Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BiocSet package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocSet.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 170/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocSet 1.6.1 (landing page) Kayla Morrell
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: BiocSet |
Version: 1.6.1 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiocSet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiocSet_1.6.1.tar.gz |
StartedAt: 2021-10-14 09:01:59 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:07:09 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 310.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BiocSet.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiocSet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiocSet_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BiocSet.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocSet/DESCRIPTION’ ... OK * this is package ‘BiocSet’ version ‘1.6.1’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BiocSet’ 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 R 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 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 mapping_set 46.197 0.809 120.953 BiocSet-methods 8.759 0.568 9.330 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("BiocSet") ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure (test_mapping_set.R:69:5): 'kegg_sets()' works ────────────────────── dim(es_set(es))[1] is not more than c(130L). Difference: -1 [ FAIL 1 | WARN 1 | SKIP 0 | PASS 557 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 See ‘/home/biocbuild/bbs-3.13-bioc/meat/BiocSet.Rcheck/00check.log’ for details.
BiocSet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BiocSet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘BiocSet’ ... ** 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 (BiocSet)
BiocSet.Rcheck/tests/testthat.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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. > library(testthat) > library(BiocSet) Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("BiocSet") ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure (test_mapping_set.R:69:5): 'kegg_sets()' works ────────────────────── dim(es_set(es))[1] is not more than c(130L). Difference: -1 [ FAIL 1 | WARN 1 | SKIP 0 | PASS 557 ] Error: Test failures Execution halted
BiocSet.Rcheck/BiocSet-Ex.timings
name | user | system | elapsed | |
BiocSet-class | 0.181 | 0.012 | 0.193 | |
BiocSet-methods | 8.759 | 0.568 | 9.330 | |
OBOSet-class | 0.130 | 0.020 | 0.149 | |
element_funs | 0.240 | 0.024 | 0.263 | |
elementset_funs | 0.177 | 0.020 | 0.197 | |
genesetcollection | 0.611 | 0.016 | 0.628 | |
import | 0.197 | 0.000 | 0.197 | |
intersect_single | 0.035 | 0.000 | 0.035 | |
mapping_element | 1.061 | 0.052 | 1.114 | |
mapping_set | 46.197 | 0.809 | 120.953 | |
obo_relations | 0.166 | 0.004 | 0.170 | |
set_funs | 0.184 | 0.004 | 0.187 | |
tblelement | 0.009 | 0.000 | 0.010 | |
tblelementset | 0.003 | 0.000 | 0.003 | |
tblset | 0.009 | 0.000 | 0.009 | |
union_single | 0.029 | 0.000 | 0.029 | |
url_ref | 0.084 | 0.000 | 0.084 | |