Michael R. Crusoe

configure should test for llvm/Pass.h and other required files

1

including a working llvm-config

Failing tests

5

``` Failure: test: crb-blast should get number of reciprocals. (TestCRBBlast) /build/ruby-crb-blast-0.6.6/test/test_test.rb:82:in `block (2 levels) in ' expected but was diff: ? 11 ? 0 ``` ruby-crb-blast Version 0.6.6 with ncbi-blast+...

Due to process substitution. Thanks to https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/jellyfish.html for highlighting this.

Fails to build from source on arm64/ppc64el: tests/generate_sequence

7

See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890137 ``` ... FAIL: tests/generate_sequence ============================= Seed: 3141592653 Creating fasta file 'seq10m.fa' Seed: 1040104553 Creating fasta file 'seq1m_0.fa' Creating fasta file 'seq1m_1.fa' Creating fasta file 'seq1m_2.fa' Creating fasta file...

py2dsp fails with local sdist

1

(Thanks for this great tool!) This is with the latest `pypi2deb` in Debian sid. ``` $ py2dsp ~/src/CTDopts/dist/CTDopts-1.1.tar.gz W: py2dsp pypi:54: cannot download CTDopts None details from PyPI: ContentTypeError("0, message='Attempt...

run doesn't respect quotes and escapes the same way exec does

13

## Version of Singularity: 3.2.1 ### Expected behavior ``` $ singularity run docker://debian /bin/sh -c 'echo \"moo\"' "moo" ``` ### Actual behavior ``` $ singularity run docker://debian /bin/sh -c 'echo...

arm64, alignment problem causes a failure to build from source

3

https://github.com/seqan/seqan/blob/master/include/seqan/misc/bit_twiddling.h#L348 Steve McIntyre at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=917851 writes: Hi! I've been doing a full rebuild of the Debian archive, building all source packages targeting armel and armhf using arm64 hardware. We are...

FormattedFile::readRecord is slow with std::string

10

`stream/tokenization.h:311 Assertion failed : optr < ochunk.end should be true but was 0` Here's a minimal test case: ``` (env)mcrusoe@athyra:~/khmer/gl-master$ g++ -I/home/mcrusoe/src/seqan/seqan-1.4.2/core/include/ seqan-std-string-test-1.4.cc -o seqan-std-string-test-1.4 -g (env)mcrusoe@athyra:~/khmer/gl-master$ g++ -I/home/mcrusoe/src/seqan/seqan-seqan-v2.0.0/include/ seqan-std-string-test-2.0.cc...

Allow seqan to be a dynamic library?

4

https://vittorioromeo.info/index/blog/2016_cpp_library_configuration_api.html This would be great for Debian as it would speed up our builds and allow us to fix bugs and security issues faster. Once multiple code paths for different...