Fernando Sola
| Snapshot Date: 2024-09-11 14:00 -0400 (Wed, 11 Sep 2024) |
| git_url: https://git.bioconductor.org/packages/ginmappeR |
| git_branch: devel |
| git_last_commit: daeae95 |
| git_last_commit_date: 2024-08-08 15:56:15 -0400 (Thu, 08 Aug 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-12 11:40 -0400 (Thu, 12 Sep 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" | 4713 |
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
| 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 855/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ginmappeR 1.1.4 (landing page) Fernando Sola
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.1.4 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ginmappeR_1.1.4.tar.gz |
| StartedAt: 2024-09-11 23:12:32 -0400 (Wed, 11 Sep 2024) |
| EndedAt: 2024-09-11 23:21:11 -0400 (Wed, 11 Sep 2024) |
| EllapsedTime: 519.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ginmappeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ginmappeR_1.1.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/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 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* 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 ‘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 4.627 0.425 16.396
getCARD2UniProt 1.071 0.133 8.528
getNCBIGene2KEGG 0.737 0.056 15.342
getNCBINucleotide2KEGG 0.703 0.067 15.502
getKEGG2NCBINucleotide 0.577 0.108 7.346
getNCBIProtein2UniProt 0.627 0.055 7.119
getNCBIProtein2KEGG 0.498 0.031 29.860
* 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-3.20-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.
ginmappeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ginmappeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * 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)
ginmappeR.Rcheck/tests/runTests.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.
> BiocGenerics:::testPackage("ginmappeR")
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
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
|=.............................| 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
|=.............................| Step 1: Translating from KEGG to UniProt
|=.............................| Step 1: Translating from KEGG to UniProt
|==............................| Step 2: Connecting to KEGG web services
|===...........................| Step 3: Connecting to KEGG API and translating id eco:b0204 to Uniprot
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene
|=.............................| Step 1: Translating from KEGG to NCBI Nucleotide
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|===...........................| Step 3: Connecting to KEGG web services
|====..........................| Step 4: Connecting to KEGG API and translating id llo:LLO_2673 to Uniprot
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for UniProt id D3HKY4 to NCBI
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Translating from KEGG to NCBI Nucleotide
|=.............................| Step 1: Translating from KEGG to NCBI Gene
|==............................| Step 2: Trying to get a direct translation for KEGG id aag:5579347 to NCBI
|=.............................| Step 1: Translating from KEGG to NCBI Gene
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/RtmpelEIoj/card-data
CARD database version 3.3.0 (2024-08-26)
|==............................| Step 2: Searching CARD database and translating to KEGG
|===...........................| Step 3: Trying to get a direct translation for KEGG id ag:ACC85616 to CARD
|=.............................| Step 1: Translating from KEGG to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from KEGG to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Searching CARD database and translating to KEGG
|===...........................| Step 3: Trying to get a direct translation for KEGG id ag:ACC85616 to CARD
|=.............................| Step 1: Translating from KEGG to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Searching CARD database and translating to KEGG
|===...........................| Step 3: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|====..........................| Step 4: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for UniProt id D3HKY4 to NCBI
|==............................| Step 2: Translating UniProt id D3HKY4 to NCBI through similar genes strategy
|===...........................| Step 3: Searching CARD database and translating to KEGG
|====..........................| Step 4: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|=====.........................| Step 5: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|======........................| Step 6: Searching CARD database and translating to KEGG
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for UniProt id D3HKY4 to NCBI
|==............................| Step 2: Translating UniProt id D3HKY4 to NCBI through similar genes strategy
|===...........................| Step 3: Searching CARD database and translating to KEGG
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|===...........................| Step 3: Searching CARD database and translating to KEGG
|=.............................| Step 1: Translating from KEGG to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Searching CARD database and translating to KEGG
|=.............................| Step 1: Translating from KEGG to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Searching CARD database and translating to KEGG
|===...........................| Step 3: Trying to get a direct translation for KEGG id llo:LLO_2673 to CARD
|====..........................| Step 4: Translating KEGG id llo:LLO_2673 to CARD through similar genes strategy
|=====.........................| Step 5: Trying to get a direct translation for KEGG id llo:LLO_2673 to CARD
|======........................| Step 6: Translating KEGG id llo:LLO_2673 to CARD through similar genes strategy
|=.............................| Step 1: Translating from KEGG to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Searching CARD database and translating to KEGG
|===...........................| Step 3: Trying to get a direct translation for KEGG id llo:LLO_2673 to CARD
|====..........................| Step 4: Translating KEGG id llo:LLO_2673 to CARD through similar genes strategy
|=====.........................| Step 5: Trying to get a direct translation for KEGG id llo:LLO_2673 to CARD
|======........................| Step 6: Translating KEGG id llo:LLO_2673 to CARD through similar genes strategy
Testing getUniProtSimilarGenes
|=.............................| Step 1: Accessing UniProt similar genes database
|==............................| Step 2: Connecting to UniProt API and retrieving cluster of id G0L217
|===...........................| Step 3: Retrieving and parsing genes of cluster UniRef50_A0A6L9EH79
|=.............................| Step 1: Accessing UniProt similar genes database
|==............................| Step 2: Connecting to UniProt API and retrieving cluster of id G0L217
|===...........................| Step 3: Retrieving and parsing genes of cluster UniRef100_G0L217
|=.............................| Step 1: Accessing UniProt similar genes database
|=.............................| Step 1: Accessing UniProt similar genes database
|=.............................| Step 1: Accessing UniProt similar genes database
|==............................| Step 2: Connecting to UniProt API and retrieving cluster of id G0L217
|===...........................| Step 3: Retrieving and parsing genes of cluster UniRef100_G0L217
|=.............................| Step 1: Accessing UniProt similar genes database
|=.............................| Step 1: Accessing UniProt similar genes database
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Accessing UniProt similar genes database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
Testing getUniProt2KEGG
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id Q6R7P5 to KEGG
|===...........................| Step 3: Translating UniProt id Q6R7P5 to KEGG through similar genes strategy
|====..........................| Step 4: Connecting to UniProt API and retrieving cluster of id Q6R7P5
|=====.........................| Step 5: Retrieving and parsing genes of cluster UniRef100_Q6R7P5
|======........................| Step 6: Trying to get a direct translation for UniProt id Q6R7P5 to KEGG
|=======.......................| Step 7: Translating UniProt id Q6R7P5 to KEGG through similar genes strategy
|========......................| Step 8: Connecting to UniProt API and retrieving cluster of id Q6R7P5
|=========.....................| Step 9: Retrieving and parsing genes of cluster UniRef90_Q6R7P5
|==========....................| Step 10: Trying to get a direct translation for UniProt id Q6R7P5 to KEGG
|===========...................| Step 11: Translating UniProt id Q6R7P5 to KEGG through similar genes strategy
|============..................| Step 12: Connecting to UniProt API and retrieving cluster of id Q6R7P5
|=============.................| Step 13: Retrieving and parsing genes of cluster UniRef50_Q6R7P5
|==============................| Step 14: Trying to get a direct translation for UniProt id Q6R7P5 to KEGG
|===============...............| Step 15: Translating UniProt id Q6R7P5 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id Q6R7P5 to KEGG
|===...........................| Step 3: Translating UniProt id Q6R7P5 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id Q6R7P5 to KEGG
|===...........................| Step 3: Translating UniProt id Q6R7P5 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id Q6R7P5 to KEGG
|===...........................| Step 3: Translating UniProt id Q6R7P5 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Translating from UniProt to KEGG
|=.............................| Step 1: Translating from UniProt to KEGG
|=.............................| Step 1: Translating from UniProt to KEGG
|=.............................| Step 1: Translating from UniProt to KEGG
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id A0A2R4PHC7 to KEGG
|===...........................| Step 3: Translating UniProt id A0A2R4PHC7 to KEGG through similar genes strategy
|====..........................| Step 4: Connecting to UniProt API and retrieving cluster of id A0A2R4PHC7
|=====.........................| Step 5: Retrieving and parsing genes of cluster UniRef100_A0A2R4PHC7
|======........................| Step 6: Trying to get a direct translation for UniProt id A0A2R4PHC7 to KEGG
|=======.......................| Step 7: Translating UniProt id A0A2R4PHC7 to KEGG through similar genes strategy
|========......................| Step 8: Connecting to UniProt API and retrieving cluster of id A0A2R4PHC7
|=========.....................| Step 9: Retrieving and parsing genes of cluster UniRef90_A0A2R4PHC7
|==========....................| Step 10: Trying to get a direct translation for UniProt id A0A2R4PHC7 to KEGG
|===========...................| Step 11: Translating UniProt id A0A2R4PHC7 to KEGG through similar genes strategy
|============..................| Step 12: Connecting to UniProt API and retrieving cluster of id A0A2R4PHC7
|=============.................| Step 13: Retrieving and parsing genes of cluster UniRef50_A0A6J4GZE2
|==============................| Step 14: Trying to get a direct translation for UniProt id A0A2R4PHC7 to KEGG
|===============...............| Step 15: Translating UniProt id A0A2R4PHC7 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id A0A2R4PHC7 to KEGG
|===...........................| Step 3: Translating UniProt id A0A2R4PHC7 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id A0A2R4PHC7 to KEGG
|===...........................| Step 3: Translating UniProt id A0A2R4PHC7 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
|==............................| Step 2: Trying to get a direct translation for UniProt id A0A2R4PHC7 to KEGG
|===...........................| Step 3: Translating UniProt id A0A2R4PHC7 to KEGG through similar genes strategy
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
|=.............................| Step 1: Translating from UniProt to KEGG
The given ID "test" is not registered in UniProt database
Testing getUniProt2NCBIProtein, getUniProt2NCBINucleotide, getUniProt2NCBIGene
|=.............................| Step 1: Translating from UniProt to NCBI Protein
|==............................| Step 2: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI
|=.............................| Step 1: Translating from UniProt to NCBI Nucleotide
|=.............................| Step 1: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI
|==............................| Step 2: Translating UniProt id A0A6H2TXZ6 to NCBI through similar genes strategy
|===...........................| Step 3: Connecting to UniProt API and retrieving cluster of id A0A6H2TXZ6
|====..........................| Step 4: Retrieving and parsing genes of cluster UniRef100_A0A6H2TXZ6
|=.............................| Step 1: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI
|==............................| Step 2: Translating UniProt id A0A6H2TXZ6 to NCBI through similar genes strategy
|===...........................| Step 3: Connecting to UniProt API and retrieving cluster of id A0A6H2TXZ6
|====..........................| Step 4: Retrieving and parsing genes of cluster UniRef90_A0A6H2TY05
|=.............................| Step 1: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI
|==............................| Step 2: Translating UniProt id A0A6H2TXZ6 to NCBI through similar genes strategy
|=.............................| Step 1: Connecting to UniProt API and retrieving cluster of id A0A6H2TXZ6
|==............................| Step 2: Retrieving and parsing genes of cluster UniRef50_A0A0U3EIS7
|=.............................| Step 1: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI
|==............................| Step 2: Translating UniProt id A0A6H2TXZ6 to NCBI through similar genes strategy
|=.............................| Step 1: Translating from UniProt to NCBI Gene
|=.............................| Step 1: Trying to get a direct translation for UniProt id A0A1S7BGS4 to NCBI
|==............................| Step 2: Translating UniProt id A0A1S7BGS4 to NCBI through similar genes strategy
Testing getUniProt2CARD
|=.............................| Step 1: Translating from UniProt to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, 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
|=.............................| Step 1: Translating from UniProt to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|=.............................| Step 1: Translating from UniProt to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating Uniprot id Q8GNY5 to CARD
|===...........................| Step 3: Trying to get a direct translation for Uniprot id Q8GNY5 to CARD
|=.............................| Step 1: Translating from UniProt to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating Uniprot id A0A6H2TXZ6 to CARD
|===...........................| Step 3: Trying to get a direct translation for Uniprot id A0A6H2TXZ6 to CARD
|=.............................| Step 1: Translating from UniProt to CARD
Using a CARD database version downloaded on Wed 09/11/2024 23:16:45, please consider updating it with updateCARDDataBase() function.
|==............................| Step 2: Translating Uniprot id A0A4R5XW64 to CARD
|===...........................| Step 3: Trying to get a direct translation for Uniprot id A0A4R5XW64 to CARD
|====..........................| Step 4: Translating UniProt id A0A4R5XW64 to CARD through similar genes strategy
|=====.........................| Step 5: Trying to get a direct translation for Uniprot id A0A4R5XW64 to CARD
|======........................| Step 6: Translating UniProt id A0A4R5XW64 to CARD through similar genes strategy
RUNIT TEST PROTOCOL -- Wed Sep 11 23:21:07 2024
***********************************************
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
24.747 1.631 279.437
ginmappeR.Rcheck/ginmappeR-Ex.timings
| name | user | system | elapsed | |
| getCARD2KEGG | 4.627 | 0.425 | 16.396 | |
| getCARD2NCBIGene | 0.279 | 0.008 | 1.418 | |
| getCARD2NCBINucleotide | 0.303 | 0.015 | 0.720 | |
| getCARD2NCBIProtein | 0.005 | 0.003 | 0.408 | |
| getCARD2UniProt | 1.071 | 0.133 | 8.528 | |
| getKEGG2CARD | 0.186 | 0.016 | 0.996 | |
| getKEGG2NCBIGene | 0.210 | 0.024 | 1.954 | |
| getKEGG2NCBINucleotide | 0.577 | 0.108 | 7.346 | |
| getKEGG2NCBIProtein | 0.141 | 0.054 | 1.490 | |
| getKEGG2UniProt | 0.002 | 0.000 | 0.102 | |
| getNCBIGene2CARD | 0.208 | 0.008 | 3.908 | |
| getNCBIGene2KEGG | 0.737 | 0.056 | 15.342 | |
| getNCBIGene2NCBINucleotide | 0.052 | 0.000 | 2.218 | |
| getNCBIGene2NCBIProtein | 0.059 | 0.007 | 1.891 | |
| getNCBIGene2UniProt | 0.001 | 0.000 | 0.101 | |
| getNCBIIdenticalProteins | 0.037 | 0.000 | 1.501 | |
| getNCBINucleotide2CARD | 0.096 | 0.008 | 1.340 | |
| getNCBINucleotide2KEGG | 0.703 | 0.067 | 15.502 | |
| getNCBINucleotide2NCBIGene | 0.039 | 0.012 | 1.005 | |
| getNCBINucleotide2NCBIProtein | 0.069 | 0.000 | 0.623 | |
| getNCBINucleotide2UniProt | 0.002 | 0.001 | 0.102 | |
| getNCBIProtein2CARD | 0.059 | 0.000 | 0.626 | |
| getNCBIProtein2KEGG | 0.498 | 0.031 | 29.860 | |
| getNCBIProtein2NCBIGene | 0.088 | 0.000 | 1.096 | |
| getNCBIProtein2NCBINucleotide | 0.058 | 0.003 | 0.638 | |
| getNCBIProtein2UniProt | 0.627 | 0.055 | 7.119 | |
| getUniProt2CARD | 0.359 | 0.004 | 1.913 | |
| getUniProt2KEGG | 0.037 | 0.007 | 0.825 | |
| getUniProt2NCBIGene | 0 | 0 | 0 | |
| getUniProt2NCBINucleotide | 0.290 | 0.001 | 3.512 | |
| getUniProt2NCBIProtein | 0 | 0 | 0 | |
| getUniProtSimilarGenes | 0.145 | 0.008 | 1.368 | |