[R-pkg-team] Bug#980082: r-bioc-shortread: autopkgtest failure in testing and unstable

[Graham Inggs]

Source: r-bioc-shortread
Version: 1.48.0-1
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
Tags: bullseye sid
User: debian-ci at lists.debian.org
Usertags: needs-update

Hi Maintainer

The autopkgtests of r-bioc-shortread are failing in testing and unstable [1].

I've copied what I hope is the relevant part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/r/r-bioc-shortread/


Timing stopped at: 0.053 0 0.053
Error in checkIdentical(exp, as(readPrb(sp, ".*prb.txt", as =
"FastqEncoding"),  :
  FALSE

In addition: Warning messages:
1: In .Internal(vapply(X, FUN, FUN.VALUE, USE.NAMES)) :
  closing unused connection 6
(/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: In .Internal(vapply(X, FUN, FUN.VALUE, USE.NAMES)) :
  closing unused connection 5
(/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
Timing stopped at: 0.032 0 0.032
Error in checkIdentical(36L, unique(width(obj))) : FALSE



RUNIT TEST PROTOCOL -- Thu Jan 14 00:29:24 2021
***********************************************
Number of test functions: 104
Number of errors: 0
Number of failures: 2


1 Test Suite :
ShortRead RUnit Tests - 104 test functions, 0 errors, 2 failures
FAILURE in test_readPrb_consistent: Error in checkIdentical(exp,
as(readPrb(sp, ".*prb.txt", as = "FastqEncoding"),  :
  FALSE

FAILURE in test_readPrb_input: Error in checkIdentical(36L,
unique(width(obj))) : FALSE


Test files with failing tests

   test_readPrb.R
     test_readPrb_consistent
     test_readPrb_input


Error in BiocGenerics:::testPackage("ShortRead") :
  unit tests failed for package ShortRead
Execution halted
autopkgtest [08:29:24]: test run-unit-test: -----------------------]
autopkgtest [08:29:25]: test run-unit-test:  - - - - - - - - - -
results - - - - - - - - - -
run-unit-test        FAIL non-zero exit status 1