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bwa-mem2 2.0 #1034

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merged 1 commit into from
Jul 17, 2020
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SeekingMeaning
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Created with brew bump-formula-pr.

@SeekingMeaning SeekingMeaning changed the base branch from master to develop July 9, 2020 10:32
@kokyriakidis
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Can you add the new production version please?

@SeekingMeaning
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This patch fixes the safe_mem_lib.h: No such file or directory error:

-  url "https://github.com/bwa-mem2/bwa-mem2/archive/v2.0.tar.gz"
+  url "https://github.com/bwa-mem2/bwa-mem2.git",
+      :tag      => "v2.0",
+      :revision => "cbcc183c0843d20d45c84e066177eb8d58be2f9b"

However, this only results in another error:

ext/safestringlib/include/safe_mem_lib.h:100:16: error: conflicting types for 'memset_s'
extern errno_t memset_s(void *dest, rsize_t dmax, uint8_t value);
               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/string.h:145:9: note: previous declaration is here
errno_t memset_s(void *__s, rsize_t __smax, int __c, rsize_t __n) __OSX_AVAILABLE_STARTING(__MAC_10_9, __IPHONE_7_0);
        ^

Because of this, bwa-mem2 2.0 is currently unable to build on macOS: intel/safestringlib#14

Bioconda "works around" this by not building for macOS at all: bioconda/bioconda-recipes@f1f3925

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@SeekingMeaning SeekingMeaning merged commit b6a1826 into brewsci:develop Jul 17, 2020
@SeekingMeaning SeekingMeaning deleted the bwa-mem2-2.0pre2 branch July 17, 2020 19:06
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3 participants