Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the perturbatr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/perturbatr.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 1374/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
perturbatr 1.12.0 (landing page) Simon Dirmeier
| 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: perturbatr |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings perturbatr_1.12.0.tar.gz |
StartedAt: 2021-10-14 10:59:58 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:06:33 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 394.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: perturbatr.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings perturbatr_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/perturbatr.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 ‘perturbatr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘perturbatr’ version ‘1.12.0’ * 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 ‘perturbatr’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bootstrap 159.845 0.744 160.598 * 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: Attaching package: 'perturbatr' The following object is masked from 'package:stats': filter > > test_check("perturbatr") ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure (test_util.R:29:3): data plots ────────────────────────────────────── `s <- plot(rnaiscreen)` produced warnings. [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ] 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/perturbatr.Rcheck/00check.log’ for details.
perturbatr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL perturbatr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘perturbatr’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (perturbatr)
perturbatr.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. > # perturbatr: analysis of high-throughput gene perturbation screens > # > # Copyright (C) 2018 Simon Dirmeier > # > # This file is part of perturbatr > # > # perturbatr is free software: you can redistribute it and/or modify > # it under the terms of the GNU General Public License as published by > # the Free Software Foundation, either version 3 of the License, or > # (at your option) any later version. > # > # perturbatr is distributed in the hope that it will be useful, > # but WITHOUT ANY WARRANTY; without even the implied warranty of > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the > # GNU General Public License for more details. > # > # You should have received a copy of the GNU General Public License > # along with perturbatr If not, see <http://www.gnu.org/licenses/>. > > > library(testthat) > library(perturbatr) Attaching package: 'perturbatr' The following object is masked from 'package:stats': filter > > test_check("perturbatr") ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure (test_util.R:29:3): data plots ────────────────────────────────────── `s <- plot(rnaiscreen)` produced warnings. [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ] Error: Test failures Execution halted
perturbatr.Rcheck/perturbatr-Ex.timings
name | user | system | elapsed | |
HMAnalysedPerturbationData-class | 2.794 | 0.172 | 2.967 | |
NetworkAnalysedPerturbationData-class | 2.699 | 0.072 | 2.776 | |
PerturbationData-class | 0.019 | 0.000 | 0.019 | |
bootstrap | 159.845 | 0.744 | 160.598 | |
dataSet-methods | 0.721 | 0.032 | 0.752 | |
diffuse-methods | 1.972 | 0.016 | 1.988 | |
filter-methods | 0.344 | 0.024 | 0.368 | |
geneEffects-methods | 2.277 | 0.052 | 2.329 | |
graph-methods | 2.249 | 0.052 | 2.301 | |
hm-methods | 2.334 | 0.052 | 2.386 | |
inference-methods | 2.258 | 0.044 | 2.304 | |
isBootstrapped-methods | 2.340 | 0.048 | 2.388 | |
modelFit-methods | 2.257 | 0.036 | 2.297 | |
nestedGeneEffects-methods | 2.294 | 0.040 | 2.334 | |
params-methods | 2.468 | 0.045 | 2.513 | |
rbind.PerturbationData | 0.398 | 0.034 | 0.433 | |
rnaiscreen | 2.383 | 0.020 | 2.403 | |