Fernando Sola
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/ginmappeR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 488e384 |
| git_last_commit_date: 2024-12-02 11:34:13 -0500 (Mon, 02 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:09 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 864/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ginmappeR 1.2.3 (landing page) Fernando Sola
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.2.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ginmappeR_1.2.3.tar.gz |
| StartedAt: 2025-01-03 20:44:16 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 20:54:11 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 595.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ginmappeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ginmappeR_1.2.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.2.3’
* 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 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 8.879 0.221 33.359
getCARD2UniProt 3.087 0.174 25.061
getUniProt2CARD 2.927 0.131 11.791
getKEGG2NCBINucleotide 2.124 0.169 40.593
getNCBINucleotide2KEGG 1.061 0.129 210.251
getNCBIProtein2UniProt 0.635 0.067 22.737
getNCBIGene2UniProt 0.566 0.054 20.945
getNCBINucleotide2UniProt 0.558 0.054 19.592
getUniProt2NCBINucleotide 0.516 0.052 8.734
getNCBIGene2CARD 0.149 0.010 7.571
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.
ginmappeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ginmappeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.
> 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, saveRDS, 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
[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/RtmpWcULf9/card-data
CARD database version 4.0.0 (2024-12-17)
|==............................| 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
[1] NA
Test failed:
NA != QIB98918.1
Testing getUniProt2CARD
|=.............................| Step 1: Translating from UniProt to CARD
Using a CARD database version downloaded on Fri 01/03/2025 20:53:30, 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 4: Translating Uniprot id A0A1S7BGS4 to CARD
|=====.........................| Step 5: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|======........................| Step 6: Translating Uniprot id A0A1S7BGS4 to CARD
|=======.......................| Step 7: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|========......................| Step 8: Translating Uniprot id A0A1S7BGS4 to CARD
|=========.....................| Step 9: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|==========....................| Step 10: Translating Uniprot id A0A1S7BGS4 to CARD
|===========...................| Step 11: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|============..................| Step 12: Translating Uniprot id A0A1S7BGS4 to CARD
|=============.................| Step 13: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|==============................| Step 14: Translating Uniprot id A0A1S7BGS4 to CARD
|===============...............| Step 15: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|================..............| Step 16: Translating Uniprot id A0A1S7BGS4 to CARD
|=================.............| Step 17: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|==================............| Step 18: Translating Uniprot id A0A1S7BGS4 to CARD
|===================...........| Step 19: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|====================..........| Step 20: Translating Uniprot id A0A1S7BGS4 to CARD
|=====================.........| Step 21: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|======================........| Step 22: Translating Uniprot id A0A1S7BGS4 to CARD
|=======================.......| Step 23: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|========================......| Step 24: Translating Uniprot id A0A1S7BGS4 to CARD
|=========================.....| Step 25: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|==========================....| Step 26: Translating Uniprot id A0A1S7BGS4 to CARD
|===========================...| Step 27: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|============================..| Step 28: Translating Uniprot id A0A1S7BGS4 to CARD
|=============================.| Step 29: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|..............................| Step 30: Translating Uniprot id A0A1S7BGS4 to CARD
|=.............................| Step 31: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|==............................| Step 32: Translating Uniprot id A0A1S7BGS4 to CARD
|===...........................| Step 33: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|====..........................| Step 34: Translating Uniprot id A0A1S7BGS4 to CARD
|=====.........................| Step 35: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|======........................| Step 36: Translating Uniprot id A0A1S7BGS4 to CARD
|=======.......................| Step 37: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|========......................| Step 38: Translating Uniprot id A0A1S7BGS4 to CARD
|=========.....................| Step 39: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
|==========....................| Step 40: Translating Uniprot id A0A1S7BGS4 to CARD
|===========...................| Step 41: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD
[1] NA
Test failed:
NA != ARO:3004185
RUNIT TEST PROTOCOL -- Fri Jan 3 20:54:00 2025
***********************************************
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
15.459 0.668 38.743
ginmappeR.Rcheck/ginmappeR-Ex.timings
| name | user | system | elapsed | |
| getCARD2KEGG | 8.879 | 0.221 | 33.359 | |
| getCARD2NCBIGene | 0.260 | 0.014 | 2.284 | |
| getCARD2NCBINucleotide | 0.350 | 0.019 | 1.368 | |
| getCARD2NCBIProtein | 0.006 | 0.002 | 1.009 | |
| getCARD2UniProt | 3.087 | 0.174 | 25.061 | |
| getKEGG2CARD | 0.180 | 0.005 | 1.365 | |
| getKEGG2NCBIGene | 0.071 | 0.003 | 2.566 | |
| getKEGG2NCBINucleotide | 2.124 | 0.169 | 40.593 | |
| getKEGG2NCBIProtein | 0.069 | 0.005 | 1.864 | |
| getKEGG2UniProt | 0.001 | 0.000 | 0.252 | |
| getNCBIGene2CARD | 0.149 | 0.010 | 7.571 | |
| getNCBIGene2KEGG | 0.020 | 0.002 | 2.316 | |
| getNCBIGene2NCBINucleotide | 0.033 | 0.002 | 3.294 | |
| getNCBIGene2NCBIProtein | 0.032 | 0.002 | 2.396 | |
| getNCBIGene2UniProt | 0.566 | 0.054 | 20.945 | |
| getNCBIIdenticalProteins | 0.024 | 0.002 | 1.859 | |
| getNCBINucleotide2CARD | 0.084 | 0.004 | 0.950 | |
| getNCBINucleotide2KEGG | 1.061 | 0.129 | 210.251 | |
| getNCBINucleotide2NCBIGene | 0.025 | 0.002 | 1.722 | |
| getNCBINucleotide2NCBIProtein | 0.082 | 0.003 | 0.957 | |
| getNCBINucleotide2UniProt | 0.558 | 0.054 | 19.592 | |
| getNCBIProtein2CARD | 0.077 | 0.004 | 0.940 | |
| getNCBIProtein2KEGG | 0.020 | 0.002 | 2.254 | |
| getNCBIProtein2NCBIGene | 0.023 | 0.002 | 1.598 | |
| getNCBIProtein2NCBINucleotide | 0.090 | 0.004 | 0.954 | |
| getNCBIProtein2UniProt | 0.635 | 0.067 | 22.737 | |
| getUniProt2CARD | 2.927 | 0.131 | 11.791 | |
| getUniProt2KEGG | 0.024 | 0.002 | 3.617 | |
| getUniProt2NCBIGene | 0 | 0 | 0 | |
| getUniProt2NCBINucleotide | 0.516 | 0.052 | 8.734 | |
| getUniProt2NCBIProtein | 0.000 | 0.001 | 0.000 | |
| getUniProtSimilarGenes | 0.041 | 0.005 | 1.014 | |