Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1.2.1 (landing page) Fernando Sola
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | 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 | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ginmappeR |
Version: 1.2.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ginmappeR_1.2.1.tar.gz |
StartedAt: 2024-11-20 08:24:01 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 08:31:20 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 438.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ginmappeR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ginmappeR_1.2.1.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: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ginmappeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ginmappeR’ version ‘1.2.1’ * 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 6.154 0.358 67.772 getCARD2UniProt 0.909 0.120 19.917 getKEGG2NCBINucleotide 0.530 0.052 11.441 getNCBIGene2UniProt 0.482 0.044 11.864 getNCBIProtein2UniProt 0.504 0.019 13.891 getNCBINucleotide2UniProt 0.467 0.025 11.590 getNCBINucleotide2KEGG 0.372 0.118 41.003 getUniProt2NCBINucleotide 0.235 0.013 6.678 getNCBIGene2CARD 0.136 0.020 8.239 getNCBIGene2NCBINucleotide 0.040 0.009 6.766 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: ginmappeR RUnit Tests - 1 test function, 1 error, 0 failures ERROR in /home/biocbuild/tmp/Rtmpw8EGm5/RLIBS_b5c1b79131938/ginmappeR/unitTests/test_KEGG.R: Error while sourcing /home/biocbuild/tmp/Rtmpw8EGm5/RLIBS_b5c1b79131938/ginmappeR/unitTests/test_KEGG.R : Error in RUnit::checkEquals(testFunction, result) : Modes: logical, character target is logical, current is character Test files with failing tests test_KEGG.R /home/biocbuild/tmp/Rtmpw8EGm5/RLIBS_b5c1b79131938/ginmappeR/unitTests/test_KEGG.R Error in BiocGenerics:::testPackage("ginmappeR") : unit tests failed for package ginmappeR Execution halted * 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 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck/00check.log’ for details.
ginmappeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ginmappeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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, 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 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 |=.............................| Step 1: Translating from KEGG to NCBI Gene |=.............................| Step 1: Trying to get a direct translation for KEGG id aag:5579347 to NCBI |==............................| Step 2: Translating KEGG id aag:5579347 to NCBI through similar genes strategy |===...........................| Step 3: Trying to get a direct translation for UniProt id A0A1S4G4Z1 to NCBI |====..........................| Step 4: Translating UniProt id A0A1S4G4Z1 to NCBI through similar genes strategy |=====.........................| Step 5: Trying to get a direct translation for KEGG id aag:5579347 to NCBI |======........................| Step 6: Translating KEGG id aag:5579347 to NCBI through similar genes strategy API(s) connection failed: Error in RUnit::checkEquals(testFunction, result) : Modes: logical, character target is logical, current is character 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 Testing getUniProt2KEGG |=.............................| Step 1: Translating from UniProt to KEGG |==............................| Step 2: Trying to get a direct translation for UniProt id A0A6I6H1L5 to KEGG 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 Testing getUniProt2CARD |=.............................| Step 1: Translating from UniProt to CARD Updating CARD database data... Deleting previous versions of CARD if any. Downloading latest version Extracting database CARD database downloaded successfully! Located at /home/biocbuild/tmp/Rtmp3WJgr4/card-data CARD database version 3.3.0 (2024-08-26) |==............................| Step 2: Translating Uniprot id A0A1S7BGS4 to CARD |===...........................| Step 3: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD RUNIT TEST PROTOCOL -- Wed Nov 20 08:31:17 2024 *********************************************** Number of test functions: 1 Number of errors: 1 Number of failures: 0 1 Test Suite : ginmappeR RUnit Tests - 1 test function, 1 error, 0 failures ERROR in /home/biocbuild/tmp/Rtmpw8EGm5/RLIBS_b5c1b79131938/ginmappeR/unitTests/test_KEGG.R: Error while sourcing /home/biocbuild/tmp/Rtmpw8EGm5/RLIBS_b5c1b79131938/ginmappeR/unitTests/test_KEGG.R : Error in RUnit::checkEquals(testFunction, result) : Modes: logical, character target is logical, current is character Test files with failing tests test_KEGG.R /home/biocbuild/tmp/Rtmpw8EGm5/RLIBS_b5c1b79131938/ginmappeR/unitTests/test_KEGG.R Error in BiocGenerics:::testPackage("ginmappeR") : unit tests failed for package ginmappeR Execution halted
ginmappeR.Rcheck/ginmappeR-Ex.timings
name | user | system | elapsed | |
getCARD2KEGG | 6.154 | 0.358 | 67.772 | |
getCARD2NCBIGene | 0.211 | 0.032 | 3.794 | |
getCARD2NCBINucleotide | 0.264 | 0.040 | 0.705 | |
getCARD2NCBIProtein | 0.004 | 0.004 | 0.409 | |
getCARD2UniProt | 0.909 | 0.120 | 19.917 | |
getKEGG2CARD | 0.160 | 0.016 | 0.628 | |
getKEGG2NCBIGene | 0.105 | 0.012 | 2.979 | |
getKEGG2NCBINucleotide | 0.530 | 0.052 | 11.441 | |
getKEGG2NCBIProtein | 0.086 | 0.004 | 1.474 | |
getKEGG2UniProt | 0.002 | 0.000 | 0.102 | |
getNCBIGene2CARD | 0.136 | 0.020 | 8.239 | |
getNCBIGene2KEGG | 0.022 | 0.008 | 1.894 | |
getNCBIGene2NCBINucleotide | 0.040 | 0.009 | 6.766 | |
getNCBIGene2NCBIProtein | 0.043 | 0.003 | 3.124 | |
getNCBIGene2UniProt | 0.482 | 0.044 | 11.864 | |
getNCBIIdenticalProteins | 0.028 | 0.008 | 2.694 | |
getNCBINucleotide2CARD | 0.057 | 0.008 | 0.894 | |
getNCBINucleotide2KEGG | 0.372 | 0.118 | 41.003 | |
getNCBINucleotide2NCBIGene | 0.040 | 0.000 | 2.132 | |
getNCBINucleotide2NCBIProtein | 0.062 | 0.004 | 0.871 | |
getNCBINucleotide2UniProt | 0.467 | 0.025 | 11.590 | |
getNCBIProtein2CARD | 0.068 | 0.000 | 1.329 | |
getNCBIProtein2KEGG | 0.021 | 0.008 | 1.946 | |
getNCBIProtein2NCBIGene | 0.034 | 0.000 | 2.902 | |
getNCBIProtein2NCBINucleotide | 0.064 | 0.000 | 0.855 | |
getNCBIProtein2UniProt | 0.504 | 0.019 | 13.891 | |
getUniProt2CARD | 0.277 | 0.008 | 4.978 | |
getUniProt2KEGG | 0.035 | 0.000 | 0.720 | |
getUniProt2NCBIGene | 0 | 0 | 0 | |
getUniProt2NCBINucleotide | 0.235 | 0.013 | 6.678 | |
getUniProt2NCBIProtein | 0 | 0 | 0 | |
getUniProtSimilarGenes | 0.062 | 0.000 | 2.369 | |