[R-pkg-team] Bug#980082: ShortRead fails test test_readPrb.R for non-Intel architectures

[Andreas Tille]

Control: tags -1 upstream
Control: forwarded -1 Bioconductor Package Maintainer <maintainer at bioconductor.org>

Hi,

the Debian packaged ShortRead is tested in CI test on different hardware
architectures.  On the debci page[1] you can see the matrix for success
and failure which shows that amd64 and i386 are passing the complete
test suite while other architectures are failing.  In those failing cases
the test log says something like


Timing stopped at: 1.012 0.02 1.031
Error in checkIdentical(exp, as(readPrb(sp, ".*prb.txt", as = "FastqEncoding"),  : 
  FALSE 
 
In addition: Warning messages:
1: In .class1(object) :
  closing unused connection 6 (/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: In .class1(object) :
  closing unused connection 5 (/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
Timing stopped at: 0.028 0.001 0.031
Error in checkIdentical(36L, unique(width(obj))) : FALSE 
 


RUNIT TEST PROTOCOL -- Sun Jan 24 21:54:15 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
In addition: Warning message:
In is.factor(x) :
  closing unused connection 3 (/tmp/RtmpEinleR/file1d7b55bbcf1b)
Execution halted


When removing the file test_readPrb.R from the installation the tests
are passing but before I do such nasty things I'd like to clarify the
situation with you.

Kind regards

      Andreas.

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

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