Back to Multiple platform build/check report for BioC 3.8 experimental data

CHECK report for RegParallel on malbec1

This page was generated on 2019-04-11 16:57:00 -0400 (Thu, 11 Apr 2019).

Package 275/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RegParallel 1.0.0
Kevin Blighe
Snapshot Date: 2019-04-11 11:00:25 -0400 (Thu, 11 Apr 2019)
URL: https://git.bioconductor.org/packages/RegParallel
Branch: RELEASE_3_8
Last Commit: 5178d6f
Last Changed Date: 2018-10-30 11:36:26 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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.



Installation output

RegParallel.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output

RegParallel.Rcheck/tests/runTests.Rout


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 

Example timings

RegParallel.Rcheck/RegParallel-Ex.timings

nameusersystemelapsed
RegParallel80.872 2.41642.869
bayesglmParallel28.132 0.41614.851
clogitParallel5.1120.2683.263
coxphParallel4.9280.3122.860
glm.nbParallel28.748 0.38815.137
glmParallel9.1441.2404.322
lmParallel1.0920.1440.865