Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 872/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ginmappeR 1.0.2 (landing page) Fernando Sola
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | |||||||||
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: 1.0.2 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ginmappeR_1.0.2.tar.gz |
StartedAt: 2024-07-22 00:50:13 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 00:57:26 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 432.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ginmappeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ginmappeR_1.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-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 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ginmappeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ginmappeR’ version ‘1.0.2’ * 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 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 1.697 0.132 14.685 getCARD2UniProt 0.938 0.135 7.163 getNCBIGene2KEGG 0.452 0.063 7.247 getNCBINucleotide2KEGG 0.417 0.041 6.913 getNCBIProtein2KEGG 0.311 0.023 10.768 * 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-3.19-bioc/meat/ginmappeR.Rcheck/00check.log’ for details.
ginmappeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ginmappeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene Testing getKEGG2CARD Updating CARD database data... CARD database downloaded successfully! Located at /tmp/RtmpFQFjEv/card-data Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Testing getUniProtSimilarGenes The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database Testing getUniProt2KEGG The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database The given ID "test" is not registered in UniProt database Testing getUniProt2NCBIProtein, getUniProt2NCBINucleotide, getUniProt2NCBIGene Testing getUniProt2CARD Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. Using a CARD database version downloaded on Mon 07/22/2024 00:53:35, please consider updating it with updateCARDDataBase() function. RUNIT TEST PROTOCOL -- Mon Jul 22 00:57:22 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 19.618 1.587 241.822
ginmappeR.Rcheck/ginmappeR-Ex.timings
name | user | system | elapsed | |
getCARD2KEGG | 1.697 | 0.132 | 14.685 | |
getCARD2NCBIGene | 0.167 | 0.012 | 1.181 | |
getCARD2NCBINucleotide | 0.555 | 0.048 | 1.003 | |
getCARD2NCBIProtein | 0.005 | 0.000 | 0.405 | |
getCARD2UniProt | 0.938 | 0.135 | 7.163 | |
getKEGG2CARD | 0.176 | 0.000 | 0.922 | |
getKEGG2NCBIGene | 0.137 | 0.005 | 1.851 | |
getKEGG2NCBINucleotide | 0.309 | 0.060 | 4.465 | |
getKEGG2NCBIProtein | 0.105 | 0.012 | 1.304 | |
getKEGG2UniProt | 0.000 | 0.002 | 0.102 | |
getNCBIGene2CARD | 0.145 | 0.016 | 3.078 | |
getNCBIGene2KEGG | 0.452 | 0.063 | 7.247 | |
getNCBIGene2NCBINucleotide | 0.042 | 0.015 | 2.762 | |
getNCBIGene2NCBIProtein | 0.043 | 0.004 | 1.756 | |
getNCBIGene2UniProt | 0.002 | 0.000 | 0.101 | |
getNCBIIdenticalProteins | 0.034 | 0.003 | 1.684 | |
getNCBINucleotide2CARD | 0.045 | 0.000 | 0.145 | |
getNCBINucleotide2KEGG | 0.417 | 0.041 | 6.913 | |
getNCBINucleotide2NCBIGene | 0.048 | 0.008 | 1.003 | |
getNCBINucleotide2NCBIProtein | 0.136 | 0.008 | 0.675 | |
getNCBINucleotide2UniProt | 0.002 | 0.000 | 0.102 | |
getNCBIProtein2CARD | 0.046 | 0.000 | 0.146 | |
getNCBIProtein2KEGG | 0.311 | 0.023 | 10.768 | |
getNCBIProtein2NCBIGene | 0.062 | 0.000 | 1.502 | |
getNCBIProtein2NCBINucleotide | 0.056 | 0.008 | 0.587 | |
getNCBIProtein2UniProt | 0.353 | 0.042 | 4.808 | |
getUniProt2CARD | 0.365 | 0.056 | 1.912 | |
getUniProt2KEGG | 0.033 | 0.000 | 0.660 | |
getUniProt2NCBIGene | 0 | 0 | 0 | |
getUniProt2NCBINucleotide | 0.254 | 0.025 | 3.418 | |
getUniProt2NCBIProtein | 0 | 0 | 0 | |
getUniProtSimilarGenes | 0.087 | 0.003 | 0.756 | |