Multiple platform build/check report for BioC 3.14 - CHECK results for perturbatr on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: perturbatr

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings perturbatr_1.14.0.tar.gz

StartedAt: 2022-04-13 00:25:36 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:55:25 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 1788.9 seconds

RetCode: 1

Status: ERROR

CheckDir: perturbatr.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings perturbatr_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/perturbatr.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'perturbatr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'perturbatr' version '1.14.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
bootstrap 362.46  21.43  383.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
bootstrap 395.15  37.43  432.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("perturbatr")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]
  
  == 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
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("perturbatr")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]
  
  == 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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/perturbatr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/perturbatr_1.14.0.tar.gz && rm -rf perturbatr.buildbin-libdir && mkdir perturbatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=perturbatr.buildbin-libdir perturbatr_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL perturbatr_1.14.0.zip && rm perturbatr_1.14.0.tar.gz perturbatr_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 29 3995k   29 1162k    0     0  1373k      0  0:00:02 --:--:--  0:00:02 1374k
 84 3995k   84 3378k    0     0  1857k      0  0:00:02  0:00:01  0:00:01 1857k
100 3995k  100 3995k    0     0  1990k      0  0:00:02  0:00:02 --:--:-- 1990k

install for i386

* 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
  converting help for package 'perturbatr'
    finding HTML links ... done
    HMAnalysedPerturbationData-class        html  
    NetworkAnalysedPerturbationData-class   html  
    PerturbationData-class                  html  
    bootstrap                               html  
    dataSet-methods                         html  
    diffuse-methods                         html  
    filter-methods                          html  
    geneEffects-methods                     html  
    graph-methods                           html  
    hm-methods                              html  
    inference-methods                       html  
    isBootstrapped-methods                  html  
    modelFit-methods                        html  
    nestedGeneEffects-methods               html  
    params-methods                          html  
    perturbatr-package                      html  
    plot.NetworkAnalysedPerturbationData    html  
    plot.PerturbationData                   html  
    rbind.PerturbationData                  html  
    rnaiscreen                              html  
    setModelData-methods                    html  
** 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

install for x64

* installing *source* package 'perturbatr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'perturbatr' as perturbatr_1.14.0.zip
* DONE (perturbatr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'perturbatr' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]

== 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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]

== 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

name	user	system	elapsed
HMAnalysedPerturbationData-class	3.28	0.38	3.66
NetworkAnalysedPerturbationData-class	2.86	0.37	3.25
PerturbationData-class	0.03	0.00	0.03
bootstrap	362.46	21.43	383.92
dataSet-methods	0.84	0.01	0.86
diffuse-methods	3.36	0.36	3.72
filter-methods	0.44	0.02	0.46
geneEffects-methods	3.42	0.28	3.70
graph-methods	3.00	0.11	3.11
hm-methods	2.83	0.26	3.09
inference-methods	2.59	0.21	2.80
isBootstrapped-methods	3.19	0.37	3.56
modelFit-methods	3.09	0.28	3.38
nestedGeneEffects-methods	2.88	0.33	3.20
params-methods	3.20	0.31	3.52
rbind.PerturbationData	0.50	0.05	0.54
rnaiscreen	3.09	0.34	3.44

name	user	system	elapsed
HMAnalysedPerturbationData-class	3.31	0.39	3.70
NetworkAnalysedPerturbationData-class	2.71	0.29	3.03
PerturbationData-class	0.02	0.00	0.01
bootstrap	395.15	37.43	432.58
dataSet-methods	0.39	0.04	0.44
diffuse-methods	3.39	0.25	3.64
filter-methods	0.38	0.03	0.40
geneEffects-methods	2.91	0.19	3.10
graph-methods	3.29	0.17	3.47
hm-methods	3.06	0.25	3.31
inference-methods	2.91	0.08	2.99
isBootstrapped-methods	2.51	0.05	2.56
modelFit-methods	2.94	0.17	3.11
nestedGeneEffects-methods	2.56	0.06	2.63
params-methods	2.91	0.10	3.00
rbind.PerturbationData	0.37	0.04	0.42
rnaiscreen	3.89	0.16	4.04

CHECK results for perturbatr on tokay2

Summary

Command output

Installation output

Tests output

Example timings