Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-11 23:55:02 -0400 (Sat, 11 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 24/33HostnameOS / ArchCHECK
ginmappeR 1.0.0  (landing page)
Fernando Sola
Snapshot Date: 2024-05-11 09:55:01 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/ginmappeR
git_branch: RELEASE_3_19
git_last_commit: f482726
git_last_commit_date: 2024-04-30 11:54:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for ginmappeR on lconway


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.

raw results

Summary

Package: ginmappeR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ginmappeR_1.0.0.tar.gz
StartedAt: 2024-05-11 16:05:21 -0400 (Sat, 11 May 2024)
EndedAt: 2024-05-11 16:13:11 -0400 (Sat, 11 May 2024)
EllapsedTime: 470.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ginmappeR.Rcheck
Warnings: 0

Tests output

ginmappeR.Rcheck/tests/test_CARD.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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, 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...
CARD database downloaded successfully!
Located at /tmp/RtmpBGSPAj/card-data
[1] TRUE
> .testEquals(getCARD2NCBIProtein('ARO:3002535'), 'CAA38525.1')
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBIProtein('3003988'), 'APB03221.1')
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBIProtein(c('3003988', 'ARO:3002535')), c('APB03221.1', 'CAA38525.1'))
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBIProtein('test'), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
The given ID "test" is not registered in CARD database
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBIProtein(c(character(0), '3002535')), c('CAA38525.1'))
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> 
> 
> 
> ### Test getCARD2NCBINucleotide
> message('Testing getCARD2NCBINucleotide')
Testing getCARD2NCBINucleotide
> # Positive cases
> .testEquals(getCARD2NCBINucleotide('3002535'), 'X54723.1')
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBINucleotide('ARO:3002535'), 'X54723.1')
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBINucleotide('3003988'), 'KX531051.1')
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBINucleotide(c('3003988', 'ARO:3002535')), c('KX531051.1', 'X54723.1'))
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2NCBINucleotide('test'), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
The given ID "test" is not registered in CARD database
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2UniProt('3006267', detailedMapping=TRUE), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2UniProt('test'), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
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 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2KEGG('3006267', detailedMapping = TRUE, bySimilarGenes = FALSE), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # Incorrect CARD ID case
> .testEquals(getCARD2KEGG('test'), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:06:45, please consider updating it with updateCARDDataBase() function.
The given ID "test" is not registered in CARD database
[1] TRUE
> 
> 
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
 29.435   1.187 110.933

ginmappeR.Rcheck/tests/test_NCBI.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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, 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'))
[1] TRUE
> .testEquals(getNCBIGene2NCBIProtein(c('76524190', '76524190')), c('WP_001082319','WP_001082319'))
[1] TRUE
> .testEquals(getNCBIGene2NCBIProtein('76524190', exhaustiveMapping = TRUE), list(c('WP_001082319')))
[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'))
[1] TRUE
> .testEquals(getNCBIProtein2NCBIGene(c('CAA79696','CAA79696')), c('1272', '1272'))
[1] TRUE
> .testEquals(getNCBIProtein2NCBIGene('CAA79696', exhaustiveMapping = TRUE), list(c('1272')))
[1] TRUE
> .testEquals(getNCBIProtein2NCBIGene(c('CAA79696','CAA79696'), exhaustiveMapping = TRUE), list(c('1272'), c('1272')))
[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'))
Updating CARD database data...
CARD database downloaded successfully!
Located at /tmp/RtmpQw8nA1/card-data
[1] TRUE
> .testEquals(getNCBIProtein2NCBINucleotide(c('AFH35853','AFH35853')), c('JQ394987', 'JQ394987'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBIProtein2NCBINucleotide('AFH35853', exhaustiveMapping = TRUE), list(c('JQ394987')))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # ID not registered case
> # .testEquals(getNCBIProtein2NCBINucleotide('test'), NA)
> 
> ### Test getNCBINucleotide2NCBIProtein
> message('Testing getNCBINucleotide2NCBIProtein')
Testing getNCBINucleotide2NCBIProtein
> # Positive case
> .testEquals(getNCBINucleotide2NCBIProtein('JQ394987'), c('AFH35853'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBINucleotide2NCBIProtein(c('JQ394987','JQ394987')), c('AFH35853', 'AFH35853'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[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'))
[1] TRUE
> .testEquals(getNCBIGene2NCBINucleotide(c('76524190','76524190')), c('NZ_CP059690', 'NZ_CP059690'))
[1] TRUE
> .testEquals(getNCBIGene2NCBINucleotide('76524190', exhaustiveMapping = TRUE), list(c('NZ_CP059690')))
[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'))
[1] TRUE
> .testEquals(getNCBINucleotide2NCBIGene(c('Z21488','Z21488')), c('1272', '1272'))
[1] TRUE
> .testEquals(getNCBINucleotide2NCBIGene('Z21488', exhaustiveMapping = TRUE), list(c('1272')))
[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")))
[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")))
[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)
[1] TRUE
> .testEquals(getNCBIIdenticalProteins(c('AHA80958','AHA80958'), format = 'dataframe'), list(dummyDf, dummyDf))
[1] TRUE
> # Incorrect format request case
> Sys.sleep(3)
> RUnit::checkException(getNCBIIdenticalProteins('AHA80958', format='test'))
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'))
[1] TRUE
> .testEquals(getNCBIProtein2UniProt(c('WP_010896559.1','WP_010896559.1')), c('Q7AJZ0', 'Q7AJZ0'))
[1] TRUE
> # .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'))
[1] TRUE
> .testEquals(getNCBINucleotide2UniProt(c('AY536519', 'AY536519')), c('Q6QJ79','Q6QJ79'))
[1] TRUE
> .testEquals(getNCBINucleotide2UniProt('AY536519', detailedMapping = TRUE), list('1.0'=c('Q6QJ79')))
[1] TRUE
> # .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'))
[1] TRUE
> .testEquals(getNCBIGene2UniProt(c('76524190','76524190')), c('A0A1W6DPG3','A0A1W6DPG3'))
[1] TRUE
> .testEquals(getNCBIGene2UniProt('76524190', detailedMapping = TRUE), list('1.0'=c('A0A1W6DPG3')))
[1] TRUE
> .testEquals(getNCBIGene2UniProt('76524190', byIdenticalProteins =  FALSE), NA)
[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"))
[1] TRUE
> .testEquals(getNCBIProtein2KEGG(c('WP_010896559.1','WP_010896559.1'), exhaustiveMapping = FALSE, detailedMapping = FALSE, byIdenticalProteins = FALSE),
+            c("bha:BH0380", "bha:BH0380"))
[1] TRUE
> .testEquals(getNCBIProtein2KEGG('WP_010896559.1', exhaustiveMapping = FALSE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
+             list('DT'=c("bha:BH0380")))
[1] TRUE
> .testEquals(getNCBIProtein2KEGG(c('WP_010896559.1','WP_010896559.1'), exhaustiveMapping = FALSE, detailedMapping = TRUE, byIdenticalProteins = FALSE),
+             c('DT'=c("bha:BH0380"),'DT'=c("bha:BH0380")))
[1] TRUE
> # .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"))
[1] TRUE
> .testEquals(getNCBINucleotide2KEGG(c('AY536519','AY536519'), exhaustiveMapping = FALSE, detailedMapping = FALSE),
+            c("ag:AAS48620", "ag:AAS48620"))
[1] TRUE
> # .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)
[1] TRUE
> .testEquals(getNCBINucleotide2KEGG('AY536519', detailedMapping = TRUE, byIdenticalProteins = FALSE), NA)
[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"))
[1] TRUE
> .testEquals(getNCBIGene2KEGG(c('76524190','76524190'), exhaustiveMapping = FALSE, detailedMapping = FALSE),
+            c("cet:B8281_09025","cet:B8281_09025"))
[1] TRUE
> # .testEquals(getNCBIGene2KEGG('76524190', exhaustiveMapping = FALSE, detailedMapping = TRUE),
> #             list('DT'=c("cet:B8281_09025")))
> # No translation case
> .testEquals(getNCBIGene2KEGG('76524190', byIdenticalProteins = FALSE, bySimilarGenes = FALSE), NA)
[1] TRUE
> .testEquals(getNCBIGene2KEGG('76524190', detailedMapping = TRUE, byIdenticalProteins = FALSE, bySimilarGenes = FALSE), NA)
[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'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBIProtein2CARD(c('AAK64581','AAK64581')), c('ARO:3004568', 'ARO:3004568'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBIProtein2CARD('AAK64581.1'), c('ARO:3004568'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBIProtein2CARD('CAC81324'), c('ARO:3003015'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBIProtein2CARD('CAC81324.1'), c('ARO:3003015'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # No translation case
> .testEquals(getNCBIProtein2CARD('EAT32321.1'), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[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'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBINucleotide2CARD(c('AY034138','AY034138')), c('ARO:3004568','ARO:3004568'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBINucleotide2CARD('AY034138.1'), c('ARO:3004568'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBINucleotide2CARD('AJ310778'), c('ARO:3003015'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBINucleotide2CARD('AJ310778.1'), c('ARO:3003015'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # No translation case
> .testEquals(getNCBINucleotide2CARD('JH725437.1'), NA)
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[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'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getNCBIGene2CARD(c('3510143','3510143')), c('ARO:3003942','ARO:3003942'))
Using a CARD database version downloaded on Sat 05/11/2024 16:08:53, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> # .testEquals(getNCBIGene2CARD('WP_001082319'), NA)
> # NCBI ID not registered case
> # .testEquals(getNCBIGene2CARD('test'), NA)
> 
> 
> proc.time()
   user  system elapsed 
 10.514   0.500 278.624

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ginmappeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/ginmappeR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ginmappeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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
  ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/ginmappeR.Rcheck/00check.log’
for details.

Installation output

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)