| Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-10-05 23:55 -0400 (Sat, 05 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| 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 1.1.4 (landing page) Fernando Sola
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
|
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: 1.1.4 |
| 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_1.1.4.tar.gz |
| StartedAt: 2024-10-05 16:17:15 -0400 (Sat, 05 Oct 2024) |
| EndedAt: 2024-10-05 16:39:23 -0400 (Sat, 05 Oct 2024) |
| EllapsedTime: 1328.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ginmappeR.Rcheck |
| Warnings: 0 |
ginmappeR.Rcheck/tests/test_CARD.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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/RtmpmgkEvb/card-data
CARD database version 3.3.0 (2024-08-26)
|=.............................| Step 1: Translating from CARD to NCBI Protein
|==............................| Step 2: Accessing CARD database and translating id 3002535 to NCBI
[1] TRUE
> .testEquals(getCARD2NCBIProtein('ARO:3002535'), 'CAA38525.1')
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2NCBIProtein('3003988'), 'APB03221.1')
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2NCBIProtein(c('3003988', 'ARO:3002535')), c('APB03221.1', 'CAA38525.1'))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBIProtein('test'), NA)
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2NCBIProtein(c('test', 'test')), c(NA, NA))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2NCBIProtein(character(0)), character(0))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from CARD to NCBI Protein
[1] TRUE
> .testEquals(getCARD2NCBIProtein(c(character(0), '3002535')), c('CAA38525.1'))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
>
>
>
> ### Test getCARD2NCBINucleotide
> message('Testing getCARD2NCBINucleotide')
Testing getCARD2NCBINucleotide
> # Positive cases
> .testEquals(getCARD2NCBINucleotide('3002535'), 'X54723.1')
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2NCBINucleotide('ARO:3002535'), 'X54723.1')
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2NCBINucleotide('3003988'), 'KX531051.1')
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2NCBINucleotide(c('3003988', 'ARO:3002535')), c('KX531051.1', 'X54723.1'))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBINucleotide('test'), NA)
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
|=.............................| 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
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
[1] TRUE
> .testEquals(getCARD2NCBINucleotide(c('test','test')), c(NA,NA))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
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
|=.............................| Step 1: Accessing CARD database and translating id test to NCBI
The given ID "test" is not registered in CARD database
[1] TRUE
>
>
> ### Test getCARD2NCBIGene
> message('Testing getCARD2NCBIGene')
Testing getCARD2NCBIGene
> # Positive cases
> .testEquals(getCARD2NCBIGene('3002525'), c('886648'))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getCARD2NCBIGene(c('3002525','3002525')), c('886648', '886648'))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> # # No translation case
> # .testEquals(getCARD2NCBIGene('3005061'), NA)
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBIGene('test'), NA)
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
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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
|=.............................| 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] TRUE
>
> ############################
> # 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 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getCARD2UniProt('3002867', detailedMapping=TRUE), list('DT'=c('Q9ZIF9')))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, list
names for current but not for target
target is logical, current is list
> .testEquals(getCARD2UniProt(c('3002867', '3002867'), detailedMapping=TRUE), c('DT'=c('Q9ZIF9'),'DT'=c('Q9ZIF9')))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, character
names for current but not for target
target is logical, current is character
> # 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 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2UniProt('3006267', detailedMapping=TRUE), NA)
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2UniProt('test'), NA)
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
>
> #########################
> # 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 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getCARD2KEGG('3000938', detailedMapping = TRUE), list('DT'='ag:AAF19151'))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, list
names for current but not for target
target is logical, current is list
> .testEquals(getCARD2KEGG(c('3000938','3000938'), detailedMapping = TRUE), c('DT'=c('ag:AAF19151'), 'DT'=c('ag:AAF19151')))
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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
API(s) connection failed:
Modes: logical, character
names for current but not for target
target is logical, current is character
> # .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 10/05/2024 16:18:43, 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] TRUE
> .testEquals(getCARD2KEGG('3006267', detailedMapping = TRUE, bySimilarGenes = FALSE), NA)
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2KEGG('test'), NA)
Using a CARD database version downloaded on Sat 10/05/2024 16:18:43, 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] TRUE
>
>
>
>
>
>
>
> proc.time()
user system elapsed
35.513 1.079 86.943
ginmappeR.Rcheck/tests/test_NCBI.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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] 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] TRUE
> .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] TRUE
> # ID not registered case
> # .testEquals(getNCBIGene2NCBIProtein('test'), NA)
> # No translation case
> # .testEquals(getNCBIGene2NCBIProtein('WP_001082319'), NA)
>
> ### Test getNCBIProtein2NCBIGene
> message('Testing getNCBIProtein2NCBIGene')
Testing getNCBIProtein2NCBIGene
> # Positive case
> .testEquals(getNCBIProtein2NCBIGene('CAA79696'), c('1272'))
|=.............................| Step 1: Translating from NCBI Protein to NCBI Gene
|==............................| Step 2: Translating NCBI id CAA79696 to NCBI Gene
[1] TRUE
> .testEquals(getNCBIProtein2NCBIGene(c('CAA79696','CAA79696')), c('1272', '1272'))
|=.............................| Step 1: Translating from NCBI Protein to NCBI Gene
|==............................| Step 2: Translating NCBI id CAA79696 to NCBI Gene
|===...........................| Step 3: Translating NCBI id CAA79696 to NCBI Gene
[1] TRUE
> .testEquals(getNCBIProtein2NCBIGene('CAA79696', exhaustiveMapping = TRUE), list(c('1272')))
|=.............................| Step 1: Translating from NCBI Protein to NCBI Gene
|==............................| Step 2: Translating NCBI id CAA79696 to NCBI Gene
[1] TRUE
> .testEquals(getNCBIProtein2NCBIGene(c('CAA79696','CAA79696'), exhaustiveMapping = TRUE), list(c('1272'), c('1272')))
|=.............................| Step 1: Translating from NCBI Protein to NCBI Gene
|==............................| Step 2: Translating NCBI id CAA79696 to NCBI Gene
|===...........................| Step 3: Translating NCBI id CAA79696 to NCBI Gene
[1] TRUE
> # ID not registered case
> # .testEquals(getNCBIProtein2NCBIGene('test'), NA)
> # .testEquals(getNCBIProtein2NCBIGene(c('test', 'test'), exhaustiveMapping = TRUE), list(NULL, NULL))
>
> # No translation case
> # .testEquals(getNCBIProtein2NCBIGene('WP_011997479'), NA)
>
> ### Test getNCBIProtein2NCBINucleotide
> message('Testing getNCBIProtein2NCBINucleotide')
Testing getNCBIProtein2NCBINucleotide
> # Positive case
> .testEquals(getNCBIProtein2NCBINucleotide('AFH35853'), c('JQ394987'))
|=.............................| Step 1: Translating from NCBI Protein to NCBI Nucleotide
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/Rtmp6MahSY/card-data
CARD database version 3.3.0 (2024-08-26)
|==............................| Step 2: Translating NCBI id AFH35853 to NCBI Nucleotide
[1] TRUE
> .testEquals(getNCBIProtein2NCBINucleotide(c('AFH35853','AFH35853')), c('JQ394987', 'JQ394987'))
|=.............................| Step 1: Translating from NCBI Protein to NCBI Nucleotide
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating NCBI id AFH35853 to NCBI Nucleotide
|===...........................| Step 3: Translating NCBI id AFH35853 to NCBI Nucleotide
[1] TRUE
> .testEquals(getNCBIProtein2NCBINucleotide('AFH35853', exhaustiveMapping = TRUE), list(c('JQ394987')))
|=.............................| Step 1: Translating from NCBI Protein to NCBI Nucleotide
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating NCBI id AFH35853 to NCBI Nucleotide
[1] TRUE
> # ID not registered case
> # .testEquals(getNCBIProtein2NCBINucleotide('test'), NA)
>
> ### Test getNCBINucleotide2NCBIProtein
> message('Testing getNCBINucleotide2NCBIProtein')
Testing getNCBINucleotide2NCBIProtein
> # Positive case
> .testEquals(getNCBINucleotide2NCBIProtein('JQ394987'), c('AFH35853'))
|=.............................| Step 1: Translating from NCBI Nucleotide to NCBI Protein
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating NCBI id JQ394987 to NCBI Protein
[1] TRUE
> .testEquals(getNCBINucleotide2NCBIProtein(c('JQ394987','JQ394987')), c('AFH35853', 'AFH35853'))
|=.............................| Step 1: Translating from NCBI Nucleotide to NCBI Protein
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating NCBI id JQ394987 to NCBI Protein
|===...........................| Step 3: Translating NCBI id JQ394987 to NCBI Protein
[1] TRUE
> # ID not registered case
> # .testEquals(getNCBINucleotide2NCBIProtein('test'), NA)
>
> ### Test getNCBIGene2NCBINucleotide
> message('Testing getNCBIGene2NCBINucleotide')
Testing getNCBIGene2NCBINucleotide
> # Positive case
> .testEquals(getNCBIGene2NCBINucleotide('76524190'), c('NZ_CP059690'))
|=.............................| Step 1: Translating from NCBI Gene to NCBI Nucleotide
|==............................| Step 2: Translating NCBI id 76524190 to NCBI Nucleotide
[1] TRUE
> .testEquals(getNCBIGene2NCBINucleotide(c('76524190','76524190')), c('NZ_CP059690', 'NZ_CP059690'))
|=.............................| Step 1: Translating from NCBI Gene to NCBI Nucleotide
|==............................| Step 2: Translating NCBI id 76524190 to NCBI Nucleotide
|===...........................| Step 3: Translating NCBI id 76524190 to NCBI Nucleotide
[1] TRUE
> .testEquals(getNCBIGene2NCBINucleotide('76524190', exhaustiveMapping = TRUE), list(c('NZ_CP059690')))
|=.............................| Step 1: Translating from NCBI Gene to NCBI Nucleotide
|==............................| Step 2: Translating NCBI id 76524190 to NCBI Nucleotide
[1] TRUE
> # ID not registered case
> # .testEquals(getNCBIGene2NCBINucleotide('test'), NA)
> # No translation case
> # .testEquals(getNCBIGene2NCBINucleotide('WP_001082319'), NA)
>
> ### Test getNCBINucleotide2NCBIGene
> message('Testing getNCBINucleotide2NCBIGene')
Testing getNCBINucleotide2NCBIGene
> # Positive case
> .testEquals(getNCBINucleotide2NCBIGene('Z21488'), c('1272'))
|=.............................| Step 1: Translating from NCBI Nucleotide to NCBI Gene
|==............................| Step 2: Translating NCBI id Z21488 to NCBI Gene
[1] TRUE
> .testEquals(getNCBINucleotide2NCBIGene(c('Z21488','Z21488')), c('1272', '1272'))
|=.............................| Step 1: Translating from NCBI Nucleotide to NCBI Gene
|==............................| Step 2: Translating NCBI id Z21488 to NCBI Gene
|===...........................| Step 3: Translating NCBI id Z21488 to NCBI Gene
[1] TRUE
> .testEquals(getNCBINucleotide2NCBIGene('Z21488', exhaustiveMapping = TRUE), list(c('1272')))
|=.............................| Step 1: Translating from NCBI Nucleotide to NCBI Gene
|==............................| Step 2: Translating NCBI id Z21488 to NCBI Gene
[1] TRUE
> # ID not registered case
> # .testEquals(getNCBINucleotide2NCBIGene('test'), NA)
> # No translation case
> # .testEquals(getNCBINucleotide2NCBIGene('KF513177'), NA)
>
> #############################
> # NCBI databases to UniProt #
> #############################
>
> ### Test .getNCBI2UniProtDT
> # message('Testing .getNCBI2UniProtDT')
> # # Positive cases
> # .testEquals(.getNCBI2UniProtDT('AEJ08681'), c('F8TCS6'))
> # .testEquals(.getNCBI2UniProtDT('AEJ08681 AGQ48857.1 CAA79696'), c('F8TCS6','S5FUH0','Q12860'))
> # # .testEquals(.getNCBI2UniProtDT('CAA79696'), c('Q12860'))
> # # ID not registered case
> # .testEquals(.getNCBI2UniProtDT('test'), character(0))
>
> ### Test getNCBIIdenticalProteins
> message('Testing getNCBIIdenticalProteins')
Testing getNCBIIdenticalProteins
> # Positive cases
> .testEquals(getNCBIIdenticalProteins('AHA80958', format = 'ids'), list(c('WP_063864654.1','AHA80958.1', "EKD8974449.1", "EKD8979565.1")))
|=.............................| Step 1: Connecting to NCBI identical proteins database
|==............................| Step 2: Connecting to NCBI identical proteins database
|===...........................| Step 3: Looking for identical proteins for id AHA80958
|====..........................| Step 4: Retrieving and parsing identical proteins for id AHA80958
[1] TRUE
> .testEquals(getNCBIIdenticalProteins(c('AHA80958', 'AHA80958'), format = 'ids'), list(c('WP_063864654.1','AHA80958.1', "EKD8974449.1", "EKD8979565.1"),
+ c('WP_063864654.1','AHA80958.1', "EKD8974449.1", "EKD8979565.1")))
|=.............................| Step 1: Connecting to NCBI identical proteins database
|==............................| Step 2: Connecting to NCBI identical proteins database
|===...........................| Step 3: Looking for identical proteins for id AHA80958
|====..........................| Step 4: Retrieving and parsing identical proteins for id AHA80958
|=====.........................| Step 5: Connecting to NCBI identical proteins database
|======........................| Step 6: Looking for identical proteins for id AHA80958
|=======.......................| Step 7: Retrieving and parsing identical proteins for id AHA80958
[1] TRUE
> Sys.sleep(3)
> dummyDf <- data.frame(Id=c(45721358, 45721358, 45721358, 45721358),
+ Source=c('RefSeq','INSDC','INSDC','INSDC'),
+ Nucleotide.Accession=c('NG_050043.1','KF513177.1', 'ABJLVL010000001.1', 'ABJLVL010000113.1'),
+ Start=c(1,1, 124981, 1755),
+ Stop=c(861,861, 125841, 2615),Strand=c('+','+','-','+'),
+ Protein=c('WP_063864654.1','AHA80958.1', 'EKD8974449.1', 'EKD8979565.1'),
+ Protein.Name=c('class A beta-lactamase SHV-172','beta-lactamase SHV-172', 'class A beta-lactamase SHV-172',
+ 'class A beta-lactamase SHV-172'),
+ Organism=c('Klebsiella pneumoniae','Klebsiella pneumoniae','Klebsiella pneumoniae','Klebsiella pneumoniae'),
+ Strain=c(845332,845332, NA, NA),Assembly=c('', '','GCA_026265195.1','GCA_026265195.1'))
> .testEquals(getNCBIIdenticalProteins('AHA80958', format = 'dataframe'), dummyDf)
|=.............................| Step 1: Connecting to NCBI identical proteins database
|==............................| Step 2: Connecting to NCBI identical proteins database
|===...........................| Step 3: Looking for identical proteins for id AHA80958
|====..........................| Step 4: Retrieving and parsing identical proteins for id AHA80958
[1] TRUE
> .testEquals(getNCBIIdenticalProteins(c('AHA80958','AHA80958'), format = 'dataframe'), list(dummyDf, dummyDf))
|=.............................| Step 1: Connecting to NCBI identical proteins database
|==............................| Step 2: Connecting to NCBI identical proteins database
|===...........................| Step 3: Looking for identical proteins for id AHA80958
|====..........................| Step 4: Retrieving and parsing identical proteins for id AHA80958
|=====.........................| Step 5: Connecting to NCBI identical proteins database
|======........................| Step 6: Looking for identical proteins for id AHA80958
|=======.......................| Step 7: Retrieving and parsing identical proteins for id AHA80958
[1] TRUE
> # Incorrect format request case
> Sys.sleep(3)
> RUnit::checkException(getNCBIIdenticalProteins('AHA80958', format='test'))
|=.............................| Step 1: Connecting to NCBI identical proteins database
Error in f(...) : Incorrect format requested
[1] TRUE
> # No identical proteins found case
> # .testEquals(getNCBIIdenticalProteins('test'), NA)
>
> ### Test .getNCBI2UniProtBatch
> # message('Testing .getNCBI2UniProtBatch')
> # # Positive cases
> # dummyDf <- getNCBIIdenticalProteins('CAA76794', format = 'dataframe')
> # .testEquals(.getNCBI2UniProtBatch(dummyDf[which(dummyDf$Source=='INSDC'),] ,'EMBL-GenBank-DDBJ_CDS' ),
> # data.frame(From=c('AAC06040.1','AAN61404.1','CAA76794.1'),
> # Entry=c('O68642','Q8GP08','Q9R747')))
> # # No translations cases
> # dummyDf <- getNCBIIdenticalProteins('WP_041918279', format = 'dataframe')
> # .testEquals(.getNCBI2UniProtBatch(dummyDf[which(dummyDf$Source=='RefSeq'),] ,'RefSeq_Protein' ),
> # data.frame(From=logical(),Entry=logical()))
> # .testEquals(.getNCBI2UniProtBatch(dummyDf[which(dummyDf$Source=='INSDC'),] ,'EMBL-GenBank-DDBJ_CDS' ),
> # data.frame(From=logical(),Entry=logical()))
>
> ### Test .getNCBI2UniProtIP
> # message('Testing .getNCBI2UniProtIP')
> # # Positive case
> # .testEquals(.getNCBI2UniProtIP('WP_010896559.1'), c('Q7AJZ0','Q9RC37'))
> # # No identical proteins found case
> # .testEquals(.getNCBI2UniProtIP('test'), character(0))
> # # Identical proteins found, but no possible translation
> # .testEquals(.getNCBI2UniProtIP('AMR06225.1'), character(0))
>
> ### Test getNCBIProtein2UniProt
> message('Testing getNCBIProtein2UniProt')
Testing getNCBIProtein2UniProt
> # Positive cases
> .testEquals(getNCBIProtein2UniProt('WP_010896559.1'), c('Q7AJZ0'))
|=.............................| Step 1: Translating from NCBI Protein to UniProt
|==............................| Step 2: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 3: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 4: Connecting to NCBI identical proteins database
|=====.........................| Step 5: Looking for identical proteins for id WP_010896559.1
|======........................| Step 6: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 7: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 8: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 9: Connecting to NCBI identical proteins database
|==========....................| Step 10: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 11: Retrieving and parsing identical proteins for id WP_010896559.1
|============..................| Step 12: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=============.................| Step 13: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==============................| Step 14: Connecting to NCBI identical proteins database
|===============...............| Step 15: Looking for identical proteins for id WP_010896559.1
|================..............| Step 16: Retrieving and parsing identical proteins for id WP_010896559.1
|=================.............| Step 17: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==================............| Step 18: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===================...........| Step 19: Connecting to NCBI identical proteins database
|====================..........| Step 20: Looking for identical proteins for id WP_010896559.1
|=====================.........| Step 21: Retrieving and parsing identical proteins for id WP_010896559.1
|======================........| Step 22: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======================.......| Step 23: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========================......| Step 24: Connecting to NCBI identical proteins database
|=========================.....| Step 25: Looking for identical proteins for id WP_010896559.1
|==========================....| Step 26: Retrieving and parsing identical proteins for id WP_010896559.1
|===========================...| Step 27: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============================..| Step 28: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============================.| Step 29: Connecting to NCBI identical proteins database
|..............................| Step 30: Looking for identical proteins for id WP_010896559.1
|=.............................| Step 31: Retrieving and parsing identical proteins for id WP_010896559.1
|==............................| Step 32: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 33: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 34: Connecting to NCBI identical proteins database
|=====.........................| Step 35: Looking for identical proteins for id WP_010896559.1
|======........................| Step 36: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 37: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 38: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 39: Connecting to NCBI identical proteins database
|==========....................| Step 40: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 41: Retrieving and parsing identical proteins for id WP_010896559.1
|============..................| Step 42: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=============.................| Step 43: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==============................| Step 44: Connecting to NCBI identical proteins database
|===============...............| Step 45: Looking for identical proteins for id WP_010896559.1
|================..............| Step 46: Retrieving and parsing identical proteins for id WP_010896559.1
|=================.............| Step 47: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==================............| Step 48: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===================...........| Step 49: Connecting to NCBI identical proteins database
|====================..........| Step 50: Looking for identical proteins for id WP_010896559.1
|=====================.........| Step 51: Retrieving and parsing identical proteins for id WP_010896559.1
|======================........| Step 52: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======================.......| Step 53: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========================......| Step 54: Connecting to NCBI identical proteins database
|=========================.....| Step 55: Looking for identical proteins for id WP_010896559.1
|==========================....| Step 56: Retrieving and parsing identical proteins for id WP_010896559.1
|===========================...| Step 57: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============================..| Step 58: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============================.| Step 59: Connecting to NCBI identical proteins database
|..............................| Step 60: Looking for identical proteins for id WP_010896559.1
|=.............................| Step 61: Retrieving and parsing identical proteins for id WP_010896559.1
|==............................| Step 62: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 63: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 64: Connecting to NCBI identical proteins database
|=====.........................| Step 65: Looking for identical proteins for id WP_010896559.1
|======........................| Step 66: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 67: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 68: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 69: Connecting to NCBI identical proteins database
|==========....................| Step 70: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 71: Retrieving and parsing identical proteins for id WP_010896559.1
|============..................| Step 72: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=============.................| Step 73: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==============................| Step 74: Connecting to NCBI identical proteins database
|===============...............| Step 75: Looking for identical proteins for id WP_010896559.1
|================..............| Step 76: Retrieving and parsing identical proteins for id WP_010896559.1
|=================.............| Step 77: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==================............| Step 78: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===================...........| Step 79: Connecting to NCBI identical proteins database
|====================..........| Step 80: Looking for identical proteins for id WP_010896559.1
|=====================.........| Step 81: Retrieving and parsing identical proteins for id WP_010896559.1
|======================........| Step 82: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======================.......| Step 83: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========================......| Step 84: Connecting to NCBI identical proteins database
|=========================.....| Step 85: Looking for identical proteins for id WP_010896559.1
|==========================....| Step 86: Retrieving and parsing identical proteins for id WP_010896559.1
|===========================...| Step 87: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============================..| Step 88: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============================.| Step 89: Connecting to NCBI identical proteins database
|..............................| Step 90: Looking for identical proteins for id WP_010896559.1
|=.............................| Step 91: Retrieving and parsing identical proteins for id WP_010896559.1
|==............................| Step 92: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 93: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 94: Connecting to NCBI identical proteins database
|=====.........................| Step 95: Looking for identical proteins for id WP_010896559.1
|======........................| Step 96: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 97: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 98: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 99: Connecting to NCBI identical proteins database
|==========....................| Step 100: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 101: Retrieving and parsing identical proteins for id WP_010896559.1
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIProtein2UniProt(c('WP_010896559.1','WP_010896559.1')), c('Q7AJZ0', 'Q7AJZ0'))
|=.............................| Step 1: Translating from NCBI Protein to UniProt
|==............................| Step 2: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 3: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 4: Connecting to NCBI identical proteins database
|=====.........................| Step 5: Looking for identical proteins for id WP_010896559.1
|======........................| Step 6: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 7: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 8: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 9: Connecting to NCBI identical proteins database
|==========....................| Step 10: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 11: Retrieving and parsing identical proteins for id WP_010896559.1
|============..................| Step 12: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=============.................| Step 13: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==============................| Step 14: Connecting to NCBI identical proteins database
|===============...............| Step 15: Looking for identical proteins for id WP_010896559.1
|================..............| Step 16: Retrieving and parsing identical proteins for id WP_010896559.1
|=================.............| Step 17: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==================............| Step 18: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===================...........| Step 19: Connecting to NCBI identical proteins database
|====================..........| Step 20: Looking for identical proteins for id WP_010896559.1
|=====================.........| Step 21: Retrieving and parsing identical proteins for id WP_010896559.1
|======================........| Step 22: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======================.......| Step 23: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========================......| Step 24: Connecting to NCBI identical proteins database
|=========================.....| Step 25: Looking for identical proteins for id WP_010896559.1
|==========================....| Step 26: Retrieving and parsing identical proteins for id WP_010896559.1
|===========================...| Step 27: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============================..| Step 28: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============================.| Step 29: Connecting to NCBI identical proteins database
|..............................| Step 30: Looking for identical proteins for id WP_010896559.1
|=.............................| Step 31: Retrieving and parsing identical proteins for id WP_010896559.1
|==............................| Step 32: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 33: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 34: Connecting to NCBI identical proteins database
|=====.........................| Step 35: Looking for identical proteins for id WP_010896559.1
|======........................| Step 36: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 37: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 38: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 39: Connecting to NCBI identical proteins database
|==========....................| Step 40: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 41: Retrieving and parsing identical proteins for id WP_010896559.1
|============..................| Step 42: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=============.................| Step 43: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==============................| Step 44: Connecting to NCBI identical proteins database
|===============...............| Step 45: Looking for identical proteins for id WP_010896559.1
|================..............| Step 46: Retrieving and parsing identical proteins for id WP_010896559.1
|=================.............| Step 47: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==================............| Step 48: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===================...........| Step 49: Connecting to NCBI identical proteins database
|====================..........| Step 50: Looking for identical proteins for id WP_010896559.1
|=====================.........| Step 51: Retrieving and parsing identical proteins for id WP_010896559.1
|======================........| Step 52: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======================.......| Step 53: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========================......| Step 54: Connecting to NCBI identical proteins database
|=========================.....| Step 55: Looking for identical proteins for id WP_010896559.1
|==========================....| Step 56: Retrieving and parsing identical proteins for id WP_010896559.1
|===========================...| Step 57: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============================..| Step 58: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============================.| Step 59: Connecting to NCBI identical proteins database
|..............................| Step 60: Looking for identical proteins for id WP_010896559.1
|=.............................| Step 61: Retrieving and parsing identical proteins for id WP_010896559.1
|==............................| Step 62: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 63: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 64: Connecting to NCBI identical proteins database
|=====.........................| Step 65: Looking for identical proteins for id WP_010896559.1
|======........................| Step 66: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 67: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 68: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 69: Connecting to NCBI identical proteins database
|==========....................| Step 70: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 71: Retrieving and parsing identical proteins for id WP_010896559.1
|============..................| Step 72: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=============.................| Step 73: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==============................| Step 74: Connecting to NCBI identical proteins database
|===============...............| Step 75: Looking for identical proteins for id WP_010896559.1
|================..............| Step 76: Retrieving and parsing identical proteins for id WP_010896559.1
|=================.............| Step 77: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==================............| Step 78: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===================...........| Step 79: Connecting to NCBI identical proteins database
|====================..........| Step 80: Looking for identical proteins for id WP_010896559.1
|=====================.........| Step 81: Retrieving and parsing identical proteins for id WP_010896559.1
|======================........| Step 82: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======================.......| Step 83: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========================......| Step 84: Connecting to NCBI identical proteins database
|=========================.....| Step 85: Looking for identical proteins for id WP_010896559.1
|==========================....| Step 86: Retrieving and parsing identical proteins for id WP_010896559.1
|===========================...| Step 87: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============================..| Step 88: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============================.| Step 89: Connecting to NCBI identical proteins database
|..............................| Step 90: Looking for identical proteins for id WP_010896559.1
|=.............................| Step 91: Retrieving and parsing identical proteins for id WP_010896559.1
|==............................| Step 92: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===...........................| Step 93: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|====..........................| Step 94: Connecting to NCBI identical proteins database
|=====.........................| Step 95: Looking for identical proteins for id WP_010896559.1
|======........................| Step 96: Retrieving and parsing identical proteins for id WP_010896559.1
|=======.......................| Step 97: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|========......................| Step 98: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=========.....................| Step 99: Connecting to NCBI identical proteins database
|==========....................| Step 100: Looking for identical proteins for id WP_010896559.1
|===========...................| Step 101: Retrieving and parsing identical proteins for id WP_010896559.1
|============..................| Step 102: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=============.................| Step 103: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==============................| Step 104: Connecting to NCBI identical proteins database
|===============...............| Step 105: Looking for identical proteins for id WP_010896559.1
|================..............| Step 106: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=================.............| Step 107: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==================............| Step 108: Connecting to NCBI identical proteins database
|===================...........| Step 109: Looking for identical proteins for id WP_010896559.1
|====================..........| Step 110: Retrieving and parsing identical proteins for id WP_010896559.1
|=====================.........| Step 111: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|======================........| Step 112: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=======================.......| Step 113: Connecting to NCBI identical proteins database
|========================......| Step 114: Looking for identical proteins for id WP_010896559.1
|=========================.....| Step 115: Retrieving and parsing identical proteins for id WP_010896559.1
|==========================....| Step 116: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===========================...| Step 117: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|============================..| Step 118: Connecting to NCBI identical proteins database
|=============================.| Step 119: Looking for identical proteins for id WP_010896559.1
|..............................| Step 120: Retrieving and parsing identical proteins for id WP_010896559.1
|=.............................| Step 121: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==............................| Step 122: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===...........................| Step 123: Connecting to NCBI identical proteins database
|====..........................| Step 124: Looking for identical proteins for id WP_010896559.1
|=====.........................| Step 125: Retrieving and parsing identical proteins for id WP_010896559.1
|======........................| Step 126: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======.......................| Step 127: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========......................| Step 128: Connecting to NCBI identical proteins database
|=========.....................| Step 129: Looking for identical proteins for id WP_010896559.1
|==========....................| Step 130: Retrieving and parsing identical proteins for id WP_010896559.1
|===========...................| Step 131: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============..................| Step 132: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============.................| Step 133: Connecting to NCBI identical proteins database
|==============................| Step 134: Looking for identical proteins for id WP_010896559.1
|===============...............| Step 135: Retrieving and parsing identical proteins for id WP_010896559.1
|================..............| Step 136: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=================.............| Step 137: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==================............| Step 138: Connecting to NCBI identical proteins database
|===================...........| Step 139: Looking for identical proteins for id WP_010896559.1
|====================..........| Step 140: Retrieving and parsing identical proteins for id WP_010896559.1
|=====================.........| Step 141: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|======================........| Step 142: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=======================.......| Step 143: Connecting to NCBI identical proteins database
|========================......| Step 144: Looking for identical proteins for id WP_010896559.1
|=========================.....| Step 145: Retrieving and parsing identical proteins for id WP_010896559.1
|==========================....| Step 146: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===========================...| Step 147: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|============================..| Step 148: Connecting to NCBI identical proteins database
|=============================.| Step 149: Looking for identical proteins for id WP_010896559.1
|..............................| Step 150: Retrieving and parsing identical proteins for id WP_010896559.1
|=.............................| Step 151: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==............................| Step 152: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===...........................| Step 153: Connecting to NCBI identical proteins database
|====..........................| Step 154: Looking for identical proteins for id WP_010896559.1
|=====.........................| Step 155: Retrieving and parsing identical proteins for id WP_010896559.1
|======........................| Step 156: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======.......................| Step 157: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========......................| Step 158: Connecting to NCBI identical proteins database
|=========.....................| Step 159: Looking for identical proteins for id WP_010896559.1
|==========....................| Step 160: Retrieving and parsing identical proteins for id WP_010896559.1
|===========...................| Step 161: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============..................| Step 162: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============.................| Step 163: Connecting to NCBI identical proteins database
|==============................| Step 164: Looking for identical proteins for id WP_010896559.1
|===============...............| Step 165: Retrieving and parsing identical proteins for id WP_010896559.1
|================..............| Step 166: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=================.............| Step 167: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==================............| Step 168: Connecting to NCBI identical proteins database
|===================...........| Step 169: Looking for identical proteins for id WP_010896559.1
|====================..........| Step 170: Retrieving and parsing identical proteins for id WP_010896559.1
|=====================.........| Step 171: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|======================........| Step 172: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=======================.......| Step 173: Connecting to NCBI identical proteins database
|========================......| Step 174: Looking for identical proteins for id WP_010896559.1
|=========================.....| Step 175: Retrieving and parsing identical proteins for id WP_010896559.1
|==========================....| Step 176: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|===========================...| Step 177: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|============================..| Step 178: Connecting to NCBI identical proteins database
|=============================.| Step 179: Looking for identical proteins for id WP_010896559.1
|..............................| Step 180: Retrieving and parsing identical proteins for id WP_010896559.1
|=.............................| Step 181: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|==............................| Step 182: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|===...........................| Step 183: Connecting to NCBI identical proteins database
|====..........................| Step 184: Looking for identical proteins for id WP_010896559.1
|=====.........................| Step 185: Retrieving and parsing identical proteins for id WP_010896559.1
|======........................| Step 186: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=======.......................| Step 187: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|========......................| Step 188: Connecting to NCBI identical proteins database
|=========.....................| Step 189: Looking for identical proteins for id WP_010896559.1
|==========....................| Step 190: Retrieving and parsing identical proteins for id WP_010896559.1
|===========...................| Step 191: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|============..................| Step 192: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|=============.................| Step 193: Connecting to NCBI identical proteins database
|==============................| Step 194: Looking for identical proteins for id WP_010896559.1
|===============...............| Step 195: Retrieving and parsing identical proteins for id WP_010896559.1
|================..............| Step 196: Trying to get a direct translation for NCBI id WP_010896559.1 to UniProt
|=================.............| Step 197: Translating NCBI id WP_010896559.1 to UniProt through identical proteins strategy
|==================............| Step 198: Connecting to NCBI identical proteins database
|===================...........| Step 199: Looking for identical proteins for id WP_010896559.1
|====================..........| Step 200: Retrieving and parsing identical proteins for id WP_010896559.1
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> # .testEquals(getNCBIProtein2UniProt('WP_010896559.1', exhaustiveMapping = TRUE), c('Q7AJZ0','Q9RC37'))
> # .testEquals(getNCBIProtein2UniProt('WP_010896559.1', exhaustiveMapping = TRUE, detailedMapping = TRUE), list('DT'=c('Q7AJZ0', 'Q9RC37'),'1.0'=c('Q7AJZ0', 'Q9RC37')))
> # .testEquals(getNCBIProtein2UniProt('WP_010896559.1', exhaustiveMapping = FALSE, detailedMapping = TRUE), list('DT'=c('Q7AJZ0')))
> # .testEquals(getNCBIProtein2UniProt('WP_039189232.1'), c('A0A2A2MC99'))
> # .testEquals(getNCBIProtein2UniProt('WP_039189232.1', exhaustiveMapping = TRUE, byIdenticalProteins = FALSE), c('A0A2A2MC99','Q9K351'))
> # .testEquals(getNCBIProtein2UniProt('WP_039189232.1', byIdenticalProteins = FALSE), c('A0A2A2MC99'))
> # No translation case
> # .testEquals(getNCBIProtein2UniProt('WP_188331862.1'), NA)
> # .testEquals(getNCBIProtein2UniProt('WP_188331862.1', detailedMapping = TRUE), NA)
> # NCBI Protein ID not registered case
> # .testEquals(getNCBIProtein2UniProt('test'), NA)
>
> ### Test getNCBINucleotide2UniProt
> message('Testing getNCBINucleotide2UniProt')
Testing getNCBINucleotide2UniProt
> # Positive case
> .testEquals(getNCBINucleotide2UniProt('AY536519'), c('Q6QJ79'))
|=.............................| Step 1: Translating from NCBI Nucleotide to UniProt
|==............................| Step 2: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 3: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 4: Connecting to NCBI identical proteins database
|=====.........................| Step 5: Looking for identical proteins for id AY536519
|======........................| Step 6: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 7: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 8: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 9: Connecting to NCBI identical proteins database
|==========....................| Step 10: Looking for identical proteins for id AY536519
|===========...................| Step 11: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 12: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 13: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 14: Connecting to NCBI identical proteins database
|===============...............| Step 15: Looking for identical proteins for id AY536519
|================..............| Step 16: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 17: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 18: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 19: Connecting to NCBI identical proteins database
|====================..........| Step 20: Looking for identical proteins for id AY536519
|=====================.........| Step 21: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 22: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 23: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 24: Connecting to NCBI identical proteins database
|=========================.....| Step 25: Looking for identical proteins for id AY536519
|==========================....| Step 26: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 27: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 28: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 29: Connecting to NCBI identical proteins database
|..............................| Step 30: Looking for identical proteins for id AY536519
|=.............................| Step 31: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 32: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 33: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 34: Connecting to NCBI identical proteins database
|=====.........................| Step 35: Looking for identical proteins for id AY536519
|======........................| Step 36: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 37: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 38: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 39: Connecting to NCBI identical proteins database
|==========....................| Step 40: Looking for identical proteins for id AY536519
|===========...................| Step 41: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 42: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 43: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 44: Connecting to NCBI identical proteins database
|===============...............| Step 45: Looking for identical proteins for id AY536519
|================..............| Step 46: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 47: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 48: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 49: Connecting to NCBI identical proteins database
|====================..........| Step 50: Looking for identical proteins for id AY536519
|=====================.........| Step 51: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 52: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 53: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 54: Connecting to NCBI identical proteins database
|=========================.....| Step 55: Looking for identical proteins for id AY536519
|==========================....| Step 56: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 57: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 58: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 59: Connecting to NCBI identical proteins database
|..............................| Step 60: Looking for identical proteins for id AY536519
|=.............................| Step 61: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 62: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 63: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 64: Connecting to NCBI identical proteins database
|=====.........................| Step 65: Looking for identical proteins for id AY536519
|======........................| Step 66: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 67: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 68: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 69: Connecting to NCBI identical proteins database
|==========....................| Step 70: Looking for identical proteins for id AY536519
|===========...................| Step 71: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 72: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 73: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 74: Connecting to NCBI identical proteins database
|===============...............| Step 75: Looking for identical proteins for id AY536519
|================..............| Step 76: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 77: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 78: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 79: Connecting to NCBI identical proteins database
|====================..........| Step 80: Looking for identical proteins for id AY536519
|=====================.........| Step 81: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 82: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 83: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 84: Connecting to NCBI identical proteins database
|=========================.....| Step 85: Looking for identical proteins for id AY536519
|==========================....| Step 86: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 87: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 88: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 89: Connecting to NCBI identical proteins database
|..............................| Step 90: Looking for identical proteins for id AY536519
|=.............................| Step 91: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 92: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 93: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 94: Connecting to NCBI identical proteins database
|=====.........................| Step 95: Looking for identical proteins for id AY536519
|======........................| Step 96: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 97: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 98: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 99: Connecting to NCBI identical proteins database
|==========....................| Step 100: Looking for identical proteins for id AY536519
|===========...................| Step 101: Retrieving and parsing identical proteins for id AY536519
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBINucleotide2UniProt(c('AY536519', 'AY536519')), c('Q6QJ79','Q6QJ79'))
|=.............................| Step 1: Translating from NCBI Nucleotide to UniProt
|==............................| Step 2: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 3: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 4: Connecting to NCBI identical proteins database
|=====.........................| Step 5: Looking for identical proteins for id AY536519
|======........................| Step 6: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 7: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 8: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 9: Connecting to NCBI identical proteins database
|==========....................| Step 10: Looking for identical proteins for id AY536519
|===========...................| Step 11: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 12: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 13: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 14: Connecting to NCBI identical proteins database
|===============...............| Step 15: Looking for identical proteins for id AY536519
|================..............| Step 16: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 17: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 18: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 19: Connecting to NCBI identical proteins database
|====================..........| Step 20: Looking for identical proteins for id AY536519
|=====================.........| Step 21: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 22: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 23: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 24: Connecting to NCBI identical proteins database
|=========================.....| Step 25: Looking for identical proteins for id AY536519
|==========================....| Step 26: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 27: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 28: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 29: Connecting to NCBI identical proteins database
|..............................| Step 30: Looking for identical proteins for id AY536519
|=.............................| Step 31: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 32: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 33: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 34: Connecting to NCBI identical proteins database
|=====.........................| Step 35: Looking for identical proteins for id AY536519
|======........................| Step 36: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 37: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 38: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 39: Connecting to NCBI identical proteins database
|==========....................| Step 40: Looking for identical proteins for id AY536519
|===========...................| Step 41: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 42: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 43: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 44: Connecting to NCBI identical proteins database
|===============...............| Step 45: Looking for identical proteins for id AY536519
|================..............| Step 46: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 47: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 48: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 49: Connecting to NCBI identical proteins database
|====================..........| Step 50: Looking for identical proteins for id AY536519
|=====================.........| Step 51: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 52: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 53: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 54: Connecting to NCBI identical proteins database
|=========================.....| Step 55: Looking for identical proteins for id AY536519
|==========================....| Step 56: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 57: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 58: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 59: Connecting to NCBI identical proteins database
|..............................| Step 60: Looking for identical proteins for id AY536519
|=.............................| Step 61: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 62: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 63: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 64: Connecting to NCBI identical proteins database
|=====.........................| Step 65: Looking for identical proteins for id AY536519
|======........................| Step 66: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 67: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 68: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 69: Connecting to NCBI identical proteins database
|==========....................| Step 70: Looking for identical proteins for id AY536519
|===========...................| Step 71: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 72: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 73: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 74: Connecting to NCBI identical proteins database
|===============...............| Step 75: Looking for identical proteins for id AY536519
|================..............| Step 76: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 77: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 78: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 79: Connecting to NCBI identical proteins database
|====================..........| Step 80: Looking for identical proteins for id AY536519
|=====================.........| Step 81: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 82: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 83: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 84: Connecting to NCBI identical proteins database
|=========================.....| Step 85: Looking for identical proteins for id AY536519
|==========================....| Step 86: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 87: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 88: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 89: Connecting to NCBI identical proteins database
|..............................| Step 90: Looking for identical proteins for id AY536519
|=.............................| Step 91: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 92: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 93: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 94: Connecting to NCBI identical proteins database
|=====.........................| Step 95: Looking for identical proteins for id AY536519
|======........................| Step 96: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 97: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 98: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 99: Connecting to NCBI identical proteins database
|==========....................| Step 100: Looking for identical proteins for id AY536519
|===========...................| Step 101: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 102: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 103: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 104: Connecting to NCBI identical proteins database
|===============...............| Step 105: Looking for identical proteins for id AY536519
|================..............| Step 106: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 107: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 108: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 109: Connecting to NCBI identical proteins database
|====================..........| Step 110: Looking for identical proteins for id AY536519
|=====================.........| Step 111: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 112: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 113: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 114: Connecting to NCBI identical proteins database
|=========================.....| Step 115: Looking for identical proteins for id AY536519
|==========================....| Step 116: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 117: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 118: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 119: Connecting to NCBI identical proteins database
|..............................| Step 120: Looking for identical proteins for id AY536519
|=.............................| Step 121: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 122: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 123: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 124: Connecting to NCBI identical proteins database
|=====.........................| Step 125: Looking for identical proteins for id AY536519
|======........................| Step 126: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 127: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 128: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 129: Connecting to NCBI identical proteins database
|==========....................| Step 130: Looking for identical proteins for id AY536519
|===========...................| Step 131: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 132: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 133: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 134: Connecting to NCBI identical proteins database
|===============...............| Step 135: Looking for identical proteins for id AY536519
|================..............| Step 136: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 137: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 138: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 139: Connecting to NCBI identical proteins database
|====================..........| Step 140: Looking for identical proteins for id AY536519
|=====================.........| Step 141: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 142: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 143: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 144: Connecting to NCBI identical proteins database
|=========================.....| Step 145: Looking for identical proteins for id AY536519
|==========================....| Step 146: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 147: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 148: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 149: Connecting to NCBI identical proteins database
|..............................| Step 150: Looking for identical proteins for id AY536519
|=.............................| Step 151: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 152: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 153: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 154: Connecting to NCBI identical proteins database
|=====.........................| Step 155: Looking for identical proteins for id AY536519
|======........................| Step 156: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 157: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 158: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 159: Connecting to NCBI identical proteins database
|==========....................| Step 160: Looking for identical proteins for id AY536519
|===========...................| Step 161: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 162: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 163: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 164: Connecting to NCBI identical proteins database
|===============...............| Step 165: Looking for identical proteins for id AY536519
|================..............| Step 166: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 167: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 168: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 169: Connecting to NCBI identical proteins database
|====================..........| Step 170: Looking for identical proteins for id AY536519
|=====================.........| Step 171: Retrieving and parsing identical proteins for id AY536519
|======================........| Step 172: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=======================.......| Step 173: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|========================......| Step 174: Connecting to NCBI identical proteins database
|=========================.....| Step 175: Looking for identical proteins for id AY536519
|==========================....| Step 176: Retrieving and parsing identical proteins for id AY536519
|===========================...| Step 177: Trying to get a direct translation for NCBI id AY536519 to UniProt
|============================..| Step 178: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=============================.| Step 179: Connecting to NCBI identical proteins database
|..............................| Step 180: Looking for identical proteins for id AY536519
|=.............................| Step 181: Retrieving and parsing identical proteins for id AY536519
|==............................| Step 182: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 183: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 184: Connecting to NCBI identical proteins database
|=====.........................| Step 185: Looking for identical proteins for id AY536519
|======........................| Step 186: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 187: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 188: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 189: Connecting to NCBI identical proteins database
|==========....................| Step 190: Looking for identical proteins for id AY536519
|===========...................| Step 191: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 192: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 193: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 194: Connecting to NCBI identical proteins database
|===============...............| Step 195: Looking for identical proteins for id AY536519
|================..............| Step 196: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 197: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 198: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 199: Connecting to NCBI identical proteins database
|====================..........| Step 200: Looking for identical proteins for id AY536519
|=====================.........| Step 201: Retrieving and parsing identical proteins for id AY536519
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBINucleotide2UniProt('AY536519', detailedMapping = TRUE), list('1.0'=c('Q6QJ79')))
|=.............................| Step 1: Translating from NCBI Nucleotide to UniProt
|==............................| Step 2: Trying to get a direct translation for NCBI id AY536519 to UniProt
|===...........................| Step 3: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|====..........................| Step 4: Connecting to NCBI identical proteins database
|=====.........................| Step 5: Looking for identical proteins for id AY536519
|======........................| Step 6: Retrieving and parsing identical proteins for id AY536519
|=======.......................| Step 7: Trying to get a direct translation for NCBI id AY536519 to UniProt
|========......................| Step 8: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|=========.....................| Step 9: Connecting to NCBI identical proteins database
|==========....................| Step 10: Looking for identical proteins for id AY536519
|===========...................| Step 11: Retrieving and parsing identical proteins for id AY536519
|============..................| Step 12: Trying to get a direct translation for NCBI id AY536519 to UniProt
|=============.................| Step 13: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|==============................| Step 14: Connecting to NCBI identical proteins database
|===============...............| Step 15: Looking for identical proteins for id AY536519
|================..............| Step 16: Retrieving and parsing identical proteins for id AY536519
|=================.............| Step 17: Trying to get a direct translation for NCBI id AY536519 to UniProt
|==================............| Step 18: Translating NCBI id AY536519 to UniProt through identical proteins strategy
|===================...........| Step 19: Connecting to NCBI identical proteins database
|====================..........| Step 20: Looking for identical proteins for id AY536519
|=====================.........| Step 21: Retrieving and parsing identical proteins for id AY536519
API(s) connection failed:
Modes: logical, list
names for current but not for target
target is logical, current is list
> # .testEquals(getNCBINucleotide2UniProt('AY536519', exhaustiveMapping = TRUE), c('Q6QJ79','A0A7G1KXU2','A0A6I4WTI5','D0UY02'))
> # .testEquals(getNCBINucleotide2UniProt('AY536519', exhaustiveMapping = TRUE, detailedMapping = TRUE), list('1.0'=c('Q6QJ79','A0A7G1KXU2','A0A6I4WTI5','D0UY02')))
> # .testEquals(getNCBINucleotide2UniProt('AY536519', byIdenticalProteins = FALSE), character(0))
> # No translation case
> # .testEquals(getNCBINucleotide2UniProt('Z21488'), NA)
> # .testEquals(getNCBINucleotide2UniProt('Z21488', detailedMapping = TRUE), NA)
> # NCBI Nucleotide ID not registered case
> # .testEquals(getNCBINucleotide2UniProt('test'), NA)
>
> ### Test getNCBIGene2UniProt
> message('Testing getNCBIGene2UniProt')
Testing getNCBIGene2UniProt
> # Positive case
> .testEquals(getNCBIGene2UniProt('76524190'), c('A0A1W6DPG3'))
|=.............................| Step 1: Translating from NCBI Gene to UniProt
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIGene2UniProt(c('76524190','76524190')), c('A0A1W6DPG3','A0A1W6DPG3'))
|=.............................| Step 1: Translating from NCBI Gene to UniProt
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIGene2UniProt('76524190', detailedMapping = TRUE), list('1.0'=c('A0A1W6DPG3')))
|=.............................| Step 1: Translating from NCBI Gene to UniProt
API(s) connection failed:
Modes: logical, list
names for current but not for target
target is logical, current is list
> .testEquals(getNCBIGene2UniProt('76524190', byIdenticalProteins = FALSE), NA)
|=.............................| Step 1: Translating from NCBI Gene to UniProt
[1] TRUE
> # No translation case
> # .testEquals(getNCBIGene2UniProt('69412715'), NA)
> # .testEquals(getNCBIGene2UniProt('69412715', detailedMapping = TRUE), NA)
> # NCBI Gene ID not registered case
> # .testEquals(getNCBIGene2UniProt('test'), NA)
>
> ##########################
> # NCBI databases to KEGG #
> ##########################
>
> ### Test .getNCBI2KEGGDT
> # message('Testing .getNCBI2KEGGDT')
> # # Positive cases
> # .testEquals(.getNCBI2KEGGDT('AAC44793.1'), c('ag:AAC44793'))
> # .testEquals(.getNCBI2KEGGDT('AAO66446.1'), c('ag:AAO66446'))
> # .testEquals(.getNCBI2KEGGDT('NP_059345'), c('hsa:10458'))
> # .testEquals(.getNCBI2KEGGDT('AAG58814'), c('ece:Z5100'))
> # # No translation case
> # .testEquals(.getNCBI2KEGGDT('CAD69003.1'), character(0))
>
> ### Test .getNCBI2KEGGTUP
> # message('Testing .getNCBI2KEGGTUP')
> # # Positive cases
> # # .testEquals(.getNCBI2KEGGTUP('WP_010896559.1', 'protein', exhaustiveMapping = TRUE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
> # # list('DT'=c('bha:BH0380'), '0.5'=c("ag:AAA22599","vpn:A21D_00889","ag:AAP74657","ddh:Desde_1644","bcl:ABC3508","scib:HUG20_05815","bha:BH0380"),
> # # '1.0'=c('bha:BH0380'), '0.9'=c('bha:BH0380')))
> # # .testEquals(.getNCBI2KEGGTUP('WP_010896559.1', 'protein', exhaustiveMapping = TRUE, detailedMapping = FALSE, byIdenticalProteins = FALSE),
> # # c("bha:BH0380","ag:AAA22599","vpn:A21D_00889","ag:AAP74657","ddh:Desde_1644","bcl:ABC3508","scib:HUG20_05815"))
> # .testEquals(.getNCBI2KEGGTUP('WP_010896559.1', 'protein', exhaustiveMapping = FALSE, detailedMapping = FALSE, byIdenticalProteins = FALSE),
> # c("bha:BH0380"))
> # .testEquals(.getNCBI2KEGGTUP('WP_010896559.1', 'protein', exhaustiveMapping = FALSE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
> # list('DT'=c("bha:BH0380")))
> # # No translation case
> # .testEquals(.getNCBI2KEGGTUP('WP_188331862.1', 'protein'), character(0))
> # .testEquals(.getNCBI2KEGGTUP('WP_188331862.1', 'protein', detailedMapping = TRUE), list())
>
>
> ### Test getNCBIProtein2KEGG
> message('Testing getNCBIProtein2KEGG')
Testing getNCBIProtein2KEGG
> # Positive cases
> .testEquals(getNCBIProtein2KEGG('WP_010896559.1', exhaustiveMapping = FALSE, detailedMapping = FALSE, byIdenticalProteins = FALSE),
+ c("bha:BH0380"))
|=.............................| Step 1: Translating from NCBI Protein to KEGG
|==............................| Step 2: Translating from NCBI Protein to KEGG
|===...........................| Step 3: Translating from NCBI Protein to KEGG
|====..........................| Step 4: Translating from NCBI Protein to KEGG
|=====.........................| Step 5: Translating from NCBI Protein to KEGG
|======........................| Step 6: Translating from NCBI Protein to KEGG
|=======.......................| Step 7: Translating from NCBI Protein to KEGG
|========......................| Step 8: Translating from NCBI Protein to KEGG
|=========.....................| Step 9: Translating from NCBI Protein to KEGG
|==========....................| Step 10: Translating from NCBI Protein to KEGG
|===========...................| Step 11: Translating from NCBI Protein to KEGG
|============..................| Step 12: Translating from NCBI Protein to KEGG
|=============.................| Step 13: Translating from NCBI Protein to KEGG
|==============................| Step 14: Translating from NCBI Protein to KEGG
|===============...............| Step 15: Translating from NCBI Protein to KEGG
|================..............| Step 16: Translating from NCBI Protein to KEGG
|=================.............| Step 17: Translating from NCBI Protein to KEGG
|==================............| Step 18: Translating from NCBI Protein to KEGG
|===================...........| Step 19: Translating from NCBI Protein to KEGG
|====================..........| Step 20: Translating from NCBI Protein to KEGG
|=====================.........| Step 21: Translating from NCBI Protein to KEGG
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIProtein2KEGG(c('WP_010896559.1','WP_010896559.1'), exhaustiveMapping = FALSE, detailedMapping = FALSE, byIdenticalProteins = FALSE),
+ c("bha:BH0380", "bha:BH0380"))
|=.............................| Step 1: Translating from NCBI Protein to KEGG
|==............................| Step 2: Translating from NCBI Protein to KEGG
|===...........................| Step 3: Translating from NCBI Protein to KEGG
|====..........................| Step 4: Translating from NCBI Protein to KEGG
|=====.........................| Step 5: Translating from NCBI Protein to KEGG
|======........................| Step 6: Translating from NCBI Protein to KEGG
|=======.......................| Step 7: Translating from NCBI Protein to KEGG
|========......................| Step 8: Translating from NCBI Protein to KEGG
|=========.....................| Step 9: Translating from NCBI Protein to KEGG
|==========....................| Step 10: Translating from NCBI Protein to KEGG
|===========...................| Step 11: Translating from NCBI Protein to KEGG
|============..................| Step 12: Translating from NCBI Protein to KEGG
|=============.................| Step 13: Translating from NCBI Protein to KEGG
|==============................| Step 14: Translating from NCBI Protein to KEGG
|===============...............| Step 15: Translating from NCBI Protein to KEGG
|================..............| Step 16: Translating from NCBI Protein to KEGG
|=================.............| Step 17: Translating from NCBI Protein to KEGG
|==================............| Step 18: Translating from NCBI Protein to KEGG
|===================...........| Step 19: Translating from NCBI Protein to KEGG
|====================..........| Step 20: Translating from NCBI Protein to KEGG
|=====================.........| Step 21: Translating from NCBI Protein to KEGG
|======================........| Step 22: Translating from NCBI Protein to KEGG
|=======================.......| Step 23: Translating from NCBI Protein to KEGG
|========================......| Step 24: Translating from NCBI Protein to KEGG
|=========================.....| Step 25: Translating from NCBI Protein to KEGG
|==========================....| Step 26: Translating from NCBI Protein to KEGG
|===========================...| Step 27: Translating from NCBI Protein to KEGG
|============================..| Step 28: Translating from NCBI Protein to KEGG
|=============================.| Step 29: Translating from NCBI Protein to KEGG
|..............................| Step 30: Translating from NCBI Protein to KEGG
|=.............................| Step 31: Translating from NCBI Protein to KEGG
|==............................| Step 32: Translating from NCBI Protein to KEGG
|===...........................| Step 33: Translating from NCBI Protein to KEGG
|====..........................| Step 34: Translating from NCBI Protein to KEGG
|=====.........................| Step 35: Translating from NCBI Protein to KEGG
|======........................| Step 36: Translating from NCBI Protein to KEGG
|=======.......................| Step 37: Translating from NCBI Protein to KEGG
|========......................| Step 38: Translating from NCBI Protein to KEGG
|=========.....................| Step 39: Translating from NCBI Protein to KEGG
|==========....................| Step 40: Translating from NCBI Protein to KEGG
|===========...................| Step 41: Translating from NCBI Protein to KEGG
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIProtein2KEGG('WP_010896559.1', exhaustiveMapping = FALSE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
+ list('DT'=c("bha:BH0380")))
|=.............................| Step 1: Translating from NCBI Protein to KEGG
|==............................| Step 2: Translating from NCBI Protein to KEGG
|===...........................| Step 3: Translating from NCBI Protein to KEGG
|====..........................| Step 4: Translating from NCBI Protein to KEGG
|=====.........................| Step 5: Translating from NCBI Protein to KEGG
|======........................| Step 6: Translating from NCBI Protein to KEGG
|=======.......................| Step 7: Translating from NCBI Protein to KEGG
|========......................| Step 8: Translating from NCBI Protein to KEGG
|=========.....................| Step 9: Translating from NCBI Protein to KEGG
|==========....................| Step 10: Translating from NCBI Protein to KEGG
|===========...................| Step 11: Translating from NCBI Protein to KEGG
|============..................| Step 12: Translating from NCBI Protein to KEGG
|=============.................| Step 13: Translating from NCBI Protein to KEGG
|==============................| Step 14: Translating from NCBI Protein to KEGG
|===============...............| Step 15: Translating from NCBI Protein to KEGG
|================..............| Step 16: Translating from NCBI Protein to KEGG
|=================.............| Step 17: Translating from NCBI Protein to KEGG
|==================............| Step 18: Translating from NCBI Protein to KEGG
|===================...........| Step 19: Translating from NCBI Protein to KEGG
|====================..........| Step 20: Translating from NCBI Protein to KEGG
|=====================.........| Step 21: Translating from NCBI Protein to KEGG
API(s) connection failed:
Modes: logical, list
names for current but not for target
target is logical, current is list
> .testEquals(getNCBIProtein2KEGG(c('WP_010896559.1','WP_010896559.1'), exhaustiveMapping = FALSE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
+ c('DT'=c("bha:BH0380"),'DT'=c("bha:BH0380")))
|=.............................| Step 1: Translating from NCBI Protein to KEGG
|==............................| Step 2: Translating from NCBI Protein to KEGG
|===...........................| Step 3: Translating from NCBI Protein to KEGG
|====..........................| Step 4: Translating from NCBI Protein to KEGG
|=====.........................| Step 5: Translating from NCBI Protein to KEGG
|======........................| Step 6: Translating from NCBI Protein to KEGG
|=======.......................| Step 7: Translating from NCBI Protein to KEGG
|========......................| Step 8: Translating from NCBI Protein to KEGG
|=========.....................| Step 9: Translating from NCBI Protein to KEGG
|==========....................| Step 10: Translating from NCBI Protein to KEGG
|===========...................| Step 11: Translating from NCBI Protein to KEGG
|============..................| Step 12: Translating from NCBI Protein to KEGG
|=============.................| Step 13: Translating from NCBI Protein to KEGG
|==============................| Step 14: Translating from NCBI Protein to KEGG
|===============...............| Step 15: Translating from NCBI Protein to KEGG
|================..............| Step 16: Translating from NCBI Protein to KEGG
|=================.............| Step 17: Translating from NCBI Protein to KEGG
|==================............| Step 18: Translating from NCBI Protein to KEGG
|===================...........| Step 19: Translating from NCBI Protein to KEGG
|====================..........| Step 20: Translating from NCBI Protein to KEGG
|=====================.........| Step 21: Translating from NCBI Protein to KEGG
|======================........| Step 22: Translating from NCBI Protein to KEGG
|=======================.......| Step 23: Translating from NCBI Protein to KEGG
|========================......| Step 24: Translating from NCBI Protein to KEGG
|=========================.....| Step 25: Translating from NCBI Protein to KEGG
|==========================....| Step 26: Translating from NCBI Protein to KEGG
|===========================...| Step 27: Translating from NCBI Protein to KEGG
|============================..| Step 28: Translating from NCBI Protein to KEGG
|=============================.| Step 29: Translating from NCBI Protein to KEGG
|..............................| Step 30: Translating from NCBI Protein to KEGG
|=.............................| Step 31: Translating from NCBI Protein to KEGG
|==............................| Step 32: Translating from NCBI Protein to KEGG
|===...........................| Step 33: Translating from NCBI Protein to KEGG
|====..........................| Step 34: Translating from NCBI Protein to KEGG
|=====.........................| Step 35: Translating from NCBI Protein to KEGG
|======........................| Step 36: Translating from NCBI Protein to KEGG
|=======.......................| Step 37: Translating from NCBI Protein to KEGG
|========......................| Step 38: Translating from NCBI Protein to KEGG
|=========.....................| Step 39: Translating from NCBI Protein to KEGG
|==========....................| Step 40: Translating from NCBI Protein to KEGG
|===========...................| Step 41: Translating from NCBI Protein to KEGG
API(s) connection failed:
Modes: logical, character
names for current but not for target
target is logical, current is character
> # .testEquals(getNCBIProtein2KEGG('WP_010896559.1',exhaustiveMapping = TRUE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
> # list('DT'=c('bha:BH0380'), '0.5'=c("ag:AAA22599","vpn:A21D_00889","ag:AAP74657","ddh:Desde_1644","bcl:ABC3508","scib:HUG20_05815","bha:BH0380"),
> # '1.0'=c('bha:BH0380'), '0.9'=c('bha:BH0380')))
> # .testEquals(getNCBIProtein2KEGG('WP_010896559.1',exhaustiveMapping = TRUE, detailedMapping = FALSE, byIdenticalProteins = FALSE),
> # c("bha:BH0380","ag:AAA22599","vpn:A21D_00889","ag:AAP74657","ddh:Desde_1644","bcl:ABC3508","scib:HUG20_05815"))
> # No translation case
> # .testEquals(getNCBIProtein2KEGG('WP_188331862.1'), NA)
> # .testEquals(getNCBIProtein2KEGG('WP_188331862.1', detailedMapping = TRUE), NA)
> # NCBI Protein ID not registered case
> # .testEquals(getNCBIProtein2KEGG('test'), NA)
>
> ### Test getNCBINucleotide2KEGG
> message('Testing getNCBINucleotide2KEGG')
Testing getNCBINucleotide2KEGG
> # Positive cases
> .testEquals(getNCBINucleotide2KEGG('AY536519', exhaustiveMapping = FALSE, detailedMapping = FALSE),
+ c("ag:AAS48620"))
|=.............................| Step 1: Translating from NCBI Nucleotide to KEGG
|==............................| Step 2: Translating from NCBI Nucleotide to KEGG
|===...........................| Step 3: Translating from NCBI Nucleotide to KEGG
|====..........................| Step 4: Translating from NCBI Nucleotide to KEGG
|=====.........................| Step 5: Translating from NCBI Nucleotide to KEGG
|======........................| Step 6: Translating from NCBI Nucleotide to KEGG
|=======.......................| Step 7: Translating from NCBI Nucleotide to KEGG
|========......................| Step 8: Translating from NCBI Nucleotide to KEGG
|=========.....................| Step 9: Translating from NCBI Nucleotide to KEGG
|==========....................| Step 10: Translating from NCBI Nucleotide to KEGG
|===========...................| Step 11: Translating from NCBI Nucleotide to KEGG
|============..................| Step 12: Translating from NCBI Nucleotide to KEGG
|=============.................| Step 13: Translating from NCBI Nucleotide to KEGG
|==============................| Step 14: Translating from NCBI Nucleotide to KEGG
|===============...............| Step 15: Translating from NCBI Nucleotide to KEGG
|================..............| Step 16: Translating from NCBI Nucleotide to KEGG
|=================.............| Step 17: Translating from NCBI Nucleotide to KEGG
|==================............| Step 18: Translating from NCBI Nucleotide to KEGG
|===================...........| Step 19: Translating from NCBI Nucleotide to KEGG
|====================..........| Step 20: Translating from NCBI Nucleotide to KEGG
|=====================.........| Step 21: Translating from NCBI Nucleotide to KEGG
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBINucleotide2KEGG(c('AY536519','AY536519'), exhaustiveMapping = FALSE, detailedMapping = FALSE),
+ c("ag:AAS48620", "ag:AAS48620"))
|=.............................| Step 1: Translating from NCBI Nucleotide to KEGG
|==............................| Step 2: Translating from NCBI Nucleotide to KEGG
|===...........................| Step 3: Translating from NCBI Nucleotide to KEGG
|====..........................| Step 4: Translating from NCBI Nucleotide to KEGG
|=====.........................| Step 5: Translating from NCBI Nucleotide to KEGG
|======........................| Step 6: Translating from NCBI Nucleotide to KEGG
|=======.......................| Step 7: Translating from NCBI Nucleotide to KEGG
|========......................| Step 8: Translating from NCBI Nucleotide to KEGG
|=========.....................| Step 9: Translating from NCBI Nucleotide to KEGG
|==========....................| Step 10: Translating from NCBI Nucleotide to KEGG
|===========...................| Step 11: Translating from NCBI Nucleotide to KEGG
|============..................| Step 12: Translating from NCBI Nucleotide to KEGG
|=============.................| Step 13: Translating from NCBI Nucleotide to KEGG
|==============................| Step 14: Translating from NCBI Nucleotide to KEGG
|===============...............| Step 15: Translating from NCBI Nucleotide to KEGG
|================..............| Step 16: Translating from NCBI Nucleotide to KEGG
|=================.............| Step 17: Translating from NCBI Nucleotide to KEGG
|==================............| Step 18: Translating from NCBI Nucleotide to KEGG
|===================...........| Step 19: Translating from NCBI Nucleotide to KEGG
|====================..........| Step 20: Translating from NCBI Nucleotide to KEGG
|=====================.........| Step 21: Translating from NCBI Nucleotide to KEGG
|======================........| Step 22: Translating from NCBI Nucleotide to KEGG
|=======================.......| Step 23: Translating from NCBI Nucleotide to KEGG
|========================......| Step 24: Translating from NCBI Nucleotide to KEGG
|=========================.....| Step 25: Translating from NCBI Nucleotide to KEGG
|==========================....| Step 26: Translating from NCBI Nucleotide to KEGG
|===========================...| Step 27: Translating from NCBI Nucleotide to KEGG
|============================..| Step 28: Translating from NCBI Nucleotide to KEGG
|=============================.| Step 29: Translating from NCBI Nucleotide to KEGG
|..............................| Step 30: Translating from NCBI Nucleotide to KEGG
|=.............................| Step 31: Translating from NCBI Nucleotide to KEGG
|==............................| Step 32: Translating from NCBI Nucleotide to KEGG
|===...........................| Step 33: Translating from NCBI Nucleotide to KEGG
|====..........................| Step 34: Translating from NCBI Nucleotide to KEGG
|=====.........................| Step 35: Translating from NCBI Nucleotide to KEGG
|======........................| Step 36: Translating from NCBI Nucleotide to KEGG
|=======.......................| Step 37: Translating from NCBI Nucleotide to KEGG
|========......................| Step 38: Translating from NCBI Nucleotide to KEGG
|=========.....................| Step 39: Translating from NCBI Nucleotide to KEGG
|==========....................| Step 40: Translating from NCBI Nucleotide to KEGG
|===========...................| Step 41: Translating from NCBI Nucleotide to KEGG
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> # .testEquals(getNCBINucleotide2KEGG('NZ_CP059690', exhaustiveMapping = FALSE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
> # list('1.0'=c("apa:APP7_0365")))
> # No translation case
> .testEquals(getNCBINucleotide2KEGG('AY536519', byIdenticalProteins = FALSE), NA)
|=.............................| Step 1: Translating from NCBI Nucleotide to KEGG
|==............................| Step 2: Translating from NCBI Nucleotide to KEGG
|===...........................| Step 3: Translating from NCBI Nucleotide to KEGG
|====..........................| Step 4: Translating from NCBI Nucleotide to KEGG
|=====.........................| Step 5: Translating from NCBI Nucleotide to KEGG
|======........................| Step 6: Translating from NCBI Nucleotide to KEGG
|=======.......................| Step 7: Translating from NCBI Nucleotide to KEGG
|========......................| Step 8: Translating from NCBI Nucleotide to KEGG
|=========.....................| Step 9: Translating from NCBI Nucleotide to KEGG
|==========....................| Step 10: Translating from NCBI Nucleotide to KEGG
|===========...................| Step 11: Translating from NCBI Nucleotide to KEGG
|============..................| Step 12: Translating from NCBI Nucleotide to KEGG
|=============.................| Step 13: Translating from NCBI Nucleotide to KEGG
|==============................| Step 14: Translating from NCBI Nucleotide to KEGG
|===============...............| Step 15: Translating from NCBI Nucleotide to KEGG
|================..............| Step 16: Translating from NCBI Nucleotide to KEGG
|=================.............| Step 17: Translating from NCBI Nucleotide to KEGG
|==================............| Step 18: Translating from NCBI Nucleotide to KEGG
|===================...........| Step 19: Translating from NCBI Nucleotide to KEGG
|====================..........| Step 20: Translating from NCBI Nucleotide to KEGG
|=====================.........| Step 21: Translating from NCBI Nucleotide to KEGG
[1] TRUE
> .testEquals(getNCBINucleotide2KEGG('AY536519', detailedMapping = TRUE, byIdenticalProteins = FALSE), NA)
|=.............................| Step 1: Translating from NCBI Nucleotide to KEGG
|==............................| Step 2: Translating from NCBI Nucleotide to KEGG
|===...........................| Step 3: Translating from NCBI Nucleotide to KEGG
|====..........................| Step 4: Translating from NCBI Nucleotide to KEGG
|=====.........................| Step 5: Translating from NCBI Nucleotide to KEGG
|======........................| Step 6: Translating from NCBI Nucleotide to KEGG
|=======.......................| Step 7: Translating from NCBI Nucleotide to KEGG
|========......................| Step 8: Translating from NCBI Nucleotide to KEGG
|=========.....................| Step 9: Translating from NCBI Nucleotide to KEGG
|==========....................| Step 10: Translating from NCBI Nucleotide to KEGG
|===========...................| Step 11: Translating from NCBI Nucleotide to KEGG
|============..................| Step 12: Translating from NCBI Nucleotide to KEGG
|=============.................| Step 13: Translating from NCBI Nucleotide to KEGG
|==============................| Step 14: Translating from NCBI Nucleotide to KEGG
|===============...............| Step 15: Translating from NCBI Nucleotide to KEGG
|================..............| Step 16: Translating from NCBI Nucleotide to KEGG
|=================.............| Step 17: Translating from NCBI Nucleotide to KEGG
|==================............| Step 18: Translating from NCBI Nucleotide to KEGG
|===================...........| Step 19: Translating from NCBI Nucleotide to KEGG
|====================..........| Step 20: Translating from NCBI Nucleotide to KEGG
|=====================.........| Step 21: Translating from NCBI Nucleotide to KEGG
[1] TRUE
> # NCBI Nucleotide ID not registered case
> # .testEquals(getNCBINucleotide2KEGG('test'), NA)
>
> ### Test getNCBIGene2KEGG
> message('Testing getNCBIGene2KEGG')
Testing getNCBIGene2KEGG
> # Positive cases
> .testEquals(getNCBIGene2KEGG('76524190', exhaustiveMapping = FALSE, detailedMapping = FALSE),
+ c("cet:B8281_09025"))
|=.............................| Step 1: Translating from NCBI Gene to KEGG
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIGene2KEGG(c('76524190','76524190'), exhaustiveMapping = FALSE, detailedMapping = FALSE),
+ c("cet:B8281_09025","cet:B8281_09025"))
|=.............................| Step 1: Translating from NCBI Gene to KEGG
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> # .testEquals(getNCBIGene2KEGG('76524190', exhaustiveMapping = FALSE, detailedMapping = TRUE),
> # list('DT'=c("cet:B8281_09025")))
> # No translation case
> .testEquals(getNCBIGene2KEGG('76524190', byIdenticalProteins = FALSE, bySimilarGenes = FALSE), NA)
|=.............................| Step 1: Translating from NCBI Gene to KEGG
[1] TRUE
> .testEquals(getNCBIGene2KEGG('76524190', detailedMapping = TRUE, byIdenticalProteins = FALSE, bySimilarGenes = FALSE), NA)
|=.............................| Step 1: Translating from NCBI Gene to KEGG
[1] TRUE
> # NCBI Gene ID not registered case
> # .testEquals(getNCBIGene2KEGG('test'), NA)
>
> ##########################
> # NCBI databases to CARD #
> ##########################
>
> ### Test getNCBIProtein2CARD
> message('Testing getNCBIProtein2CARD')
Testing getNCBIProtein2CARD
> # Positive cases
> .testEquals(getNCBIProtein2CARD('AAK64581'), c('ARO:3004568'))
|=.............................| Step 1: Translating from NCBI Protein to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AAK64581
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AAK64581
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AAK64581
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AAK64581
|======........................| Step 6: Accesing and searching CARD database for NCBI id AAK64581
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AAK64581
|========......................| Step 8: Accesing and searching CARD database for NCBI id AAK64581
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AAK64581
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AAK64581
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AAK64581
|============..................| Step 12: Accesing and searching CARD database for NCBI id AAK64581
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AAK64581
|==============................| Step 14: Accesing and searching CARD database for NCBI id AAK64581
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AAK64581
|================..............| Step 16: Accesing and searching CARD database for NCBI id AAK64581
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AAK64581
|==================............| Step 18: Accesing and searching CARD database for NCBI id AAK64581
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AAK64581
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AAK64581
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AAK64581
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIProtein2CARD(c('AAK64581','AAK64581')), c('ARO:3004568', 'ARO:3004568'))
|=.............................| Step 1: Translating from NCBI Protein to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AAK64581
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AAK64581
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AAK64581
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AAK64581
|======........................| Step 6: Accesing and searching CARD database for NCBI id AAK64581
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AAK64581
|========......................| Step 8: Accesing and searching CARD database for NCBI id AAK64581
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AAK64581
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AAK64581
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AAK64581
|============..................| Step 12: Accesing and searching CARD database for NCBI id AAK64581
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AAK64581
|==============................| Step 14: Accesing and searching CARD database for NCBI id AAK64581
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AAK64581
|================..............| Step 16: Accesing and searching CARD database for NCBI id AAK64581
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AAK64581
|==================............| Step 18: Accesing and searching CARD database for NCBI id AAK64581
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AAK64581
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AAK64581
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AAK64581
|======================........| Step 22: Accesing and searching CARD database for NCBI id AAK64581
|=======================.......| Step 23: Accesing and searching CARD database for NCBI id AAK64581
|========================......| Step 24: Accesing and searching CARD database for NCBI id AAK64581
|=========================.....| Step 25: Accesing and searching CARD database for NCBI id AAK64581
|==========================....| Step 26: Accesing and searching CARD database for NCBI id AAK64581
|===========================...| Step 27: Accesing and searching CARD database for NCBI id AAK64581
|============================..| Step 28: Accesing and searching CARD database for NCBI id AAK64581
|=============================.| Step 29: Accesing and searching CARD database for NCBI id AAK64581
|..............................| Step 30: Accesing and searching CARD database for NCBI id AAK64581
|=.............................| Step 31: Accesing and searching CARD database for NCBI id AAK64581
|==............................| Step 32: Accesing and searching CARD database for NCBI id AAK64581
|===...........................| Step 33: Accesing and searching CARD database for NCBI id AAK64581
|====..........................| Step 34: Accesing and searching CARD database for NCBI id AAK64581
|=====.........................| Step 35: Accesing and searching CARD database for NCBI id AAK64581
|======........................| Step 36: Accesing and searching CARD database for NCBI id AAK64581
|=======.......................| Step 37: Accesing and searching CARD database for NCBI id AAK64581
|========......................| Step 38: Accesing and searching CARD database for NCBI id AAK64581
|=========.....................| Step 39: Accesing and searching CARD database for NCBI id AAK64581
|==========....................| Step 40: Accesing and searching CARD database for NCBI id AAK64581
|===========...................| Step 41: Accesing and searching CARD database for NCBI id AAK64581
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIProtein2CARD('AAK64581.1'), c('ARO:3004568'))
|=.............................| Step 1: Translating from NCBI Protein to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AAK64581.1
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AAK64581.1
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AAK64581.1
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AAK64581.1
|======........................| Step 6: Accesing and searching CARD database for NCBI id AAK64581.1
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AAK64581.1
|========......................| Step 8: Accesing and searching CARD database for NCBI id AAK64581.1
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AAK64581.1
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AAK64581.1
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AAK64581.1
|============..................| Step 12: Accesing and searching CARD database for NCBI id AAK64581.1
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AAK64581.1
|==============................| Step 14: Accesing and searching CARD database for NCBI id AAK64581.1
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AAK64581.1
|================..............| Step 16: Accesing and searching CARD database for NCBI id AAK64581.1
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AAK64581.1
|==================............| Step 18: Accesing and searching CARD database for NCBI id AAK64581.1
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AAK64581.1
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AAK64581.1
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AAK64581.1
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIProtein2CARD('CAC81324'), c('ARO:3003015'))
|=.............................| Step 1: Translating from NCBI Protein to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id CAC81324
|===...........................| Step 3: Accesing and searching CARD database for NCBI id CAC81324
|====..........................| Step 4: Accesing and searching CARD database for NCBI id CAC81324
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id CAC81324
|======........................| Step 6: Accesing and searching CARD database for NCBI id CAC81324
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id CAC81324
|========......................| Step 8: Accesing and searching CARD database for NCBI id CAC81324
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id CAC81324
|==========....................| Step 10: Accesing and searching CARD database for NCBI id CAC81324
|===========...................| Step 11: Accesing and searching CARD database for NCBI id CAC81324
|============..................| Step 12: Accesing and searching CARD database for NCBI id CAC81324
|=============.................| Step 13: Accesing and searching CARD database for NCBI id CAC81324
|==============................| Step 14: Accesing and searching CARD database for NCBI id CAC81324
|===============...............| Step 15: Accesing and searching CARD database for NCBI id CAC81324
|================..............| Step 16: Accesing and searching CARD database for NCBI id CAC81324
|=================.............| Step 17: Accesing and searching CARD database for NCBI id CAC81324
|==================............| Step 18: Accesing and searching CARD database for NCBI id CAC81324
|===================...........| Step 19: Accesing and searching CARD database for NCBI id CAC81324
|====================..........| Step 20: Accesing and searching CARD database for NCBI id CAC81324
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id CAC81324
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIProtein2CARD('CAC81324.1'), c('ARO:3003015'))
|=.............................| Step 1: Translating from NCBI Protein to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id CAC81324.1
|===...........................| Step 3: Accesing and searching CARD database for NCBI id CAC81324.1
|====..........................| Step 4: Accesing and searching CARD database for NCBI id CAC81324.1
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id CAC81324.1
|======........................| Step 6: Accesing and searching CARD database for NCBI id CAC81324.1
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id CAC81324.1
|========......................| Step 8: Accesing and searching CARD database for NCBI id CAC81324.1
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id CAC81324.1
|==========....................| Step 10: Accesing and searching CARD database for NCBI id CAC81324.1
|===========...................| Step 11: Accesing and searching CARD database for NCBI id CAC81324.1
|============..................| Step 12: Accesing and searching CARD database for NCBI id CAC81324.1
|=============.................| Step 13: Accesing and searching CARD database for NCBI id CAC81324.1
|==============................| Step 14: Accesing and searching CARD database for NCBI id CAC81324.1
|===============...............| Step 15: Accesing and searching CARD database for NCBI id CAC81324.1
|================..............| Step 16: Accesing and searching CARD database for NCBI id CAC81324.1
|=================.............| Step 17: Accesing and searching CARD database for NCBI id CAC81324.1
|==================............| Step 18: Accesing and searching CARD database for NCBI id CAC81324.1
|===================...........| Step 19: Accesing and searching CARD database for NCBI id CAC81324.1
|====================..........| Step 20: Accesing and searching CARD database for NCBI id CAC81324.1
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id CAC81324.1
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> # No translation case
> .testEquals(getNCBIProtein2CARD('EAT32321.1'), NA)
|=.............................| Step 1: Translating from NCBI Protein to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id EAT32321.1
|===...........................| Step 3: Accesing and searching CARD database for NCBI id EAT32321.1
|====..........................| Step 4: Accesing and searching CARD database for NCBI id EAT32321.1
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id EAT32321.1
|======........................| Step 6: Accesing and searching CARD database for NCBI id EAT32321.1
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id EAT32321.1
|========......................| Step 8: Accesing and searching CARD database for NCBI id EAT32321.1
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id EAT32321.1
|==========....................| Step 10: Accesing and searching CARD database for NCBI id EAT32321.1
|===========...................| Step 11: Accesing and searching CARD database for NCBI id EAT32321.1
|============..................| Step 12: Accesing and searching CARD database for NCBI id EAT32321.1
|=============.................| Step 13: Accesing and searching CARD database for NCBI id EAT32321.1
|==============................| Step 14: Accesing and searching CARD database for NCBI id EAT32321.1
|===============...............| Step 15: Accesing and searching CARD database for NCBI id EAT32321.1
|================..............| Step 16: Accesing and searching CARD database for NCBI id EAT32321.1
|=================.............| Step 17: Accesing and searching CARD database for NCBI id EAT32321.1
|==================............| Step 18: Accesing and searching CARD database for NCBI id EAT32321.1
|===================...........| Step 19: Accesing and searching CARD database for NCBI id EAT32321.1
|====================..........| Step 20: Accesing and searching CARD database for NCBI id EAT32321.1
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id EAT32321.1
[1] TRUE
> # NCBI ID not registered case
> # .testEquals(getNCBIProtein2CARD('test'), NA)
>
> ### Test getNCBINucleotide2CARD
> message('Testing getNCBINucleotide2CARD')
Testing getNCBINucleotide2CARD
> # Positive cases
> .testEquals(getNCBINucleotide2CARD('AY034138'), c('ARO:3004568'))
|=.............................| Step 1: Translating from NCBI Nucleotide to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AY034138
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AY034138
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AY034138
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AY034138
|======........................| Step 6: Accesing and searching CARD database for NCBI id AY034138
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AY034138
|========......................| Step 8: Accesing and searching CARD database for NCBI id AY034138
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AY034138
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AY034138
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AY034138
|============..................| Step 12: Accesing and searching CARD database for NCBI id AY034138
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AY034138
|==============................| Step 14: Accesing and searching CARD database for NCBI id AY034138
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AY034138
|================..............| Step 16: Accesing and searching CARD database for NCBI id AY034138
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AY034138
|==================............| Step 18: Accesing and searching CARD database for NCBI id AY034138
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AY034138
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AY034138
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AY034138
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBINucleotide2CARD(c('AY034138','AY034138')), c('ARO:3004568','ARO:3004568'))
|=.............................| Step 1: Translating from NCBI Nucleotide to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AY034138
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AY034138
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AY034138
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AY034138
|======........................| Step 6: Accesing and searching CARD database for NCBI id AY034138
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AY034138
|========......................| Step 8: Accesing and searching CARD database for NCBI id AY034138
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AY034138
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AY034138
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AY034138
|============..................| Step 12: Accesing and searching CARD database for NCBI id AY034138
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AY034138
|==============................| Step 14: Accesing and searching CARD database for NCBI id AY034138
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AY034138
|================..............| Step 16: Accesing and searching CARD database for NCBI id AY034138
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AY034138
|==================............| Step 18: Accesing and searching CARD database for NCBI id AY034138
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AY034138
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AY034138
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AY034138
|======================........| Step 22: Accesing and searching CARD database for NCBI id AY034138
|=======================.......| Step 23: Accesing and searching CARD database for NCBI id AY034138
|========================......| Step 24: Accesing and searching CARD database for NCBI id AY034138
|=========================.....| Step 25: Accesing and searching CARD database for NCBI id AY034138
|==========================....| Step 26: Accesing and searching CARD database for NCBI id AY034138
|===========================...| Step 27: Accesing and searching CARD database for NCBI id AY034138
|============================..| Step 28: Accesing and searching CARD database for NCBI id AY034138
|=============================.| Step 29: Accesing and searching CARD database for NCBI id AY034138
|..............................| Step 30: Accesing and searching CARD database for NCBI id AY034138
|=.............................| Step 31: Accesing and searching CARD database for NCBI id AY034138
|==............................| Step 32: Accesing and searching CARD database for NCBI id AY034138
|===...........................| Step 33: Accesing and searching CARD database for NCBI id AY034138
|====..........................| Step 34: Accesing and searching CARD database for NCBI id AY034138
|=====.........................| Step 35: Accesing and searching CARD database for NCBI id AY034138
|======........................| Step 36: Accesing and searching CARD database for NCBI id AY034138
|=======.......................| Step 37: Accesing and searching CARD database for NCBI id AY034138
|========......................| Step 38: Accesing and searching CARD database for NCBI id AY034138
|=========.....................| Step 39: Accesing and searching CARD database for NCBI id AY034138
|==========....................| Step 40: Accesing and searching CARD database for NCBI id AY034138
|===========...................| Step 41: Accesing and searching CARD database for NCBI id AY034138
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBINucleotide2CARD('AY034138.1'), c('ARO:3004568'))
|=.............................| Step 1: Translating from NCBI Nucleotide to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AY034138.1
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AY034138.1
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AY034138.1
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AY034138.1
|======........................| Step 6: Accesing and searching CARD database for NCBI id AY034138.1
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AY034138.1
|========......................| Step 8: Accesing and searching CARD database for NCBI id AY034138.1
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AY034138.1
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AY034138.1
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AY034138.1
|============..................| Step 12: Accesing and searching CARD database for NCBI id AY034138.1
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AY034138.1
|==============................| Step 14: Accesing and searching CARD database for NCBI id AY034138.1
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AY034138.1
|================..............| Step 16: Accesing and searching CARD database for NCBI id AY034138.1
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AY034138.1
|==================............| Step 18: Accesing and searching CARD database for NCBI id AY034138.1
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AY034138.1
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AY034138.1
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AY034138.1
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBINucleotide2CARD('AJ310778'), c('ARO:3003015'))
|=.............................| Step 1: Translating from NCBI Nucleotide to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AJ310778
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AJ310778
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AJ310778
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AJ310778
|======........................| Step 6: Accesing and searching CARD database for NCBI id AJ310778
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AJ310778
|========......................| Step 8: Accesing and searching CARD database for NCBI id AJ310778
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AJ310778
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AJ310778
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AJ310778
|============..................| Step 12: Accesing and searching CARD database for NCBI id AJ310778
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AJ310778
|==============................| Step 14: Accesing and searching CARD database for NCBI id AJ310778
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AJ310778
|================..............| Step 16: Accesing and searching CARD database for NCBI id AJ310778
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AJ310778
|==================............| Step 18: Accesing and searching CARD database for NCBI id AJ310778
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AJ310778
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AJ310778
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AJ310778
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBINucleotide2CARD('AJ310778.1'), c('ARO:3003015'))
|=.............................| Step 1: Translating from NCBI Nucleotide to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id AJ310778.1
|===...........................| Step 3: Accesing and searching CARD database for NCBI id AJ310778.1
|====..........................| Step 4: Accesing and searching CARD database for NCBI id AJ310778.1
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id AJ310778.1
|======........................| Step 6: Accesing and searching CARD database for NCBI id AJ310778.1
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id AJ310778.1
|========......................| Step 8: Accesing and searching CARD database for NCBI id AJ310778.1
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id AJ310778.1
|==========....................| Step 10: Accesing and searching CARD database for NCBI id AJ310778.1
|===========...................| Step 11: Accesing and searching CARD database for NCBI id AJ310778.1
|============..................| Step 12: Accesing and searching CARD database for NCBI id AJ310778.1
|=============.................| Step 13: Accesing and searching CARD database for NCBI id AJ310778.1
|==============................| Step 14: Accesing and searching CARD database for NCBI id AJ310778.1
|===============...............| Step 15: Accesing and searching CARD database for NCBI id AJ310778.1
|================..............| Step 16: Accesing and searching CARD database for NCBI id AJ310778.1
|=================.............| Step 17: Accesing and searching CARD database for NCBI id AJ310778.1
|==================............| Step 18: Accesing and searching CARD database for NCBI id AJ310778.1
|===================...........| Step 19: Accesing and searching CARD database for NCBI id AJ310778.1
|====================..........| Step 20: Accesing and searching CARD database for NCBI id AJ310778.1
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id AJ310778.1
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> # No translation case
> .testEquals(getNCBINucleotide2CARD('JH725437.1'), NA)
|=.............................| Step 1: Translating from NCBI Nucleotide to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id JH725437.1
|===...........................| Step 3: Accesing and searching CARD database for NCBI id JH725437.1
|====..........................| Step 4: Accesing and searching CARD database for NCBI id JH725437.1
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id JH725437.1
|======........................| Step 6: Accesing and searching CARD database for NCBI id JH725437.1
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id JH725437.1
|========......................| Step 8: Accesing and searching CARD database for NCBI id JH725437.1
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id JH725437.1
|==========....................| Step 10: Accesing and searching CARD database for NCBI id JH725437.1
|===========...................| Step 11: Accesing and searching CARD database for NCBI id JH725437.1
|============..................| Step 12: Accesing and searching CARD database for NCBI id JH725437.1
|=============.................| Step 13: Accesing and searching CARD database for NCBI id JH725437.1
|==============................| Step 14: Accesing and searching CARD database for NCBI id JH725437.1
|===============...............| Step 15: Accesing and searching CARD database for NCBI id JH725437.1
|================..............| Step 16: Accesing and searching CARD database for NCBI id JH725437.1
|=================.............| Step 17: Accesing and searching CARD database for NCBI id JH725437.1
|==================............| Step 18: Accesing and searching CARD database for NCBI id JH725437.1
|===================...........| Step 19: Accesing and searching CARD database for NCBI id JH725437.1
|====================..........| Step 20: Accesing and searching CARD database for NCBI id JH725437.1
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id JH725437.1
[1] TRUE
> # NCBI ID not registered case
> # .testEquals(getNCBINucleotide2CARD('test'), NA)
>
> ### Test getNCBIGene2CARD
> message('Testing getNCBIGene2CARD')
Testing getNCBIGene2CARD
> # Positive case
> .testEquals(getNCBIGene2CARD('3510143'), c('ARO:3003942'))
|=.............................| Step 1: Translating from NCBI Gene to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id 3510143
|===...........................| Step 3: Accesing and searching CARD database for NCBI id 3510143
|====..........................| Step 4: Accesing and searching CARD database for NCBI id 3510143
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id 3510143
|======........................| Step 6: Accesing and searching CARD database for NCBI id 3510143
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id 3510143
|========......................| Step 8: Accesing and searching CARD database for NCBI id 3510143
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id 3510143
|==========....................| Step 10: Accesing and searching CARD database for NCBI id 3510143
|===========...................| Step 11: Accesing and searching CARD database for NCBI id 3510143
|============..................| Step 12: Accesing and searching CARD database for NCBI id 3510143
|=============.................| Step 13: Accesing and searching CARD database for NCBI id 3510143
|==============................| Step 14: Accesing and searching CARD database for NCBI id 3510143
|===============...............| Step 15: Accesing and searching CARD database for NCBI id 3510143
|================..............| Step 16: Accesing and searching CARD database for NCBI id 3510143
|=================.............| Step 17: Accesing and searching CARD database for NCBI id 3510143
|==================............| Step 18: Accesing and searching CARD database for NCBI id 3510143
|===================...........| Step 19: Accesing and searching CARD database for NCBI id 3510143
|====================..........| Step 20: Accesing and searching CARD database for NCBI id 3510143
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id 3510143
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> .testEquals(getNCBIGene2CARD(c('3510143','3510143')), c('ARO:3003942','ARO:3003942'))
|=.............................| Step 1: Translating from NCBI Gene to CARD
Using a CARD database version downloaded on Sat 10/05/2024 16:20:24, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Accesing and searching CARD database for NCBI id 3510143
|===...........................| Step 3: Accesing and searching CARD database for NCBI id 3510143
|====..........................| Step 4: Accesing and searching CARD database for NCBI id 3510143
|=====.........................| Step 5: Accesing and searching CARD database for NCBI id 3510143
|======........................| Step 6: Accesing and searching CARD database for NCBI id 3510143
|=======.......................| Step 7: Accesing and searching CARD database for NCBI id 3510143
|========......................| Step 8: Accesing and searching CARD database for NCBI id 3510143
|=========.....................| Step 9: Accesing and searching CARD database for NCBI id 3510143
|==========....................| Step 10: Accesing and searching CARD database for NCBI id 3510143
|===========...................| Step 11: Accesing and searching CARD database for NCBI id 3510143
|============..................| Step 12: Accesing and searching CARD database for NCBI id 3510143
|=============.................| Step 13: Accesing and searching CARD database for NCBI id 3510143
|==============................| Step 14: Accesing and searching CARD database for NCBI id 3510143
|===============...............| Step 15: Accesing and searching CARD database for NCBI id 3510143
|================..............| Step 16: Accesing and searching CARD database for NCBI id 3510143
|=================.............| Step 17: Accesing and searching CARD database for NCBI id 3510143
|==================............| Step 18: Accesing and searching CARD database for NCBI id 3510143
|===================...........| Step 19: Accesing and searching CARD database for NCBI id 3510143
|====================..........| Step 20: Accesing and searching CARD database for NCBI id 3510143
|=====================.........| Step 21: Accesing and searching CARD database for NCBI id 3510143
|======================........| Step 22: Accesing and searching CARD database for NCBI id 3510143
|=======================.......| Step 23: Accesing and searching CARD database for NCBI id 3510143
|========================......| Step 24: Accesing and searching CARD database for NCBI id 3510143
|=========================.....| Step 25: Accesing and searching CARD database for NCBI id 3510143
|==========================....| Step 26: Accesing and searching CARD database for NCBI id 3510143
|===========================...| Step 27: Accesing and searching CARD database for NCBI id 3510143
|============================..| Step 28: Accesing and searching CARD database for NCBI id 3510143
|=============================.| Step 29: Accesing and searching CARD database for NCBI id 3510143
|..............................| Step 30: Accesing and searching CARD database for NCBI id 3510143
|=.............................| Step 31: Accesing and searching CARD database for NCBI id 3510143
|==............................| Step 32: Accesing and searching CARD database for NCBI id 3510143
|===...........................| Step 33: Accesing and searching CARD database for NCBI id 3510143
|====..........................| Step 34: Accesing and searching CARD database for NCBI id 3510143
|=====.........................| Step 35: Accesing and searching CARD database for NCBI id 3510143
|======........................| Step 36: Accesing and searching CARD database for NCBI id 3510143
|=======.......................| Step 37: Accesing and searching CARD database for NCBI id 3510143
|========......................| Step 38: Accesing and searching CARD database for NCBI id 3510143
|=========.....................| Step 39: Accesing and searching CARD database for NCBI id 3510143
|==========....................| Step 40: Accesing and searching CARD database for NCBI id 3510143
|===========...................| Step 41: Accesing and searching CARD database for NCBI id 3510143
API(s) connection failed:
Modes: logical, character
target is logical, current is character
> # .testEquals(getNCBIGene2CARD('WP_001082319'), NA)
> # NCBI ID not registered case
> # .testEquals(getNCBIGene2CARD('test'), NA)
>
>
> proc.time()
user system elapsed
257.607 6.247 1156.517
##############################################################################
##############################################################################
###
### 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_1.1.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/ginmappeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.1.4’
* 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’
OK
* DONE
Status: 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)