| Back to Long Tests report for BioC 3.20 |
This page was generated on 2025-01-25 23:55 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| 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 23/32 | Hostname | OS / Arch | CHECK | |||||||
| ginmappeR 1.2.3 (landing page) Fernando Sola
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | |||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
| merida1 | macOS 12.7.5 Monterey / 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: 1.2.3 |
| Command: /home/biocbuild/bbs-3.20-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_1.2.3.tar.gz |
| StartedAt: 2025-01-25 16:16:28 -0500 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 16:19:36 -0500 (Sat, 25 Jan 2025) |
| EllapsedTime: 188.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ginmappeR.Rcheck |
| Warnings: NA |
ginmappeR.Rcheck/tests/test_CARD.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(RUnit)
> library(ginmappeR)
> library('UniProt.ws')
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: RSQLite
> 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
Extracting database
CARD database downloaded successfully!
Located at /home/biocbuild/bbs-3.20-bioc-longtests/tmpdir/Rtmp5DUlvs/card-data
CARD database version 4.0.0 (2024-12-17)
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id 3002535 to NCBI
[1] "CAA38525.1"
[1] TRUE
> .testEquals(getCARD2NCBIProtein('ARO:3002535'), 'CAA38525.1')
Using a CARD database version downloaded on Sat 01/25/2025 16:17:55, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id ARO:3002535 to NCBI
[1] "CAA38525.1"
[1] TRUE
> .testEquals(getCARD2NCBIProtein('3003988'), 'APB03221.1')
Using a CARD database version downloaded on Sat 01/25/2025 16:17:55, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id 3003988 to NCBI
[1] "APB03221.1"
[1] TRUE
> .testEquals(getCARD2NCBIProtein(c('3003988', 'ARO:3002535')), c('APB03221.1', 'CAA38525.1'))
Using a CARD database version downloaded on Sat 01/25/2025 16:17:55, please consider updating it with updateCARDDataBase() function.
|=.............................| 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 ARO:3002535 to NCBI
[1] "APB03221.1" "CAA38525.1"
Test failed:
APB03221.1CAA38525.1 != APB03221.1CAA38525.1
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBIProtein('test'), NA)
Using a CARD database version downloaded on Sat 01/25/2025 16:17:55, please consider updating it with updateCARDDataBase() function.
|=.............................| 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
|=.............................| 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
> .testEquals(getCARD2NCBIProtein(c('test', 'test')), c(NA, NA))
Using a CARD database version downloaded on Sat 01/25/2025 16:17:55, please consider updating it with updateCARDDataBase() function.
|=.............................| 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
|=.............................| 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
|=.............................| 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
|=.............................| 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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
|=.............................| 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
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|=.............................| 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 01/25/2025 16:17:55, 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
|=.............................| 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
|=.............................| 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
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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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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
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|============..................| 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
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|==========....................| 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 01/25/2025 16:17:55, 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
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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
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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
|=.............................| 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
>
> ############################
> # 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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 01/25/2025 16:17:55, 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
41.443 0.970 92.815
ginmappeR.Rcheck/tests/test_NCBI.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(RUnit)
> library(ginmappeR)
> library('UniProt.ws')
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: RSQLite
> 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
[1] "WP_001082319"
[1] TRUE
> .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
[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
[[1]]
[1] "WP_001082319"
Error in testFunction == result :
comparison of these types is not implemented
Calls: .testEquals
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-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_1.2.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/ginmappeR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 ‘1.2.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ginmappeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 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 1: Translating from NCBI Gene to NCBI Protein
|==............................| Step 2: Translating NCBI id 76524190 to NCBI Protein
[[1]]
[1] "WP_001082319"
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-3.20-bioc-longtests/meat/ginmappeR.Rcheck/00check.log’
for details.
ginmappeR.Rcheck/00install.out
* installing *source* package ‘ginmappeR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ginmappeR)