Bug#914731: r-bioc-biocparallel: autopkgtest regression

[Graham Inggs]

Control: severity -1 important

Downgrading severity, since the autopkgtests now pass in unstable [1],
to avoid autoremoval warnings in several other packages.

[1] https://ci.debian.net/packages/r/r-bioc-biocparallel/unstable/amd64/

Bug#914731: r-bioc-biocparallel: autopkgtest regression - any idea

[Andreas Tille]

Hi folks,

after each new upload of r-bioc-biocparallel the autopkgtest fails in a
different way.  Currently I have no good idea what might be the problem
and currently its also urgent to fix it since if we don't our whole BioC
stack will be removed from testing which we need to prevent.

Any idea how to fix the autopkgtest?

Kind regards

 Andreas.

-- 
http://fam-tille.de

Bug#914731:

[Dylan Aïssi]

Hummm, it worked on my own autopkgtest instance.
I will investigate it again.

Bug#914731: r-bioc-biocparallel: autopkgtest regression

[Graham Inggs]

Control: reopen -1

Still failing.

RUNIT TEST PROTOCOL -- Mon Dec  3 19:13:50 2018
***
Number of test functions: 63
Number of deactivated test functions: 3
Number of errors: 1
Number of failures: 1


1 Test Suite :
BiocParallel RUnit Tests - 63 test functions, 1 error, 1 failure
DEACTIVATED test_SnowParam_MPI: MPI tests not run
DEACTIVATED test_SnowParam_coerce_from_MPI: 'snow' and/or 'Rmpi'
package did not load
DEACTIVATED test_SnowParam_workers: 'snow' and/or 'Rmpi' package did not load
ERROR in test_bpaggregate: Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'bpworkers<-' for
signature '"SerialParam", "numeric"'
FAILURE in test_stop.on.error: Error in
checkIdentical(c("bplist_error", "bperror", "error", "condition"),  :
  FALSE


Test files with failing tests

   test_SnowParam.R
 test_SnowParam_MPI
 test_SnowParam_coerce_from_MPI
 test_SnowParam_workers

   test_bpaggregate.R
 test_bpaggregate

   test_errorhandling.R
 test_stop.on.error


Error in BiocGenerics:::testPackage("BiocParallel") :
  unit tests failed for package BiocParallel
Execution halted
autopkgtest [19:13:50]: test run-unit-test: ---]
autopkgtest [19:13:50]: test run-unit-test:  - - - - - - - - - -
results - - - - - - - - - -
run-unit-testFAIL non-zero exit status 1

Bug#914731:

[Dylan Aïssi]

Hi Graham,

Another R package autopkgtest (r-cran-metamix) fails with this error:
> libmpi.so: cannot open shared object file: No such file or directory

This seems to be induced by one of them dependency: r-cran-rmpi which
is not loadable in R. Maybe a new occurrence of #861748 [1] ?

[1] https://bugs.debian.org/861748

Best,
Dylan

Bug#914731: r-bioc-biocparallel: autopkgtest regression

[Graham Inggs]

Source: r-bioc-biocparallel
Version: 1.14.0-1
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: regression

Hi Maintainer

Since the upload of 1.14.0-1, r-bioc-biocparallel has been failing its
own autopkgtests with the following error:

RUNIT TEST PROTOCOL -- Mon Nov 26 17:50:31 2018
***
Number of test functions: 63
Number of deactivated test functions: 1
Number of errors: 1
Number of failures: 1


1 Test Suite :
BiocParallel RUnit Tests - 63 test functions, 1 error, 1 failure
DEACTIVATED test_SnowParam_workers: 'snow' and/or 'Rmpi' package did not load
ERROR in test_bpaggregate: Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'bpworkers<-' for
signature '"SerialParam", "numeric"'
FAILURE in test_stop.on.error: Error in
checkIdentical(c("bplist_error", "bperror", "error", "condition"),  :
  FALSE

Error in BiocGenerics:::testPackage("BiocParallel") :
  unit tests failed for package BiocParallel

Test files with failing tests

   test_SnowParam.R
 test_SnowParam_workers

   test_bpaggregate.R
 test_bpaggregate

   test_errorhandling.R
 test_stop.on.error


Execution halted
autopkgtest [17:50:31]: test run-unit-test: ---]
autopkgtest [17:50:31]: test run-unit-test:  - - - - - - - - - -
results - - - - - - - - - -
run-unit-testFAIL non-zero exit status 1

Regards
Graham

[1] https://ci.debian.net/packages/r/r-bioc-biocparallel/unstable/amd64/