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CHECK report for INDEED on tokay2

This page was generated on 2020-10-17 11:56:52 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE INDEED PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 875/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INDEED 2.2.0
Ressom group
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/INDEED
Branch: RELEASE_3_11
Last Commit: 347d71d
Last Changed Date: 2020-04-27 15:18:28 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: INDEED
Version: 2.2.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:INDEED.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings INDEED_2.2.0.tar.gz
StartedAt: 2020-10-17 05:12:31 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:15:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 190.0 seconds
RetCode: 0
Status:  OK  
CheckDir: INDEED.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:INDEED.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings INDEED_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/INDEED.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'INDEED/DESCRIPTION' ... OK
* this is package 'INDEED' version '2.2.0'
* package encoding: UTF-8
* 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 'INDEED' 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
partial_cor     8.98   0.06    9.29
network_display 5.67   0.07    6.13
non_partial_cor 5.47   0.00    5.46
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
partial_cor     7.94   0.01    8.65
non_partial_cor 5.50   0.00    5.50
network_display 5.22   0.05    5.88
* 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


Installation output

INDEED.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/INDEED_2.2.0.tar.gz && rm -rf INDEED.buildbin-libdir && mkdir INDEED.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=INDEED.buildbin-libdir INDEED_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL INDEED_2.2.0.zip && rm INDEED_2.2.0.tar.gz INDEED_2.2.0.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 1898k  100 1898k    0     0  22.6M      0 --:--:-- --:--:-- --:--:-- 24.7M

install for i386

* installing *source* package 'INDEED' ...
** 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 'INDEED'
    finding HTML links ... done
    INDEED                                  html  
    Met_GU                                  html  
    Met_Group_GU                            html  
    Met_name_GU                             html  
    choose_rho                              html  
    compute_cor                             html  
    compute_dns                             html  
    compute_par                             html  
    loglik_ave                              html  
    network_display                         html  
    non_partial_cor                         html  
    partial_cor                             html  
    permutation_cor                         html  
    permutation_pc                          html  
    permutation_thres                       html  
    pvalue_M_GU                             html  
    pvalue_logit                            html  
    scale_range                             html  
    select_rho_partial                      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 'INDEED' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'INDEED' as INDEED_2.2.0.zip
* DONE (INDEED)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'INDEED' successfully unpacked and MD5 sums checked

Tests output

INDEED.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library(testthat)
> library(INDEED)
Loading required package: glasso
> 
> test_check("INDEED")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   1.40    0.15    1.54 

INDEED.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library(testthat)
> library(INDEED)
Loading required package: glasso
> 
> test_check("INDEED")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   1.76    0.10    1.87 

Example timings

INDEED.Rcheck/examples_i386/INDEED-Ex.timings

nameusersystemelapsed
network_display5.670.076.13
non_partial_cor5.470.005.46
partial_cor8.980.069.29
select_rho_partial0.850.030.87

INDEED.Rcheck/examples_x64/INDEED-Ex.timings

nameusersystemelapsed
network_display5.220.055.88
non_partial_cor5.50.05.5
partial_cor7.940.018.65
select_rho_partial0.840.050.89