| Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4408 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| 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 1.1.2 (landing page) Fernando Sola
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | TIMEOUT | ||||||||
| 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: 1.1.2 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ginmappeR_1.1.2.tar.gz |
| StartedAt: 2024-06-29 16:23:54 -0400 (Sat, 29 Jun 2024) |
| EndedAt: 2024-06-29 22:23:54 -0400 (Sat, 29 Jun 2024) |
| EllapsedTime: 21600.0 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: ginmappeR.Rcheck |
| Warnings: NA |
ginmappeR.Rcheck/tests/test_CARD.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 C:\Users\biocbuild\bbs-3.20-bioc-longtests\tmpdir\Rtmp4ANI8v/card-data
[1] TRUE
> .testEquals(getCARD2NCBIProtein('ARO:3002535'), 'CAA38525.1')
Using a CARD database version downloaded on Sat 06/29/2024 16:25:30, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBIProtein('3003988'), 'APB03221.1')
Using a CARD database version downloaded on Sat 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBINucleotide('ARO:3002535'), 'X54723.1')
Using a CARD database version downloaded on Sat 06/29/2024 16:25:30, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2NCBINucleotide('3003988'), 'KX531051.1')
Using a CARD database version downloaded on Sat 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, please consider updating it with updateCARDDataBase() function.
[1] TRUE
> .testEquals(getCARD2UniProt('3006267', detailedMapping=TRUE), NA)
Using a CARD database version downloaded on Sat 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, 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 06/29/2024 16:25:30, please consider updating it with updateCARDDataBase() function.
The given ID "test" is not registered in CARD database
[1] TRUE
>
>
>
>
>
>
>
> proc.time()
user system elapsed
25.48 1.59 165.00
ginmappeR.Rcheck/tests/test_NCBI.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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...
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ginmappeR_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/ginmappeR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.1.2'
* 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 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'
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)