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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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Incompatible with OSX Catalina #424

Closed danielecook closed 4 years ago

danielecook commented 4 years ago

Sambamba can no longer be used on the latest version of Mac OSX

Tested with version 0.6.8; I also experimented with building but I do not see a straightforward way to build for version 0.7.1.

dyld: lazy symbol binding failed: Symbol not found: _dyld_enumerate_tlv_storage
  Referenced from: /usr/local/bin/sambamba
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _dyld_enumerate_tlv_storage
  Referenced from: /usr/local/bin/sambamba
  Expected in: /usr/lib/libSystem.B.dylib

Abort trap: 6
pjotrp commented 4 years ago

Appears to be a small problem. I don't run non-free software, but if someone fixes it we are happy to accept the patches.

dpryan79 commented 4 years ago

Has there been any resolution to this? It appears to be an issue with DMD on OSX and perhaps just using a newer version of DMD to compile things will solve the issue.

I mostly ask since we have some users running into this with pipeline steps that use sambamba.

Xref: https://github.com/dlang/druntime/pull/2666

pjotrp commented 4 years ago

I'll do some work on sambamba soon. Hopeful travis-ci will help sort the OSX stuff.

marcelm commented 4 years ago

I can confirm that compiling Sambamba with LDC 1.17 will fix the problem, see bioconda/bioconda-recipes#20276.

pjotrp commented 4 years ago

That is great news :+1: