Fernando Sola
| Snapshot Date: 2026-02-12 13:45 -0500 (Thu, 12 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/ginmappeR |
| git_branch: RELEASE_3_22 |
| git_last_commit: f5ef284 |
| git_last_commit_date: 2025-10-29 11:28:37 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-16 11:57 -0500 (Mon, 16 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4889 |
| 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 887/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ginmappeR 1.6.0 (landing page) Fernando Sola
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for ginmappeR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the ginmappeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ginmappeR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ginmappeR_1.6.0.tar.gz |
| StartedAt: 2026-02-13 00:32:40 -0500 (Fri, 13 Feb 2026) |
| EndedAt: 2026-02-13 00:54:16 -0500 (Fri, 13 Feb 2026) |
| EllapsedTime: 1295.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ginmappeR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ginmappeR_1.6.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ginmappeR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.6.0’
* 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 ‘build’ 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getCARD2KEGG 5.116 0.674 19.122
getCARD2UniProt 5.316 0.441 940.601
getNCBINucleotide2KEGG 1.737 0.097 66.078
getKEGG2NCBINucleotide 0.666 0.010 9.407
getNCBIGene2UniProt 0.519 0.014 11.627
getNCBIProtein2UniProt 0.506 0.026 11.278
getNCBINucleotide2UniProt 0.446 0.025 11.394
getNCBIGene2CARD 0.413 0.002 12.019
getCARD2NCBIGene 0.306 0.027 6.092
getUniProt2NCBINucleotide 0.251 0.011 5.489
getNCBIGene2NCBINucleotide 0.214 0.006 27.607
getNCBIGene2NCBIProtein 0.117 0.010 16.657
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.
ginmappeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ginmappeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ginmappeR’ ... ** this is package ‘ginmappeR’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ginmappeR)
ginmappeR.Rcheck/tests/runTests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("ginmappeR")
Testing getKEGG2UniProt
|=.............................| Step 1: Translating from KEGG to UniProt
|==............................| Step 2: Connecting to KEGG web services
|===...........................| Step 3: Connecting to KEGG API and translating id aag:5579347 to Uniprot
[1] "A0A1S4G4Z1"
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene
|=.............................| Step 1: Translating from KEGG to NCBI Protein
|==............................| Step 2: Trying to get a direct translation for KEGG id bha:BH0380 to NCBI
[1] "BAB04099"
Testing getKEGG2CARD
|=.............................| Step 1: Translating from KEGG to CARD
Updating CARD database data...
Deleting previous versions of CARD if any.
Downloading latest version
Extracting database
CARD database downloaded successfully!
Located at /tmp/RtmpjhmidH/card-data
CARD database version 4.0.1 (2025-05-29)
|==............................| Step 2: Searching CARD database and translating to KEGG
|===...........................| Step 3: Trying to get a direct translation for KEGG id ag:ACC85616 to CARD
[1] "ARO:3002804"
Testing getUniProtSimilarGenes
|=.............................| Step 1: Accessing UniProt similar genes database
|==............................| Step 2: Connecting to UniProt API and retrieving cluster of id G9JVE6
|===...........................| Step 3: Retrieving and parsing genes of cluster UniRef100_G9JVE6
[1] "UniRef100_G9JVE6"
Testing getUniProt2KEGG
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id A0A6I6H1L5 to KEGG
[1] "fls:GLV81_10715"
Testing getUniProt2NCBIProtein, getUniProt2NCBINucleotide, getUniProt2NCBIGene
|=.............................| Step 1: Translating from UniProt to NCBI Protein
|=.............................| Step 1: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI
[1] "QIB98918.1"
Testing getUniProt2CARD
|=.............................| Step 1: Translating from UniProt to CARD
Using a CARD database version downloaded on Fri 02/13/2026 00:53:52, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating Uniprot id A0A1S7BGS4 to CARD
|===...........................| Step 3: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
[1] "ARO:3004185"
RUNIT TEST PROTOCOL -- Fri Feb 13 00:54:10 2026
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
ginmappeR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.844 1.088 27.433
ginmappeR.Rcheck/ginmappeR-Ex.timings
| name | user | system | elapsed | |
| getCARD2KEGG | 5.116 | 0.674 | 19.122 | |
| getCARD2NCBIGene | 0.306 | 0.027 | 6.092 | |
| getCARD2NCBINucleotide | 0.275 | 0.017 | 0.693 | |
| getCARD2NCBIProtein | 0.005 | 0.001 | 0.407 | |
| getCARD2UniProt | 5.316 | 0.441 | 940.601 | |
| getKEGG2CARD | 0.214 | 0.004 | 1.491 | |
| getKEGG2NCBIGene | 0.193 | 0.005 | 1.979 | |
| getKEGG2NCBINucleotide | 0.666 | 0.010 | 9.407 | |
| getKEGG2NCBIProtein | 0.130 | 0.000 | 1.327 | |
| getKEGG2UniProt | 0.003 | 0.000 | 0.103 | |
| getNCBIGene2CARD | 0.413 | 0.002 | 12.019 | |
| getNCBIGene2KEGG | 0.031 | 0.000 | 1.950 | |
| getNCBIGene2NCBINucleotide | 0.214 | 0.006 | 27.607 | |
| getNCBIGene2NCBIProtein | 0.117 | 0.010 | 16.657 | |
| getNCBIGene2UniProt | 0.519 | 0.014 | 11.627 | |
| getNCBIIdenticalProteins | 0.129 | 0.010 | 2.006 | |
| getNCBINucleotide2CARD | 0.115 | 0.004 | 0.795 | |
| getNCBINucleotide2KEGG | 1.737 | 0.097 | 66.078 | |
| getNCBINucleotide2NCBIGene | 0.103 | 0.007 | 1.902 | |
| getNCBINucleotide2NCBIProtein | 0.073 | 0.011 | 0.681 | |
| getNCBINucleotide2UniProt | 0.446 | 0.025 | 11.394 | |
| getNCBIProtein2CARD | 0.190 | 0.011 | 0.747 | |
| getNCBIProtein2KEGG | 0.035 | 0.000 | 2.230 | |
| getNCBIProtein2NCBIGene | 0.039 | 0.005 | 2.272 | |
| getNCBIProtein2NCBINucleotide | 0.067 | 0.002 | 0.609 | |
| getNCBIProtein2UniProt | 0.506 | 0.026 | 11.278 | |
| getUniProt2CARD | 0.311 | 0.004 | 4.043 | |
| getUniProt2KEGG | 0.027 | 0.002 | 0.741 | |
| getUniProt2NCBIGene | 0 | 0 | 0 | |
| getUniProt2NCBINucleotide | 0.251 | 0.011 | 5.489 | |
| getUniProt2NCBIProtein | 0 | 0 | 0 | |
| getUniProtSimilarGenes | 0.125 | 0.009 | 1.008 | |