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CHECK report for beachmat on nebbiolo1

This page was generated on 2020-09-27 10:15:13 -0400 (Sun, 27 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE beachmat PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 126/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beachmat 2.5.5
Aaron Lun
Snapshot Date: 2020-09-26 14:42:06 -0400 (Sat, 26 Sep 2020)
URL: https://git.bioconductor.org/packages/beachmat
Branch: master
Last Commit: aaaa782
Last Changed Date: 2020-09-24 01:27:58 -0400 (Thu, 24 Sep 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beachmat
Version: 2.5.5
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:beachmat.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings beachmat_2.5.5.tar.gz
StartedAt: 2020-09-26 21:41:01 -0400 (Sat, 26 Sep 2020)
EndedAt: 2020-09-26 21:45:33 -0400 (Sat, 26 Sep 2020)
EllapsedTime: 271.7 seconds
RetCode: 0
Status:  OK 
CheckDir: beachmat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:beachmat.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings beachmat_2.5.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/beachmat.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘2.5.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘beachmat’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘DelayedArray:::bplapply2’
  See the note in ?`:::` about the use of this operator.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
colBlockApply 9.196  3.478  21.009
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/beachmat.Rcheck/00check.log’
for details.



Installation output

beachmat.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL beachmat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘beachmat’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beachmat)

Tests output

beachmat.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

> library(testthat)
> library(beachmat)
> test_check("beachmat")
── Building ────────────────────────────────────────────────── morebeachtests ──
Setting env vars:
● CFLAGS    : -Wall -pedantic
● CXXFLAGS  : -Wall -pedantic
● CXX11FLAGS: -Wall -pedantic
────────────────────────────────────────────────────────────────────────────────
  
   checking for file ‘/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/newtests/DESCRIPTION’ ...
  
✔  checking for file ‘/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/newtests/DESCRIPTION’

  
─  preparing ‘morebeachtests’:
   checking DESCRIPTION meta-information ...
  
✔  checking DESCRIPTION meta-information
─  cleaning src

  
─  checking for LF line-endings in source and make files and shell scripts

  
─  checking for empty or unneeded directories
─  building ‘morebeachtests_1.0.0.tar.gz’

  
   

── Checking ────────────────────────────────────────────────── morebeachtests ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
● _R_CHECK_CRAN_INCOMING_       : FALSE
● _R_CHECK_FORCE_SUGGESTS_      : FALSE
● NOT_CRAN                      : true
── R CMD check ─────────────────────────────────────────────────────────────────
* using log directory ‘/tmp/RtmpxXzoc9/morebeachtests.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘morebeachtests/DESCRIPTION’ ... OK
* this is package ‘morebeachtests’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘morebeachtests’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 loading without being on the library search path ... 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 for missing documentation entries ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 NOTEs
See
  ‘/tmp/RtmpxXzoc9/morebeachtests.Rcheck/00check.log’
for details.


══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 141 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
100.894   6.930 177.492 

Example timings

beachmat.Rcheck/beachmat-Ex.timings

nameusersystemelapsed
colBlockApply 9.196 3.47821.009