Back to Long Tests report for BioC 3.14

This page was generated on 2022-04-09 21:00:03 -0400 (Sat, 09 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4322
riesling1Windows Server 2019 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4108
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4135
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for beachmat on riesling1


To the developers/maintainers of the beachmat package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 3/19HostnameOS / ArchCHECK
beachmat 2.10.0  (landing page)
Aaron Lun
Snapshot Date: 2022-04-09 06:55:01 -0400 (Sat, 09 Apr 2022)
git_url: https://git.bioconductor.org/packages/beachmat
git_branch: RELEASE_3_14
git_last_commit: b7cc532
git_last_commit_date: 2021-10-26 12:36:32 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  ERROR  
riesling1Windows Server 2019 Standard / x64  ERROR  
machv2macOS 10.14.6 Mojave / x86_64  ERROR  

Summary

Package: beachmat
Version: 2.10.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_2.10.0.tar.gz
StartedAt: 2022-04-09 08:04:23 -0400 (Sat, 09 Apr 2022)
EndedAt: 2022-04-09 08:41:36 -0400 (Sat, 09 Apr 2022)
EllapsedTime: 2232.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: beachmat.Rcheck
Warnings: NA

Tests output

beachmat.Rcheck/tests_i386/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 'D:\biocbuild\bbs-3.14-bioc-longtests\meat\beachmat.Rcheck\beachmat\testpkg/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 'D:/biocbuild/bbs-3.14-bioc-longtests/tmpdir/Rtmpu2aM5d/file40e812732c0f/beachtest.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'beachtest' 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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 PDF version of manual ... OK
* DONE

Status: OK

== 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:
    x
 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

beachmat.Rcheck/tests_x64/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 'D:\biocbuild\bbs-3.14-bioc-longtests\meat\beachmat.Rcheck\beachmat\testpkg/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 'D:/biocbuild/bbs-3.14-bioc-longtests/tmpdir/RtmpecifXs/file35c877cc4960/beachtest.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'beachtest' 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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 PDF version of manual ... OK
* DONE

Status: OK

== 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:
    x
 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:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 '2.10.0'
* 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 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
* 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 ... 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 tests for arch 'i386' ...
  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:
      x
   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
** running tests for arch 'x64' ...
  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:
      x
   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: 2 ERRORs, 1 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck/00check.log'
for details.


Installation output

beachmat.Rcheck/00install.out

* installing *source* package 'beachmat' ...
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o beachmat.dll tmp.def RcppExports.o fragment_sparse_rows.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck/00LOCK-beachmat/00new/beachmat/libs/i386

*** arch - x64
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o beachmat.dll tmp.def RcppExports.o fragment_sparse_rows.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck/00_pkg_src/beachmat/src-x64/RcppExports.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck/00_pkg_src/beachmat/src-x64/fragment_sparse_rows.o: file format not recognized
Warning messages:
1: In system(sprintf("%s -Pg %s", nm, shQuote(f)), intern = TRUE) :
  running command 'C:\rtools40\mingw32\bin\nm.exe -Pg "D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck/00_pkg_src/beachmat/src-x64/RcppExports.o"' had status 1
2: In system(sprintf("%s -Pg %s", nm, shQuote(f)), intern = TRUE) :
  running command 'C:\rtools40\mingw32\bin\nm.exe -Pg "D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck/00_pkg_src/beachmat/src-x64/fragment_sparse_rows.o"' had status 1
installing to D:/biocbuild/bbs-3.14-bioc-longtests/meat/beachmat.Rcheck/00LOCK-beachmat/00new/beachmat/libs/x64
** 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
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (beachmat)