Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:40 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for perturbatr on nebbiolo1


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1438/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
perturbatr 1.16.0  (landing page)
Simon Dirmeier
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/perturbatr
git_branch: RELEASE_3_15
git_last_commit: e98d45e
git_last_commit_date: 2022-04-26 11:47:58 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: perturbatr
Version: 1.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings perturbatr_1.16.0.tar.gz
StartedAt: 2022-10-18 21:06:16 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:19:13 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 777.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: perturbatr.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings perturbatr_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/perturbatr.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.16.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'perturbatr' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.15-bioc/meat/perturbatr.Rcheck/00install.out’ for details.
* 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 300.733   1.24 301.983
* 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:
  
  Warning message:
  Package 'perturbatr' is deprecated and will be removed from
    Bioconductor version 3.16 
  > 
  > test_check("perturbatr")
  [ FAIL 1 | WARN 19 | SKIP 0 | PASS 40 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_util.R:29'): data plots ──────────────────────────────────────
  `s <- plot(rnaiscreen)` produced warnings.
  
  [ FAIL 1 | WARN 19 | 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, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/perturbatr.Rcheck/00check.log’
for details.


Installation output

perturbatr.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL perturbatr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
Warning: Package 'perturbatr' is deprecated and will be removed from
  Bioconductor version 3.16
** testing if installed package can be loaded from final location
Warning: Package 'perturbatr' is deprecated and will be removed from
  Bioconductor version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (perturbatr)

Tests output

perturbatr.Rcheck/tests/testthat.Rout.fail


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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

Warning message:
Package 'perturbatr' is deprecated and will be removed from
  Bioconductor version 3.16 
> 
> test_check("perturbatr")
[ FAIL 1 | WARN 19 | SKIP 0 | PASS 40 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_util.R:29'): data plots ──────────────────────────────────────
`s <- plot(rnaiscreen)` produced warnings.

[ FAIL 1 | WARN 19 | SKIP 0 | PASS 40 ]
Error: Test failures
Execution halted

Example timings

perturbatr.Rcheck/perturbatr-Ex.timings

nameusersystemelapsed
HMAnalysedPerturbationData-class2.9690.1513.121
NetworkAnalysedPerturbationData-class2.8730.1202.994
PerturbationData-class0.0320.0000.032
bootstrap300.733 1.240301.983
dataSet-methods0.3720.0360.408
diffuse-methods2.5880.0202.608
filter-methods0.7880.0280.816
geneEffects-methods2.0720.0322.104
graph-methods2.6120.0322.644
hm-methods2.6080.0282.637
inference-methods2.2320.0282.259
isBootstrapped-methods2.090.042.13
modelFit-methods2.3860.0362.422
nestedGeneEffects-methods2.8220.0282.850
params-methods2.0370.0692.107
rbind.PerturbationData0.4510.0420.493
rnaiscreen2.5450.0482.593