Package: RegParallel

Version: 1.0.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RegParallel.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RegParallel_1.0.0.tar.gz

StartedAt: 2019-04-11 16:41:37 -0400 (Thu, 11 Apr 2019)

EndedAt: 2019-04-11 16:50:10 -0400 (Thu, 11 Apr 2019)

EllapsedTime: 512.5 seconds

RetCode: 0

Status:  OK

CheckDir: RegParallel.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RegParallel.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RegParallel_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/RegParallel.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RegParallel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegParallel’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Depends: includes the non-default packages:
  ‘doParallel’ ‘foreach’ ‘parallel’ ‘iterators’ ‘data.table’ ‘stringr’
  ‘survival’ ‘arm’ ‘MASS’
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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RegParallel      80.872  2.416  42.869
glm.nbParallel   28.748  0.388  15.137
bayesglmParallel 28.132  0.416  14.851
glmParallel       9.144  1.240   4.322
clogitParallel    5.112  0.268   3.263
coxphParallel     4.928  0.312   2.860
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.8-data-experiment/meat/RegParallel.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RegParallel
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RegParallel’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RegParallel)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1.10-1, built: 2018-4-12)

Working directory is /home/biocbuild/bbs-3.8-data-experiment/meat/RegParallel.Rcheck/tests



RUNIT TEST PROTOCOL -- Thu Apr 11 16:50:07 2019 
*********************************************** 
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 
  1.192   0.084   1.264 

name	user	system	elapsed
RegParallel	80.872	2.416	42.869
bayesglmParallel	28.132	0.416	14.851
clogitParallel	5.112	0.268	3.263
coxphParallel	4.928	0.312	2.860
glm.nbParallel	28.748	0.388	15.137
glmParallel	9.144	1.240	4.322
lmParallel	1.092	0.144	0.865