Multiple platform build/check report for BioC 3.9 - CHECK report for perturbatr on tokay2

Package: perturbatr

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings perturbatr_1.4.0.tar.gz

StartedAt: 2019-10-16 05:56:20 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:10:29 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 848.7 seconds

RetCode: 0

Status: OK

CheckDir: perturbatr.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings perturbatr_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/perturbatr.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.4.0'
* 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 or elapsed time > 5s
                                       user system elapsed
bootstrap                             76.73  29.36  106.14
HMAnalysedPerturbationData-class       6.25   4.03   10.28
NetworkAnalysedPerturbationData-class  5.93   3.85    9.86
rnaiscreen                             5.73   2.78    8.51
inference-methods                      5.86   2.43    8.28
diffuse-methods                        5.25   2.72    7.97
isBootstrapped-methods                 5.46   1.90    7.36
graph-methods                          5.25   1.86    7.11
nestedGeneEffects-methods              4.99   2.12    7.11
modelFit-methods                       5.15   1.91    7.07
params-methods                         5.12   1.94    7.06
hm-methods                             5.03   1.90    6.95
geneEffects-methods                    4.95   1.42    6.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
bootstrap                             75.33  24.83  100.19
HMAnalysedPerturbationData-class       7.27   5.01   12.28
NetworkAnalysedPerturbationData-class  5.61   5.32   10.95
diffuse-methods                        6.19   1.56    7.75
modelFit-methods                       6.19   1.29    7.48
hm-methods                             5.12   1.65    6.78
geneEffects-methods                    5.20   0.63    5.82
isBootstrapped-methods                 5.05   0.77    5.81
graph-methods                          4.66   1.14    5.80
params-methods                         4.48   1.30    5.78
rnaiscreen                             5.27   0.50    5.77
inference-methods                      5.00   0.41    5.41
* 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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/perturbatr_1.4.0.tar.gz && rm -rf perturbatr.buildbin-libdir && mkdir perturbatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=perturbatr.buildbin-libdir perturbatr_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL perturbatr_1.4.0.zip && rm perturbatr_1.4.0.tar.gz perturbatr_1.4.0.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
100 3984k  100 3984k    0     0  40.1M      0 --:--:-- --:--:-- --:--:-- 43.2M

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_1.4.0.zip
* DONE (perturbatr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'perturbatr' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 .
> 
> 
> library(testthat)
> library(perturbatr)

Attaching package: 'perturbatr'

The following object is masked from 'package:stats':

    filter

> 
> test_check("perturbatr")
== testthat results  ===========================================================
[ OK: 41 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 164.70   27.95  192.90


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 .
> 
> 
> library(testthat)
> library(perturbatr)

Attaching package: 'perturbatr'

The following object is masked from 'package:stats':

    filter

> 
> test_check("perturbatr")
== testthat results  ===========================================================
[ OK: 41 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 133.75   20.62  154.42

name	user	system	elapsed
HMAnalysedPerturbationData-class	6.25	4.03	10.28
NetworkAnalysedPerturbationData-class	5.93	3.85	9.86
PerturbationData-class	0.02	0.00	0.02
bootstrap	76.73	29.36	106.14
dataSet-methods	0.67	0.01	0.69
diffuse-methods	5.25	2.72	7.97
filter-methods	0.50	0.05	0.54
geneEffects-methods	4.95	1.42	6.39
graph-methods	5.25	1.86	7.11
hm-methods	5.03	1.90	6.95
inference-methods	5.86	2.43	8.28
isBootstrapped-methods	5.46	1.90	7.36
modelFit-methods	5.15	1.91	7.07
nestedGeneEffects-methods	4.99	2.12	7.11
params-methods	5.12	1.94	7.06
rbind.PerturbationData	0.47	0.03	0.50
rnaiscreen	5.73	2.78	8.51

name	user	system	elapsed
HMAnalysedPerturbationData-class	7.27	5.01	12.28
NetworkAnalysedPerturbationData-class	5.61	5.32	10.95
PerturbationData-class	0.02	0.00	0.01
bootstrap	75.33	24.83	100.19
dataSet-methods	1.06	0.06	1.13
diffuse-methods	6.19	1.56	7.75
filter-methods	0.58	0.03	0.61
geneEffects-methods	5.20	0.63	5.82
graph-methods	4.66	1.14	5.80
hm-methods	5.12	1.65	6.78
inference-methods	5.00	0.41	5.41
isBootstrapped-methods	5.05	0.77	5.81
modelFit-methods	6.19	1.29	7.48
nestedGeneEffects-methods	4.39	0.55	4.94
params-methods	4.48	1.30	5.78
rbind.PerturbationData	0.42	0.04	0.47
rnaiscreen	5.27	0.50	5.77

CHECK report for perturbatr on tokay2

Summary

Command output

Installation output

Tests output

Example timings