Multiple platform build/check report for BioC 3.12 - CHECK report for perturbatr on tokay1

Package: perturbatr

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings perturbatr_1.10.0.tar.gz

StartedAt: 2021-05-06 05:28:12 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:47:24 -0400 (Thu, 06 May 2021)

EllapsedTime: 1151.4 seconds

RetCode: 0

Status: OK

CheckDir: perturbatr.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings perturbatr_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/perturbatr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.10.0'
* 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 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 209.51  29.25  238.76
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
bootstrap 214.44  42.65  257.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/perturbatr_1.10.0.tar.gz && rm -rf perturbatr.buildbin-libdir && mkdir perturbatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=perturbatr.buildbin-libdir perturbatr_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL perturbatr_1.10.0.zip && rm perturbatr_1.10.0.tar.gz perturbatr_1.10.0.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
 31 3990k   31 1275k    0     0  17.1M      0 --:--:-- --:--:-- --:--:-- 17.0M
100 3990k  100 3990k    0     0  40.4M      0 --:--:-- --:--:-- --:--:-- 40.5M

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_1.10.0.zip
* DONE (perturbatr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'perturbatr' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 0 | WARN 4 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
 198.23    6.48  204.75


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 0 | WARN 4 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
 232.10    3.64  236.28

name	user	system	elapsed
HMAnalysedPerturbationData-class	4.25	0.50	4.75
NetworkAnalysedPerturbationData-class	3.50	0.44	4.05
PerturbationData-class	0.04	0.00	0.04
bootstrap	209.51	29.25	238.76
dataSet-methods	0.70	0.03	0.73
diffuse-methods	2.77	0.42	3.19
filter-methods	0.48	0.02	0.50
geneEffects-methods	3.47	0.34	3.81
graph-methods	3.20	0.39	3.59
hm-methods	3.89	0.29	4.17
inference-methods	3.26	0.39	3.66
isBootstrapped-methods	3.47	0.31	3.78
modelFit-methods	2.88	0.26	3.14
nestedGeneEffects-methods	3.06	0.41	3.47
params-methods	3.69	0.33	4.01
rbind.PerturbationData	0.50	0.05	0.55
rnaiscreen	4.51	0.17	4.69

name	user	system	elapsed
HMAnalysedPerturbationData-class	4.36	0.36	4.72
NetworkAnalysedPerturbationData-class	3.20	0.31	3.58
PerturbationData-class	0.03	0.00	0.03
bootstrap	214.44	42.65	257.09
dataSet-methods	0.47	0.01	0.48
diffuse-methods	3.01	0.24	3.25
filter-methods	0.61	0.07	0.69
geneEffects-methods	4.45	0.19	4.64
graph-methods	3.83	0.31	4.14
hm-methods	3.66	0.11	3.77
inference-methods	2.62	0.08	2.70
isBootstrapped-methods	3.61	0.13	3.74
modelFit-methods	2.75	0.07	2.82
nestedGeneEffects-methods	2.49	0.08	2.57
params-methods	4.09	0.13	4.22
rbind.PerturbationData	0.39	0.01	0.40
rnaiscreen	3.33	0.08	3.41

CHECK report for perturbatr on tokay1

Summary

Command output

Installation output

Tests output

Example timings