| Step 8: Accessing CARD database and translating id test to NCBI
|=========.....................| Step 9: Accessing CARD database and translating id test to NCBI
|==========....................| Step 10: Accessing CARD database and translating id test to NCBI
|===========...................| Step 11: Accessing CARD database and translating id test to NCBI
|============..................| Step 12: Accessing CARD database and translating id test to NCBI
|=============.................| Step 13: Accessing CARD database and translating id test to NCBI
|==============................| Step 14: Accessing CARD database and translating id test to NCBI
|===============...............| Step 15: Accessing CARD database and translating id test to NCBI
|================..............| Step 16: Accessing CARD database and translating id test to NCBI
|=================.............| Step 17: Accessing CARD database and translating id test to NCBI
|==================............| Step 18: Accessing CARD database and translating id test to NCBI
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[1] NA
Test failed:
NA != NA
> .testEquals(getCARD2NCBIProtein(c('test', 'test')), c(NA, NA))
Updating CARD database data...
Deleting previous versions of CARD if any.
Downloading latest version
Extracting database
CARD database downloaded successfully!
Located at /tmp/RtmpjOUltv/card-data
CARD database version 4.0.1 (2025-05-29)
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
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|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
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|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
[1] NA NA
Test failed:
NANA != NANA
> .testEquals(getCARD2NCBIProtein(character(0)), character(0))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Protein
character(0)
Test failed:
!=
> .testEquals(getCARD2NCBIProtein(c(character(0), '3002535')), c('CAA38525.1'))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id 3002535 to NCBI
[1] "CAA38525.1"
[1] TRUE
>
>
>
> ### Test getCARD2NCBINucleotide
> message('Testing getCARD2NCBINucleotide')
Testing getCARD2NCBINucleotide
> # Positive cases
> .testEquals(getCARD2NCBINucleotide('3002535'), 'X54723.1')
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Nucleotide
|==............................| Step 2: Accessing CARD database and translating id 3002535 to NCBI
[1] "X54723.1"
[1] TRUE
> .testEquals(getCARD2NCBINucleotide('ARO:3002535'), 'X54723.1')
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Nucleotide
|==............................| Step 2: Accessing CARD database and translating id ARO:3002535 to NCBI
[1] "X54723.1"
[1] TRUE
> .testEquals(getCARD2NCBINucleotide('3003988'), 'KX531051.1')
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Nucleotide
|==............................| Step 2: Accessing CARD database and translating id 3003988 to NCBI
[1] "KX531051.1"
[1] TRUE
> .testEquals(getCARD2NCBINucleotide(c('3003988', 'ARO:3002535')), c('KX531051.1', 'X54723.1'))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Nucleotide
|==............................| Step 2: Accessing CARD database and translating id 3003988 to NCBI
|===...........................| Step 3: Accessing CARD database and translating id ARO:3002535 to NCBI
[1] "KX531051.1" "X54723.1"
Test failed:
KX531051.1X54723.1 != KX531051.1X54723.1
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBINucleotide('test'), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Nucleotide
|==............................| Step 2: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
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|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
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|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
[1] NA
Test failed:
NA != NA
> .testEquals(getCARD2NCBINucleotide(c('test','test')), c(NA,NA))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Nucleotide
|==............................| Step 2: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
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|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
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|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
[1] NA NA
Test failed:
NANA != NANA
>
>
> ### Test getCARD2NCBIGene
> message('Testing getCARD2NCBIGene')
Testing getCARD2NCBIGene
> # Positive cases
> .testEquals(getCARD2NCBIGene('3002525'), c('886648'))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Gene
|==............................| Step 2: Accessing CARD database and translating id 3002525 to NCBI
|===...........................| Step 3: Accessing CARD database and translating id 3002525 to NCBI
|====..........................| Step 4: Accessing CARD database and translating id 3002525 to NCBI
|=====.........................| Step 5: Accessing CARD database and translating id 3002525 to NCBI
|======........................| Step 6: Accessing CARD database and translating id 3002525 to NCBI
|=======.......................| Step 7: Accessing CARD database and translating id 3002525 to NCBI
|========......................| Step 8: Accessing CARD database and translating id 3002525 to NCBI
|=========.....................| Step 9: Accessing CARD database and translating id 3002525 to NCBI
|==========....................| Step 10: Accessing CARD database and translating id 3002525 to NCBI
|===========...................| Step 11: Accessing CARD database and translating id 3002525 to NCBI
|============..................| Step 12: Accessing CARD database and translating id 3002525 to NCBI
|=============.................| Step 13: Accessing CARD database and translating id 3002525 to NCBI
|==============................| Step 14: Accessing CARD database and translating id 3002525 to NCBI
|===============...............| Step 15: Accessing CARD database and translating id 3002525 to NCBI
|================..............| Step 16: Accessing CARD database and translating id 3002525 to NCBI
|=================.............| Step 17: Accessing CARD database and translating id 3002525 to NCBI
|==================............| Step 18: Accessing CARD database and translating id 3002525 to NCBI
|===================...........| Step 19: Accessing CARD database and translating id 3002525 to NCBI
|====================..........| Step 20: Accessing CARD database and translating id 3002525 to NCBI
|=====================.........| Step 21: Accessing CARD database and translating id 3002525 to NCBI
[1] NA
Test failed:
NA != 886648
> .testEquals(getCARD2NCBIGene(c('3002525','3002525')), c('886648', '886648'))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Gene
|==............................| Step 2: Accessing CARD database and translating id 3002525 to NCBI
|===...........................| Step 3: Accessing CARD database and translating id 3002525 to NCBI
|====..........................| Step 4: Accessing CARD database and translating id 3002525 to NCBI
|=====.........................| Step 5: Accessing CARD database and translating id 3002525 to NCBI
|======........................| Step 6: Accessing CARD database and translating id 3002525 to NCBI
|=======.......................| Step 7: Accessing CARD database and translating id 3002525 to NCBI
|========......................| Step 8: Accessing CARD database and translating id 3002525 to NCBI
|=========.....................| Step 9: Accessing CARD database and translating id 3002525 to NCBI
|==========....................| Step 10: Accessing CARD database and translating id 3002525 to NCBI
|===========...................| Step 11: Accessing CARD database and translating id 3002525 to NCBI
|============..................| Step 12: Accessing CARD database and translating id 3002525 to NCBI
|=============.................| Step 13: Accessing CARD database and translating id 3002525 to NCBI
|==============................| Step 14: Accessing CARD database and translating id 3002525 to NCBI
|===============...............| Step 15: Accessing CARD database and translating id 3002525 to NCBI
|================..............| Step 16: Accessing CARD database and translating id 3002525 to NCBI
|=================.............| Step 17: Accessing CARD database and translating id 3002525 to NCBI
|==================............| Step 18: Accessing CARD database and translating id 3002525 to NCBI
|===================...........| Step 19: Accessing CARD database and translating id 3002525 to NCBI
|====================..........| Step 20: Accessing CARD database and translating id 3002525 to NCBI
|=====================.........| Step 21: Accessing CARD database and translating id 3002525 to NCBI
|======================........| Step 22: Accessing CARD database and translating id 3002525 to NCBI
|=======================.......| Step 23: Accessing CARD database and translating id 3002525 to NCBI
|========================......| Step 24: Accessing CARD database and translating id 3002525 to NCBI
|=========================.....| Step 25: Accessing CARD database and translating id 3002525 to NCBI
|==========================....| Step 26: Accessing CARD database and translating id 3002525 to NCBI
|===========================...| Step 27: Accessing CARD database and translating id 3002525 to NCBI
|============================..| Step 28: Accessing CARD database and translating id 3002525 to NCBI
|=============================.| Step 29: Accessing CARD database and translating id 3002525 to NCBI
|..............................| Step 30: Accessing CARD database and translating id 3002525 to NCBI
|=.............................| Step 31: Accessing CARD database and translating id 3002525 to NCBI
|==............................| Step 32: Accessing CARD database and translating id 3002525 to NCBI
|===...........................| Step 33: Accessing CARD database and translating id 3002525 to NCBI
|====..........................| Step 34: Accessing CARD database and translating id 3002525 to NCBI
|=====.........................| Step 35: Accessing CARD database and translating id 3002525 to NCBI
|======........................| Step 36: Accessing CARD database and translating id 3002525 to NCBI
|=======.......................| Step 37: Accessing CARD database and translating id 3002525 to NCBI
|========......................| Step 38: Accessing CARD database and translating id 3002525 to NCBI
|=========.....................| Step 39: Accessing CARD database and translating id 3002525 to NCBI
|==========....................| Step 40: Accessing CARD database and translating id 3002525 to NCBI
|===========...................| Step 41: Accessing CARD database and translating id 3002525 to NCBI
[1] NA NA
Test failed:
NANA != 886648886648
> # # No translation case
> # .testEquals(getCARD2NCBIGene('3005061'), NA)
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBIGene('test'), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Gene
|==............................| Step 2: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
[1] NA
Test failed:
NA != NA
>
> ############################
> # CARD database to UniProt #
> ############################
>
> ### Test getCARD2UniProt
> message('Testing getCARD2UniProt')
Testing getCARD2UniProt
> # Positive cases
> .testEquals(getCARD2UniProt('3002867'), c('Q9ZIF9'))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to UniProt
|==............................| Step 2: Accessing CARD database and translating id 3002867 to Uniprot
|===...........................| Step 3: Accessing CARD database and translating id 3002867 to Uniprot
|====..........................| Step 4: Accessing CARD database and translating id 3002867 to Uniprot
|=====.........................| Step 5: Accessing CARD database and translating id 3002867 to Uniprot
|======........................| Step 6: Accessing CARD database and translating id 3002867 to Uniprot
|=======.......................| Step 7: Accessing CARD database and translating id 3002867 to Uniprot
|========......................| Step 8: Accessing CARD database and translating id 3002867 to Uniprot
|=========.....................| Step 9: Accessing CARD database and translating id 3002867 to Uniprot
|==========....................| Step 10: Accessing CARD database and translating id 3002867 to Uniprot
|===========...................| Step 11: Accessing CARD database and translating id 3002867 to Uniprot
|============..................| Step 12: Accessing CARD database and translating id 3002867 to Uniprot
|=============.................| Step 13: Accessing CARD database and translating id 3002867 to Uniprot
|==============................| Step 14: Accessing CARD database and translating id 3002867 to Uniprot
|===============...............| Step 15: Accessing CARD database and translating id 3002867 to Uniprot
|================..............| Step 16: Accessing CARD database and translating id 3002867 to Uniprot
|=================.............| Step 17: Accessing CARD database and translating id 3002867 to Uniprot
|==================............| Step 18: Accessing CARD database and translating id 3002867 to Uniprot
|===================...........| Step 19: Accessing CARD database and translating id 3002867 to Uniprot
|====================..........| Step 20: Accessing CARD database and translating id 3002867 to Uniprot
|=====================.........| Step 21: Accessing CARD database and translating id 3002867 to Uniprot
[1] NA
Test failed:
NA != Q9ZIF9
> .testEquals(getCARD2UniProt('3002867', detailedMapping=TRUE), list('DT'=c('Q9ZIF9')))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to UniProt
|==............................| Step 2: Accessing CARD database and translating id 3002867 to Uniprot
|===...........................| Step 3: Accessing CARD database and translating id 3002867 to Uniprot
|====..........................| Step 4: Accessing CARD database and translating id 3002867 to Uniprot
|=====.........................| Step 5: Accessing CARD database and translating id 3002867 to Uniprot
|======........................| Step 6: Accessing CARD database and translating id 3002867 to Uniprot
|=======.......................| Step 7: Accessing CARD database and translating id 3002867 to Uniprot
|========......................| Step 8: Accessing CARD database and translating id 3002867 to Uniprot
|=========.....................| Step 9: Accessing CARD database and translating id 3002867 to Uniprot
|==========....................| Step 10: Accessing CARD database and translating id 3002867 to Uniprot
|===========...................| Step 11: Accessing CARD database and translating id 3002867 to Uniprot
|============..................| Step 12: Accessing CARD database and translating id 3002867 to Uniprot
|=============.................| Step 13: Accessing CARD database and translating id 3002867 to Uniprot
|==============................| Step 14: Accessing CARD database and translating id 3002867 to Uniprot
|===============...............| Step 15: Accessing CARD database and translating id 3002867 to Uniprot
|================..............| Step 16: Accessing CARD database and translating id 3002867 to Uniprot
|=================.............| Step 17: Accessing CARD database and translating id 3002867 to Uniprot
|==================............| Step 18: Accessing CARD database and translating id 3002867 to Uniprot
|===================...........| Step 19: Accessing CARD database and translating id 3002867 to Uniprot
|====================..........| Step 20: Accessing CARD database and translating id 3002867 to Uniprot
|=====================.........| Step 21: Accessing CARD database and translating id 3002867 to Uniprot
[1] NA
Test failed:
NA != Q9ZIF9
> .testEquals(getCARD2UniProt(c('3002867', '3002867'), detailedMapping=TRUE), c('DT'=c('Q9ZIF9'),'DT'=c('Q9ZIF9')))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to UniProt
|==............................| Step 2: Accessing CARD database and translating id 3002867 to Uniprot
|===...........................| Step 3: Accessing CARD database and translating id 3002867 to Uniprot
|====..........................| Step 4: Accessing CARD database and translating id 3002867 to Uniprot
|=====.........................| Step 5: Accessing CARD database and translating id 3002867 to Uniprot
|======........................| Step 6: Accessing CARD database and translating id 3002867 to Uniprot
|=======.......................| Step 7: Accessing CARD database and translating id 3002867 to Uniprot
|========......................| Step 8: Accessing CARD database and translating id 3002867 to Uniprot
|=========.....................| Step 9: Accessing CARD database and translating id 3002867 to Uniprot
|==========....................| Step 10: Accessing CARD database and translating id 3002867 to Uniprot
|===========...................| Step 11: Accessing CARD database and translating id 3002867 to Uniprot
|============..................| Step 12: Accessing CARD database and translating id 3002867 to Uniprot
|=============.................| Step 13: Accessing CARD database and translating id 3002867 to Uniprot
|==============................| Step 14: Accessing CARD database and translating id 3002867 to Uniprot
|===============...............| Step 15: Accessing CARD database and translating id 3002867 to Uniprot
|================..............| Step 16: Accessing CARD database and translating id 3002867 to Uniprot
|=================.............| Step 17: Accessing CARD database and translating id 3002867 to Uniprot
|==================............| Step 18: Accessing CARD database and translating id 3002867 to Uniprot
|===================...........| Step 19: Accessing CARD database and translating id 3002867 to Uniprot
|====================..........| Step 20: Accessing CARD database and translating id 3002867 to Uniprot
|=====================.........| Step 21: Accessing CARD database and translating id 3002867 to Uniprot
|======================........| Step 22: Accessing CARD database and translating id 3002867 to Uniprot
|=======================.......| Step 23: Accessing CARD database and translating id 3002867 to Uniprot
|========================......| Step 24: Accessing CARD database and translating id 3002867 to Uniprot
|=========================.....| Step 25: Accessing CARD database and translating id 3002867 to Uniprot
|==========================....| Step 26: Accessing CARD database and translating id 3002867 to Uniprot
|===========================...| Step 27: Accessing CARD database and translating id 3002867 to Uniprot
|============================..| Step 28: Accessing CARD database and translating id 3002867 to Uniprot
|=============================.| Step 29: Accessing CARD database and translating id 3002867 to Uniprot
|..............................| Step 30: Accessing CARD database and translating id 3002867 to Uniprot
|=.............................| Step 31: Accessing CARD database and translating id 3002867 to Uniprot
|==............................| Step 32: Accessing CARD database and translating id 3002867 to Uniprot
|===...........................| Step 33: Accessing CARD database and translating id 3002867 to Uniprot
|====..........................| Step 34: Accessing CARD database and translating id 3002867 to Uniprot
|=====.........................| Step 35: Accessing CARD database and translating id 3002867 to Uniprot
|======........................| Step 36: Accessing CARD database and translating id 3002867 to Uniprot
|=======.......................| Step 37: Accessing CARD database and translating id 3002867 to Uniprot
|========......................| Step 38: Accessing CARD database and translating id 3002867 to Uniprot
|=========.....................| Step 39: Accessing CARD database and translating id 3002867 to Uniprot
|==========....................| Step 40: Accessing CARD database and translating id 3002867 to Uniprot
|===========...................| Step 41: Accessing CARD database and translating id 3002867 to Uniprot
[1] NA NA
Test failed:
NANA != Q9ZIF9Q9ZIF9
> # checkTrue(length(getCARD2UniProt('3002867', TRUE)) == 35)
> # .testEquals(getCARD2UniProt('3003649'), c('A0A0K0TQH5'))
> # No translation case
> .testEquals(getCARD2UniProt('3006267'), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to UniProt
|==............................| Step 2: Accessing CARD database and translating id 3006267 to Uniprot
|===...........................| Step 3: Accessing CARD database and translating id 3006267 to Uniprot
|====..........................| Step 4: Accessing CARD database and translating id 3006267 to Uniprot
|=====.........................| Step 5: Accessing CARD database and translating id 3006267 to Uniprot
|======........................| Step 6: Accessing CARD database and translating id 3006267 to Uniprot
|=======.......................| Step 7: Accessing CARD database and translating id 3006267 to Uniprot
|========......................| Step 8: Accessing CARD database and translating id 3006267 to Uniprot
|=========.....................| Step 9: Accessing CARD database and translating id 3006267 to Uniprot
|==========....................| Step 10: Accessing CARD database and translating id 3006267 to Uniprot
|===========...................| Step 11: Accessing CARD database and translating id 3006267 to Uniprot
|============..................| Step 12: Accessing CARD database and translating id 3006267 to Uniprot
|=============.................| Step 13: Accessing CARD database and translating id 3006267 to Uniprot
|==============................| Step 14: Accessing CARD database and translating id 3006267 to Uniprot
|===============...............| Step 15: Accessing CARD database and translating id 3006267 to Uniprot
|================..............| Step 16: Accessing CARD database and translating id 3006267 to Uniprot
|=================.............| Step 17: Accessing CARD database and translating id 3006267 to Uniprot
|==================............| Step 18: Accessing CARD database and translating id 3006267 to Uniprot
|===================...........| Step 19: Accessing CARD database and translating id 3006267 to Uniprot
|====================..........| Step 20: Accessing CARD database and translating id 3006267 to Uniprot
|=====================.........| Step 21: Accessing CARD database and translating id 3006267 to Uniprot
[1] NA
Test failed:
NA != NA
> .testEquals(getCARD2UniProt('3006267', detailedMapping=TRUE), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to UniProt
|==............................| Step 2: Accessing CARD database and translating id 3006267 to Uniprot
|===...........................| Step 3: Accessing CARD database and translating id 3006267 to Uniprot
|====..........................| Step 4: Accessing CARD database and translating id 3006267 to Uniprot
|=====.........................| Step 5: Accessing CARD database and translating id 3006267 to Uniprot
|======........................| Step 6: Accessing CARD database and translating id 3006267 to Uniprot
|=======.......................| Step 7: Accessing CARD database and translating id 3006267 to Uniprot
|========......................| Step 8: Accessing CARD database and translating id 3006267 to Uniprot
|=========.....................| Step 9: Accessing CARD database and translating id 3006267 to Uniprot
|==========....................| Step 10: Accessing CARD database and translating id 3006267 to Uniprot
|===========...................| Step 11: Accessing CARD database and translating id 3006267 to Uniprot
|============..................| Step 12: Accessing CARD database and translating id 3006267 to Uniprot
|=============.................| Step 13: Accessing CARD database and translating id 3006267 to Uniprot
|==============................| Step 14: Accessing CARD database and translating id 3006267 to Uniprot
|===============...............| Step 15: Accessing CARD database and translating id 3006267 to Uniprot
|================..............| Step 16: Accessing CARD database and translating id 3006267 to Uniprot
|=================.............| Step 17: Accessing CARD database and translating id 3006267 to Uniprot
|==================............| Step 18: Accessing CARD database and translating id 3006267 to Uniprot
|===================...........| Step 19: Accessing CARD database and translating id 3006267 to Uniprot
|====================..........| Step 20: Accessing CARD database and translating id 3006267 to Uniprot
|=====================.........| Step 21: Accessing CARD database and translating id 3006267 to Uniprot
[1] NA
Test failed:
NA != NA
> # Incorrect CARD ID case
> .testEquals(getCARD2UniProt('test'), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to UniProt
|==............................| Step 2: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
|=.............................| Step 1: Accessing CARD database and translating id test to Uniprot
The given ID "test" is not registered in CARD database
[1] NA
Test failed:
NA != NA
>
> #########################
> # CARD database to KEGG #
> #########################
>
> ### Test getCARD2KEGG
> message('Testing getCARD2KEGG')
Testing getCARD2KEGG
> # Positive cases
> .testEquals(getCARD2KEGG('3000938'), c('ag:AAF19151'))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to KEGG
|==............................| Step 2: Accessing CARD database and translating id 3000938 to KEGG
|===...........................| Step 3: Accessing CARD database and translating id 3000938 to KEGG
|====..........................| Step 4: Accessing CARD database and translating id 3000938 to KEGG
|=====.........................| Step 5: Accessing CARD database and translating id 3000938 to KEGG
|======........................| Step 6: Accessing CARD database and translating id 3000938 to KEGG
|=======.......................| Step 7: Accessing CARD database and translating id 3000938 to KEGG
|========......................| Step 8: Accessing CARD database and translating id 3000938 to KEGG
|=========.....................| Step 9: Accessing CARD database and translating id 3000938 to KEGG
|==========....................| Step 10: Accessing CARD database and translating id 3000938 to KEGG
|===========...................| Step 11: Accessing CARD database and translating id 3000938 to KEGG
|============..................| Step 12: Accessing CARD database and translating id 3000938 to KEGG
|=============.................| Step 13: Accessing CARD database and translating id 3000938 to KEGG
|==============................| Step 14: Accessing CARD database and translating id 3000938 to KEGG
|===============...............| Step 15: Accessing CARD database and translating id 3000938 to KEGG
|================..............| Step 16: Accessing CARD database and translating id 3000938 to KEGG
|=================.............| Step 17: Accessing CARD database and translating id 3000938 to KEGG
|==================............| Step 18: Accessing CARD database and translating id 3000938 to KEGG
|===================...........| Step 19: Accessing CARD database and translating id 3000938 to KEGG
|====================..........| Step 20: Accessing CARD database and translating id 3000938 to KEGG
|=====================.........| Step 21: Accessing CARD database and translating id 3000938 to KEGG
[1] NA
Test failed:
NA != ag:AAF19151
> .testEquals(getCARD2KEGG('3000938', detailedMapping = TRUE), list('DT'='ag:AAF19151'))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to KEGG
|==............................| Step 2: Accessing CARD database and translating id 3000938 to KEGG
|===...........................| Step 3: Accessing CARD database and translating id 3000938 to KEGG
|====..........................| Step 4: Accessing CARD database and translating id 3000938 to KEGG
|=====.........................| Step 5: Accessing CARD database and translating id 3000938 to KEGG
|======........................| Step 6: Accessing CARD database and translating id 3000938 to KEGG
|=======.......................| Step 7: Accessing CARD database and translating id 3000938 to KEGG
|========......................| Step 8: Accessing CARD database and translating id 3000938 to KEGG
|=========.....................| Step 9: Accessing CARD database and translating id 3000938 to KEGG
|==========....................| Step 10: Accessing CARD database and translating id 3000938 to KEGG
|===========...................| Step 11: Accessing CARD database and translating id 3000938 to KEGG
|============..................| Step 12: Accessing CARD database and translating id 3000938 to KEGG
|=============.................| Step 13: Accessing CARD database and translating id 3000938 to KEGG
|==============................| Step 14: Accessing CARD database and translating id 3000938 to KEGG
|===============...............| Step 15: Accessing CARD database and translating id 3000938 to KEGG
|================..............| Step 16: Accessing CARD database and translating id 3000938 to KEGG
|=================.............| Step 17: Accessing CARD database and translating id 3000938 to KEGG
|==================............| Step 18: Accessing CARD database and translating id 3000938 to KEGG
|===================...........| Step 19: Accessing CARD database and translating id 3000938 to KEGG
|====================..........| Step 20: Accessing CARD database and translating id 3000938 to KEGG
|=====================.........| Step 21: Accessing CARD database and translating id 3000938 to KEGG
[1] NA
Test failed:
NA != ag:AAF19151
> .testEquals(getCARD2KEGG(c('3000938','3000938'), detailedMapping = TRUE), c('DT'=c('ag:AAF19151'), 'DT'=c('ag:AAF19151')))
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to KEGG
|==............................| Step 2: Accessing CARD database and translating id 3000938 to KEGG
|===...........................| Step 3: Accessing CARD database and translating id 3000938 to KEGG
|====..........................| Step 4: Accessing CARD database and translating id 3000938 to KEGG
|=====.........................| Step 5: Accessing CARD database and translating id 3000938 to KEGG
|======........................| Step 6: Accessing CARD database and translating id 3000938 to KEGG
|=======.......................| Step 7: Accessing CARD database and translating id 3000938 to KEGG
|========......................| Step 8: Accessing CARD database and translating id 3000938 to KEGG
|=========.....................| Step 9: Accessing CARD database and translating id 3000938 to KEGG
|==========....................| Step 10: Accessing CARD database and translating id 3000938 to KEGG
|===========...................| Step 11: Accessing CARD database and translating id 3000938 to KEGG
|============..................| Step 12: Accessing CARD database and translating id 3000938 to KEGG
|=============.................| Step 13: Accessing CARD database and translating id 3000938 to KEGG
|==============................| Step 14: Accessing CARD database and translating id 3000938 to KEGG
|===============...............| Step 15: Accessing CARD database and translating id 3000938 to KEGG
|================..............| Step 16: Accessing CARD database and translating id 3000938 to KEGG
|=================.............| Step 17: Accessing CARD database and translating id 3000938 to KEGG
|==================............| Step 18: Accessing CARD database and translating id 3000938 to KEGG
|===================...........| Step 19: Accessing CARD database and translating id 3000938 to KEGG
|====================..........| Step 20: Accessing CARD database and translating id 3000938 to KEGG
|=====================.........| Step 21: Accessing CARD database and translating id 3000938 to KEGG
|======================........| Step 22: Accessing CARD database and translating id 3000938 to KEGG
|=======================.......| Step 23: Accessing CARD database and translating id 3000938 to KEGG
|========================......| Step 24: Accessing CARD database and translating id 3000938 to KEGG
|=========================.....| Step 25: Accessing CARD database and translating id 3000938 to KEGG
|==========================....| Step 26: Accessing CARD database and translating id 3000938 to KEGG
|===========================...| Step 27: Accessing CARD database and translating id 3000938 to KEGG
|============================..| Step 28: Accessing CARD database and translating id 3000938 to KEGG
|=============================.| Step 29: Accessing CARD database and translating id 3000938 to KEGG
|..............................| Step 30: Accessing CARD database and translating id 3000938 to KEGG
|=.............................| Step 31: Accessing CARD database and translating id 3000938 to KEGG
|==............................| Step 32: Accessing CARD database and translating id 3000938 to KEGG
|===...........................| Step 33: Accessing CARD database and translating id 3000938 to KEGG
|====..........................| Step 34: Accessing CARD database and translating id 3000938 to KEGG
|=====.........................| Step 35: Accessing CARD database and translating id 3000938 to KEGG
|======........................| Step 36: Accessing CARD database and translating id 3000938 to KEGG
|=======.......................| Step 37: Accessing CARD database and translating id 3000938 to KEGG
|========......................| Step 38: Accessing CARD database and translating id 3000938 to KEGG
|=========.....................| Step 39: Accessing CARD database and translating id 3000938 to KEGG
|==========....................| Step 40: Accessing CARD database and translating id 3000938 to KEGG
|===========...................| Step 41: Accessing CARD database and translating id 3000938 to KEGG
[1] NA NA
Test failed:
NANA != ag:AAF19151ag:AAF19151
> # .testEquals(getCARD2KEGG('3001109', detailedMapping = TRUE), list('0.9'=c('ag:BAA84973')))
> # .testEquals(getCARD2KEGG('3002511', exhaustiveMapping = TRUE, detailedMapping = TRUE, bySimilarGenes = TRUE),
> # list('0.5'=c("chk:D4L85_28045","proe:H9L23_08075"))) # Takes a long time
> # No translation cases
> .testEquals(getCARD2KEGG('3006267', detailedMapping = FALSE, bySimilarGenes = FALSE), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to KEGG
|==............................| Step 2: Accessing CARD database and translating id 3006267 to KEGG
|===...........................| Step 3: Accessing CARD database and translating id 3006267 to KEGG
|====..........................| Step 4: Accessing CARD database and translating id 3006267 to KEGG
|=====.........................| Step 5: Accessing CARD database and translating id 3006267 to KEGG
|======........................| Step 6: Accessing CARD database and translating id 3006267 to KEGG
|=======.......................| Step 7: Accessing CARD database and translating id 3006267 to KEGG
|========......................| Step 8: Accessing CARD database and translating id 3006267 to KEGG
|=========.....................| Step 9: Accessing CARD database and translating id 3006267 to KEGG
|==========....................| Step 10: Accessing CARD database and translating id 3006267 to KEGG
|===========...................| Step 11: Accessing CARD database and translating id 3006267 to KEGG
|============..................| Step 12: Accessing CARD database and translating id 3006267 to KEGG
|=============.................| Step 13: Accessing CARD database and translating id 3006267 to KEGG
|==============................| Step 14: Accessing CARD database and translating id 3006267 to KEGG
|===============...............| Step 15: Accessing CARD database and translating id 3006267 to KEGG
|================..............| Step 16: Accessing CARD database and translating id 3006267 to KEGG
|=================.............| Step 17: Accessing CARD database and translating id 3006267 to KEGG
|==================............| Step 18: Accessing CARD database and translating id 3006267 to KEGG
|===================...........| Step 19: Accessing CARD database and translating id 3006267 to KEGG
|====================..........| Step 20: Accessing CARD database and translating id 3006267 to KEGG
|=====================.........| Step 21: Accessing CARD database and translating id 3006267 to KEGG
[1] NA
Test failed:
NA != NA
> .testEquals(getCARD2KEGG('3006267', detailedMapping = TRUE, bySimilarGenes = FALSE), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to KEGG
|==............................| Step 2: Accessing CARD database and translating id 3006267 to KEGG
|===...........................| Step 3: Accessing CARD database and translating id 3006267 to KEGG
|====..........................| Step 4: Accessing CARD database and translating id 3006267 to KEGG
|=====.........................| Step 5: Accessing CARD database and translating id 3006267 to KEGG
|======........................| Step 6: Accessing CARD database and translating id 3006267 to KEGG
|=======.......................| Step 7: Accessing CARD database and translating id 3006267 to KEGG
|========......................| Step 8: Accessing CARD database and translating id 3006267 to KEGG
|=========.....................| Step 9: Accessing CARD database and translating id 3006267 to KEGG
|==========....................| Step 10: Accessing CARD database and translating id 3006267 to KEGG
|===========...................| Step 11: Accessing CARD database and translating id 3006267 to KEGG
|============..................| Step 12: Accessing CARD database and translating id 3006267 to KEGG
|=============.................| Step 13: Accessing CARD database and translating id 3006267 to KEGG
|==============................| Step 14: Accessing CARD database and translating id 3006267 to KEGG
|===============...............| Step 15: Accessing CARD database and translating id 3006267 to KEGG
|================..............| Step 16: Accessing CARD database and translating id 3006267 to KEGG
|=================.............| Step 17: Accessing CARD database and translating id 3006267 to KEGG
|==================............| Step 18: Accessing CARD database and translating id 3006267 to KEGG
|===================...........| Step 19: Accessing CARD database and translating id 3006267 to KEGG
|====================..........| Step 20: Accessing CARD database and translating id 3006267 to KEGG
|=====================.........| Step 21: Accessing CARD database and translating id 3006267 to KEGG
[1] NA
Test failed:
NA != NA
> # Incorrect CARD ID case
> .testEquals(getCARD2KEGG('test'), NA)
Using a CARD database version downloaded on Sat 11/08/2025 16:51:27, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to KEGG
|==............................| Step 2: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
|=.............................| Step 1: Accessing CARD database and translating id test to KEGG
The given ID "test" is not registered in CARD database
[1] NA
Test failed:
NA != NA
>
>
>
>
>
>
>
> proc.time()
user system elapsed
38.852 1.461 1856.208
ginmappeR.Rcheck/tests/test_NCBI.Rout.fail
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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.
> library(RUnit)
> library(ginmappeR)
> library('UniProt.ws')
> library('KEGGREST')
> library('httr')
> library('rentrez')
> library('XML')
>
> utils::globalVariables('cardPath')
[1] "cardPath"
> cardPath <<- tempdir()
>
> # GitHub Actions imports
> # source('../../../R/NCBIFunctions.R')
> # source('../../../R/UniProtFunctions.R')
> # source('../../../R/00utils.R')
>
> # # Local execution imports
> setwd('../00_pkg_src/ginmappeR/')
> source('R/NCBIFunctions.R')
> source('R/UniProtFunctions.R')
> source('R/00utils.R')
>
> #####################################
> # NCBI databases inter-translations #
> #####################################
>
> ### Test getNCBIGene2NCBIProtein
> message('Testing getNCBIGene2NCBIProtein')
Testing getNCBIGene2NCBIProtein
> # Positive case
> .testEquals(getNCBIGene2NCBIProtein('76524190'), c('WP_001082319'))
|=.............................| Step 1: Translating from NCBI Gene to NCBI Protein
|==............................| Step 2: Translating NCBI id 76524190 to NCBI Protein
|===...........................| Step 3: Translating NCBI id 76524190 to NCBI Protein
|====..........................| Step 4: Translating NCBI id 76524190 to NCBI Protein
|=====.........................| Step 5: Translating NCBI id 76524190 to NCBI Protein
|======........................| Step 6: Translating NCBI id 76524190 to NCBI Protein
|=======.......................| Step 7: Translating NCBI id 76524190 to NCBI Protein
|========......................| Step 8: Translating NCBI id 76524190 to NCBI Protein
|=========.....................| Step 9: Translating NCBI id 76524190 to NCBI Protein
|==========....................| Step 10: Translating NCBI id 76524190 to NCBI Protein
|===========...................| Step 11: Translating NCBI id 76524190 to NCBI Protein
|============..................| Step 12: Translating NCBI id 76524190 to NCBI Protein
|=============.................| Step 13: Translating NCBI id 76524190 to NCBI Protein
|==============................| Step 14: Translating NCBI id 76524190 to NCBI Protein
|===============...............| Step 15: Translating NCBI id 76524190 to NCBI Protein
|================..............| Step 16: Translating NCBI id 76524190 to NCBI Protein
|=================.............| Step 17: Translating NCBI id 76524190 to NCBI Protein
|==================............| Step 18: Translating NCBI id 76524190 to NCBI Protein
|===================...........| Step 19: Translating NCBI id 76524190 to NCBI Protein
|====================..........| Step 20: Translating NCBI id 76524190 to NCBI Protein
|=====================.........| Step 21: Translating NCBI id 76524190 to NCBI Protein
[1] NA
Test failed:
NA != WP_001082319
> .testEquals(getNCBIGene2NCBIProtein(c('76524190', '76524190')), c('WP_001082319','WP_001082319'))
|=.............................| Step 1: Translating from NCBI Gene to NCBI Protein
|==............................| Step 2: Translating NCBI id 76524190 to NCBI Protein
|===...........................| Step 3: Translating NCBI id 76524190 to NCBI Protein
|====..........................| Step 4: Translating NCBI id 76524190 to NCBI Protein
|=====.........................| Step 5: Translating NCBI id 76524190 to NCBI Protein
|======........................| Step 6: Translating NCBI id 76524190 to NCBI Protein
|=======.......................| Step 7: Translating NCBI id 76524190 to NCBI Protein
|========......................| Step 8: Translating NCBI id 76524190 to NCBI Protein
|=========.....................| Step 9: Translating NCBI id 76524190 to NCBI Protein
|==========....................| Step 10: Translating NCBI id 76524190 to NCBI Protein
|===========...................| Step 11: Translating NCBI id 76524190 to NCBI Protein
|============..................| Step 12: Translating NCBI id 76524190 to NCBI Protein
|=============.................| Step 13: Translating NCBI id 76524190 to NCBI Protein
|==============................| Step 14: Translating NCBI id 76524190 to NCBI Protein
|===============...............| Step 15: Translating NCBI id 76524190 to NCBI Protein
|================..............| Step 16: Translating NCBI id 76524190 to NCBI Protein
|=================.............| Step 17: Translating NCBI id 76524190 to NCBI Protein
|==================............| Step 18: Translating NCBI id 76524190 to NCBI Protein
|===================...........| Step 19: Translating NCBI id 76524190 to NCBI Protein
|====================..........| Step 20: Translating NCBI id 76524190 to NCBI Protein
|=====================.........| Step 21: Translating NCBI id 76524190 to NCBI Protein
|======================........| Step 22: Translating NCBI id 76524190 to NCBI Protein
|=======================.......| Step 23: Translating NCBI id 76524190 to NCBI Protein
|========================......| Step 24: Translating NCBI id 76524190 to NCBI Protein
|=========================.....| Step 25: Translating NCBI id 76524190 to NCBI Protein
[1] "WP_001082319" "WP_001082319"
Test failed:
WP_001082319WP_001082319 != WP_001082319WP_001082319
> .testEquals(getNCBIGene2NCBIProtein('76524190', exhaustiveMapping = TRUE), list(c('WP_001082319')))
|=.............................| Step 1: Translating from NCBI Gene to NCBI Protein
|==............................| Step 2: Translating NCBI id 76524190 to NCBI Protein
|===...........................| Step 3: Translating NCBI id 76524190 to NCBI Protein
|====..........................| Step 4: Translating NCBI id 76524190 to NCBI Protein
|=====.........................| Step 5: Translating NCBI id 76524190 to NCBI Protein
|======........................| Step 6: Translating NCBI id 76524190 to NCBI Protein
|=======.......................| Step 7: Translating NCBI id 76524190 to NCBI Protein
|========......................| Step 8: Translating NCBI id 76524190 to NCBI Protein
|=========.....................| Step 9: Translating NCBI id 76524190 to NCBI Protein
|==========....................| Step 10: Translating NCBI id 76524190 to NCBI Protein
|===========...................| Step 11: Translating NCBI id 76524190 to NCBI Protein
|============..................| Step 12: Translating NCBI id 76524190 to NCBI Protein
|=============.................| Step 13: Translating NCBI id 76524190 to NCBI Protein
|==============................| Step 14: Translating NCBI id 76524190 to NCBI Protein
|===============...............| Step 15: Translating NCBI id 76524190 to NCBI Protein
|================..............| Step 16: Translating NCBI id 76524190 to NCBI Protein
|=================.............| Step 17: Translating NCBI id 76524190 to NCBI Protein
|==================............| Step 18: Translating NCBI id 76524190 to NCBI Protein
|===================...........| Step 19: Translating NCBI id 76524190 to NCBI Protein
|====================..........| Step 20: Translating NCBI id 76524190 to NCBI Protein
|=====================.........| Step 21: Translating NCBI id 76524190 to NCBI Protein
[[1]]
NULL
Error in testFunction == result :
comparison of these types is not implemented
Calls: .testEquals
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ginmappeR_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/ginmappeR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.7.0’
* 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 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘test_CARD.R’
Running ‘test_NCBI.R’
ERROR
Running the tests in ‘longtests/test_NCBI.R’ failed.
Last 13 lines of output:
|====================..........| Step 20: Translating NCBI id 76524190 to NCBI Protein
|=====================.........| Step 21: Translating NCBI id 76524190 to NCBI Protein
[[1]]
NULL
Error in testFunction == result :
comparison of these types is not implemented
Calls: .testEquals
Execution halted
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/ginmappeR.Rcheck/00check.log’
for details.
ginmappeR.Rcheck/00install.out
* installing *source* package ‘ginmappeR’ ... ** this is package ‘ginmappeR’ version ‘1.7.0’ ** 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)