Control: tags -1 upstream
Control: forwarded -1 Bioconductor Package Maintainer
<maintai...@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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