Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1.0.0 (landing page) Fernando Sola
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | 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: 1.0.0 |
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_1.0.0.tar.gz |
StartedAt: 2024-06-05 20:44:03 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 20:48:20 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 257.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ginmappeR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ginmappeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ginmappeR’ version ‘1.0.0’ * 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 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 3.222 0.115 28.234 getKEGG2NCBINucleotide 0.580 0.009 6.429 getCARD2UniProt 0.456 0.035 12.547 getNCBINucleotide2KEGG 0.256 0.025 8.157 getNCBIGene2KEGG 0.254 0.017 10.967 getNCBIProtein2KEGG 0.156 0.017 11.748 * 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: Test not TRUE Test files with failing tests test_KEGG.R /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_KEGG.R test_UniProt.R /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_UniProt.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 ‘/Users/biocbuild/bbs-3.19-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-x86_64/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.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RSQLite Testing getKEGG2UniProt API(s) connection failed: Error in RUnit::checkEquals(testFunction, result) : 1 string mismatch Testing getUniProtSimilarGenes Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5", : Test not TRUE RUNIT TEST PROTOCOL -- Wed Jun 5 20:48:08 2024 *********************************************** Number of test functions: 2 Number of errors: 2 Number of failures: 0 1 Test Suite : ginmappeR RUnit Tests - 2 test functions, 2 errors, 0 failures ERROR in /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_KEGG.R: Error while sourcing /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_KEGG.R : Error in RUnit::checkEquals(testFunction, result) : 1 string mismatch ERROR in /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_UniProt.R: Error while sourcing /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5", : Test not TRUE Test files with failing tests test_KEGG.R /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_KEGG.R test_UniProt.R /private/tmp/Rtmpvb0FJn/RLIBS_153430c379a4/ginmappeR/unitTests/test_UniProt.R Error in BiocGenerics:::testPackage("ginmappeR") : unit tests failed for package ginmappeR Execution halted
ginmappeR.Rcheck/ginmappeR-Ex.timings
name | user | system | elapsed | |
getCARD2KEGG | 3.222 | 0.115 | 28.234 | |
getCARD2NCBIGene | 0.141 | 0.007 | 1.249 | |
getCARD2NCBINucleotide | 0.423 | 0.013 | 1.182 | |
getCARD2NCBIProtein | 0.006 | 0.002 | 0.716 | |
getCARD2UniProt | 0.456 | 0.035 | 12.547 | |
getKEGG2CARD | 0.158 | 0.006 | 1.741 | |
getKEGG2NCBIGene | 0.091 | 0.004 | 3.328 | |
getKEGG2NCBINucleotide | 0.580 | 0.009 | 6.429 | |
getKEGG2NCBIProtein | 0.076 | 0.002 | 2.067 | |
getKEGG2UniProt | 0.001 | 0.001 | 0.107 | |
getNCBIGene2CARD | 0.128 | 0.006 | 4.348 | |
getNCBIGene2KEGG | 0.254 | 0.017 | 10.967 | |
getNCBIGene2NCBINucleotide | 0.035 | 0.005 | 3.204 | |
getNCBIGene2NCBIProtein | 0.034 | 0.004 | 2.147 | |
getNCBIGene2UniProt | 0.002 | 0.000 | 0.102 | |
getNCBIIdenticalProteins | 0.025 | 0.003 | 1.789 | |
getNCBINucleotide2CARD | 0.058 | 0.004 | 0.297 | |
getNCBINucleotide2KEGG | 0.256 | 0.025 | 8.157 | |
getNCBINucleotide2NCBIGene | 0.024 | 0.003 | 1.219 | |
getNCBINucleotide2NCBIProtein | 0.060 | 0.004 | 0.755 | |
getNCBINucleotide2UniProt | 0.002 | 0.001 | 0.234 | |
getNCBIProtein2CARD | 0.060 | 0.003 | 0.297 | |
getNCBIProtein2KEGG | 0.156 | 0.017 | 11.748 | |
getNCBIProtein2NCBIGene | 0.049 | 0.006 | 2.997 | |
getNCBIProtein2NCBINucleotide | 0.087 | 0.005 | 0.778 | |
getNCBIProtein2UniProt | 0.210 | 0.011 | 4.724 | |
getUniProt2CARD | 0.223 | 0.010 | 1.756 | |
getUniProt2KEGG | 0.021 | 0.002 | 0.702 | |
getUniProt2NCBIGene | 0.000 | 0.000 | 0.001 | |
getUniProt2NCBINucleotide | 0.157 | 0.005 | 3.837 | |
getUniProt2NCBIProtein | 0 | 0 | 0 | |
getUniProtSimilarGenes | 0.039 | 0.003 | 1.194 | |