Back to Multiple platform build/check report for BioC 3.12
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for beachmat on tokay1

This page was generated on 2021-05-06 12:29:59 -0400 (Thu, 06 May 2021).

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 133/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beachmat 2.6.4  (landing page)
Aaron Lun
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/beachmat
Branch: RELEASE_3_12
Last Commit: 7d9dc63
Last Changed Date: 2020-12-19 18:15:07 -0400 (Sat, 19 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: beachmat
Version: 2.6.4
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:beachmat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings beachmat_2.6.4.tar.gz
StartedAt: 2021-05-06 00:41:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:03:12 -0400 (Thu, 06 May 2021)
EllapsedTime: 1328.9 seconds
RetCode: 0
Status:   OK   
CheckDir: beachmat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:beachmat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings beachmat_2.6.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/beachmat.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beachmat/DESCRIPTION' ... OK
* this is package 'beachmat' version '2.6.4'
* 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 '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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
colBlockApply 10.92   2.93    26.1
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
colBlockApply 10.47   2.94   25.61
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/beachmat.Rcheck/00check.log'
for details.



Installation output

beachmat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/beachmat_2.6.4.tar.gz && rm -rf beachmat.buildbin-libdir && mkdir beachmat.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=beachmat.buildbin-libdir beachmat_2.6.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL beachmat_2.6.4.zip && rm beachmat_2.6.4.tar.gz beachmat_2.6.4.zip
###
##############################################################################
##############################################################################


  % 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 92085  100 92085    0     0  1891k      0 --:--:-- --:--:-- --:--:-- 1954k

install for i386

* installing *source* package 'beachmat' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'beachmat'
    finding HTML links ... done
    colBlockApply                           html  
    finding level-2 HTML links ... done

** 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 'beachmat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beachmat' as beachmat_2.6.4.zip
* DONE (beachmat)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'beachmat' successfully unpacked and MD5 sums checked

Tests output

beachmat.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(beachmat)
> test_check("beachmat")
-- R CMD build -----------------------------------------------------------------
* checking for file 'C:\Users\biocbuild\bbs-3.12-bioc\R\library\beachmat\newtests/DESCRIPTION' ... OK

* preparing 'morebeachtests':

* checking DESCRIPTION meta-information ... OK

* 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'



-- R CMD check -----------------------------------------------------------------
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpuQXwh4/file2d4439c03e48/morebeachtests.Rcheck'

* using R version 4.0.5 (2021-03-31)

* using platform: i386-w64-mingw32 (32-bit)

* using session charset: ISO8859-1

* 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 whether package 'morebeachtests' can be installed ... OK

* checking installed package size ... OK

* checking package 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 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 compiled code ... OK

* checking examples ... NONE

* checking for unstated dependencies in 'tests' ... OK

* checking tests ...

  Running 'testthat.R'

 OK

* checking PDF version of manual ... OK

* DONE



Status: OK



[ FAIL 0 | WARN 0 | SKIP 0 | PASS 171 ]
> 
> proc.time()
   user  system elapsed 
  21.84    0.79  799.04 

beachmat.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(beachmat)
> test_check("beachmat")
-- R CMD build -----------------------------------------------------------------
* checking for file 'C:\Users\biocbuild\bbs-3.12-bioc\R\library\beachmat\newtests/DESCRIPTION' ... OK

* preparing 'morebeachtests':

* checking DESCRIPTION meta-information ... OK

* 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'



-- R CMD check -----------------------------------------------------------------
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMFqyNi/file17981562750a/morebeachtests.Rcheck'

* using R version 4.0.5 (2021-03-31)

* using platform: x86_64-w64-mingw32 (64-bit)

* using session charset: ISO8859-1

* 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 whether package 'morebeachtests' can be installed ... OK

* checking installed package size ... OK

* checking package 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 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 compiled code ... OK

* checking examples ... NONE

* checking for unstated dependencies in 'tests' ... OK

* checking tests ...

  Running 'testthat.R'

 OK

* checking PDF version of manual ... OK

* DONE



Status: OK



[ FAIL 0 | WARN 0 | SKIP 0 | PASS 171 ]
> 
> proc.time()
   user  system elapsed 
  19.39    0.29  325.37 

Example timings

beachmat.Rcheck/examples_i386/beachmat-Ex.timings

nameusersystemelapsed
colBlockApply10.92 2.9326.10

beachmat.Rcheck/examples_x64/beachmat-Ex.timings

nameusersystemelapsed
colBlockApply10.47 2.9425.61