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 20:25 -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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ginmappeR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ginmappeR_1.0.0.tar.gz |
StartedAt: 2024-06-06 04:24:24 -0400 (Thu, 06 Jun 2024) |
EndedAt: 2024-06-06 04:31:34 -0400 (Thu, 06 Jun 2024) |
EllapsedTime: 429.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ginmappeR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ginmappeR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ginmappeR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 getKEGG2NCBINucleotide 0.75 0.00 6.41 getCARD2UniProt 0.56 0.11 5.81 getNCBIGene2KEGG 0.31 0.01 7.00 getNCBINucleotide2KEGG 0.25 0.06 6.84 getNCBIProtein2KEGG 0.24 0.04 11.23 getCARD2KEGG 0.14 0.12 98.97 * 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 F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/ginmappeR/unitTests/test_KEGG.R test_UniProt.R F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/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 'F:/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck/00check.log' for details.
ginmappeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ginmappeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 -- Thu Jun 6 04:31:14 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 F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/ginmappeR/unitTests/test_KEGG.R: Error while sourcing F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/ginmappeR/unitTests/test_KEGG.R : Error in RUnit::checkEquals(testFunction, result) : 1 string mismatch ERROR in F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/ginmappeR/unitTests/test_UniProt.R: Error while sourcing F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/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 F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/ginmappeR/unitTests/test_KEGG.R test_UniProt.R F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpslYD5j/RLIBS_33cc68c7491a/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 | 0.14 | 0.12 | 98.97 | |
getCARD2NCBIGene | 0.18 | 0.02 | 1.45 | |
getCARD2NCBINucleotide | 0.28 | 0.01 | 0.75 | |
getCARD2NCBIProtein | 0.00 | 0.00 | 0.44 | |
getCARD2UniProt | 0.56 | 0.11 | 5.81 | |
getKEGG2CARD | 0.13 | 0.00 | 1.62 | |
getKEGG2NCBIGene | 0.06 | 0.00 | 2.52 | |
getKEGG2NCBINucleotide | 0.75 | 0.00 | 6.41 | |
getKEGG2NCBIProtein | 0.11 | 0.00 | 1.98 | |
getKEGG2UniProt | 0.00 | 0.00 | 0.11 | |
getNCBIGene2CARD | 0.11 | 0.02 | 3.83 | |
getNCBIGene2KEGG | 0.31 | 0.01 | 7.00 | |
getNCBIGene2NCBINucleotide | 0.02 | 0.00 | 2.40 | |
getNCBIGene2NCBIProtein | 0.0 | 0.0 | 1.8 | |
getNCBIGene2UniProt | 0.00 | 0.00 | 0.11 | |
getNCBIIdenticalProteins | 0.01 | 0.02 | 1.75 | |
getNCBINucleotide2CARD | 0.07 | 0.00 | 0.19 | |
getNCBINucleotide2KEGG | 0.25 | 0.06 | 6.84 | |
getNCBINucleotide2NCBIGene | 0.01 | 0.02 | 1.03 | |
getNCBINucleotide2NCBIProtein | 0.07 | 0.00 | 0.64 | |
getNCBINucleotide2UniProt | 0.00 | 0.00 | 0.11 | |
getNCBIProtein2CARD | 0.04 | 0.00 | 0.19 | |
getNCBIProtein2KEGG | 0.24 | 0.04 | 11.23 | |
getNCBIProtein2NCBIGene | 0.01 | 0.00 | 1.10 | |
getNCBIProtein2NCBINucleotide | 0.06 | 0.02 | 0.62 | |
getNCBIProtein2UniProt | 0.30 | 0.01 | 4.39 | |
getUniProt2CARD | 0.27 | 0.04 | 1.74 | |
getUniProt2KEGG | 0.03 | 0.00 | 0.73 | |
getUniProt2NCBIGene | 0 | 0 | 0 | |
getUniProt2NCBINucleotide | 0.11 | 0.00 | 3.27 | |
getUniProt2NCBIProtein | 0 | 0 | 0 | |
getUniProtSimilarGenes | 0.03 | 0.00 | 0.62 | |