Back to Long Tests report for BioC 3.13

CHECK report for beachmat on rex3

This page was generated on 2021-12-11 17:30:01 -0500 (Sat, 11 Dec 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 3/20HostnameOS / ArchCHECK
beachmat 2.11.0  (landing page)
Aaron Lun
Snapshot Date: 2021-12-11 09:00:01 -0500 (Sat, 11 Dec 2021)
URL: https://git.bioconductor.org/packages/beachmat
Branch: master
Last Commit: dd97920
Last Changed Date: 2021-10-26 12:36:32 -0500 (Tue, 26 Oct 2021)
rex3Linux (Ubuntu 20.04.2 LTS) / x86_64  ERROR  

Summary

Package: beachmat
Version: 2.11.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_2.11.0.tar.gz
StartedAt: 2021-12-11 09:30:25 -0500 (Sat, 11 Dec 2021)
EndedAt: 2021-12-11 09:42:49 -0500 (Sat, 11 Dec 2021)
EllapsedTime: 744.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: beachmat.Rcheck
Warnings: NA

Tests output

beachmat.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2021-02-10 r79979) -- "Unsuffered Consequences"
Copyright (C) 2021 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")
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘beachtest’:
* 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 ‘beachtest_1.0.0.tar.gz’

── R CMD check ─────────────────────────────────────────────────────────────────
* using log directory ‘/tmp/Rtmp3xTjXc/file3be07d4c1f55/beachtest.Rcheck’
* using R Under development (unstable) (2021-02-10 r79979)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘beachtest/DESCRIPTION’ ... OK
* this is package ‘beachtest’ 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 whether package ‘beachtest’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 108.8Mb
  sub-directories of 1Mb or more:
    libs  108.6Mb
* 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 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 compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/tmp/Rtmp3xTjXc/file3be07d4c1f55/beachtest.Rcheck/00check.log’
for details.

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-check.R:6:5): extension test package CHECKs correctly ─────────
`rcmdcheck::rcmdcheck(...)` threw an error.
Message: unused argument (document = FALSE)
Class:   simpleError/error/condition
Backtrace:
    █
 1. └─testthat::expect_error(...) test-check.R:6:4
 2.   └─testthat:::quasi_capture(...)
 3.     ├─testthat:::.capture(...)
 4.     │ └─base::withCallingHandlers(...)
 5.     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc-longtests/meat/beachmat.Rcheck’
* using R Under development (unstable) (2021-02-10 r79979)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘2.11.0’
* 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 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 ... SKIPPED
* 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 compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure (test-check.R:6:5): extension test package CHECKs correctly ─────────
  `rcmdcheck::rcmdcheck(...)` threw an error.
  Message: unused argument (document = FALSE)
  Class:   simpleError/error/condition
  Backtrace:
      █
   1. └─testthat::expect_error(...) test-check.R:6:4
   2.   └─testthat:::quasi_capture(...)
   3.     ├─testthat:::.capture(...)
   4.     │ └─base::withCallingHandlers(...)
   5.     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc-longtests/meat/beachmat.Rcheck/00check.log’
for details.


Installation output

beachmat.Rcheck/00install.out

* installing *source* package ‘beachmat’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o beachmat.so RcppExports.o fragment_sparse_rows.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc-longtests/meat/beachmat.Rcheck/00LOCK-beachmat/00new/beachmat/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beachmat)