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CHECK report for RegParallel on riesling1

This page was generated on 2021-01-21 16:01:36 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE RegParallel PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 291/386HostnameOS / ArchINSTALLBUILDCHECK
RegParallel 1.9.0
Kevin Blighe
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/RegParallel
Branch: master
Last Commit: fec40a5
Last Changed Date: 2020-10-27 10:27:59 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: RegParallel
Version: 1.9.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RegParallel.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RegParallel_1.9.0.tar.gz
StartedAt: 2021-01-21 11:42:19 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:45:53 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 214.4 seconds
RetCode: 0
Status:  OK  
CheckDir: RegParallel.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RegParallel.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RegParallel_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RegParallel.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RegParallel/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RegParallel' version '1.9.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'doParallel', 'foreach', 'parallel', 'iterators', 'data.table',
  'stringr', 'survival', 'arm'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'RegParallel' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
RegParallel      25.74   0.18   35.51
bayesglmParallel 17.44   0.00   17.58
glmParallel       0.97   0.08    9.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
RegParallel      27.00   0.22   37.15
bayesglmParallel 18.64   0.04   18.80
glmParallel       0.98   0.04   10.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/RegParallel.Rcheck/00check.log'
for details.



Installation output

RegParallel.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/RegParallel_1.9.0.tar.gz && rm -rf RegParallel.buildbin-libdir && mkdir RegParallel.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RegParallel.buildbin-libdir RegParallel_1.9.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RegParallel_1.9.0.zip && rm RegParallel_1.9.0.tar.gz RegParallel_1.9.0.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  166k  100  166k    0     0  1424k      0 --:--:-- --:--:-- --:--:-- 1437k

install for i386

* installing *source* package 'RegParallel' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RegParallel'
    finding HTML links ... done
    RegParallel-package                     html  
REDIRECT:file	 RegParallel-package.html -> RegParallel-package.html [ SUCCESS ]
    RegParallel                             html  
REDIRECT:topic	 RegParallel -> RegParallel.html [ SUCCESS ]
    finding level-2 HTML links ... done

    bayesglmParallel                        html  
REDIRECT:topic	 bayesglmParallel -> bayesglmParallel.html [ SUCCESS ]
    clogitParallel                          html  
REDIRECT:topic	 clogitParallel -> clogitParallel.html [ SUCCESS ]
    coxphParallel                           html  
REDIRECT:topic	 coxphParallel -> coxphParallel.html [ SUCCESS ]
    glmParallel                             html  
REDIRECT:topic	 glmParallel -> glmParallel.html [ SUCCESS ]
    lmParallel                              html  
REDIRECT:topic	 lmParallel -> lmParallel.html [ SUCCESS ]
    svyglmParallel                          html  
REDIRECT:topic	 svyglmParallel -> svyglmParallel.html [ SUCCESS ]
** 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 'RegParallel' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RegParallel' as RegParallel_1.9.0.zip
* DONE (RegParallel)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RegParallel' successfully unpacked and MD5 sums checked

Tests output

RegParallel.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage('RegParallel')

arm (Version 1.11-2, built: 2020-7-27)

Working directory is D:/biocbuild/bbs-3.13-data-experiment/meat/RegParallel.Rcheck/tests_i386



RUNIT TEST PROTOCOL -- Thu Jan 21 11:45:44 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RegParallel RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.68    0.17    1.84 

RegParallel.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage('RegParallel')

arm (Version 1.11-2, built: 2020-7-27)

Working directory is D:/biocbuild/bbs-3.13-data-experiment/meat/RegParallel.Rcheck/tests_x64



RUNIT TEST PROTOCOL -- Thu Jan 21 11:45:46 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RegParallel RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.79    0.15    1.92 

Example timings

RegParallel.Rcheck/examples_i386/RegParallel-Ex.timings

nameusersystemelapsed
RegParallel25.74 0.1835.51
bayesglmParallel17.44 0.0017.58
clogitParallel3.040.033.20
coxphParallel3.250.003.38
glmParallel0.970.089.57
lmParallel0.950.001.08
svyglmParallel0.100.000.11

RegParallel.Rcheck/examples_x64/RegParallel-Ex.timings

nameusersystemelapsed
RegParallel27.00 0.2237.15
bayesglmParallel18.64 0.0418.80
clogitParallel3.230.003.46
coxphParallel3.410.003.54
glmParallel 0.98 0.0410.14
lmParallel0.860.001.00
svyglmParallel0.110.000.11