BWA compile fail with GCC 10

[fizwit]

GCC 10 defaults to -fno-common which is causing this issue.

ld.gold: error: ./libbwa.a(rope.o): multiple definition of 'rle_auxtab' ld.gold: ./libbwa.a(bwtindex.o): previous definition here ld.gold: error: ./libbwa.a(rle.o): multiple definition of 'rle_auxtab' ld.gold: ./libbwa.a(bwtindex.o): previous definition here

[fizwit]

I see that the issue is fixed in branch master, but the only tagged release is 0.7.17 which has the missing extern for rle_auxtab. I only build from tagged releases, could you create 0.7.18 ?

To promote reproducible science, could you please use git tags. Creating a tag also creates a release for your project. We require tagged releases when building scientific software. Pulling from the master is not reproducible. thanks

[dpryan79]

@lh3 Can you please tag a new release? I'm also hitting this in bioconda, since clang 11 uses -fno-common by default. I fully expect that I can work around this by passing -fcommon, but it'd be nice to have that fixed in an official release that I can distribute to everyone.

[V-Z]

I package BWA for openSUSE Linux and I patch it like:

--- Makefile.orig	2021-05-18 11:19:23.819963543 +0200
+++ Makefile	2021-05-18 11:19:45.080303226 +0200
@@ -1,6 +1,6 @@
 CC=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS=		-g -Wall -Wno-unused-function -O2 -fcommon
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)

BWA in openSUSE scientific repository contains also another patch to fix compilation with GCC 10 and 11:

Description: Fix package to build with GCC-10 from Debian
Author: Nilesh Patra <[email protected]>
Last-Update: Sat, 18 Apr 2020 20:19:30 +0530
--- a/rle.h
+++ b/rle.h
@@ -30,7 +30,7 @@
  *** 43+3 codec ***
  ******************/
 
-const uint8_t rle_auxtab[8];
+extern const uint8_t rle_auxtab[8];
 
 #define RLE_MIN_SPACE 18
 #define rle_nptr(block) ((uint16_t*)(block))

With one or the other the compilation (and packaging) works well, but, of course, upstream fix would be better. :-)

[cmccabe0728]

I see that the issue is fixed in branch master, but the only tagged release is 0.7.17 which has the missing extern for rle_auxtab. I only build from tagged releases, could you create 0.7.18 ?

To promote reproducible science, could you please use git tags. Creating a tag also creates a release for your project. We require tagged releases when building scientific software. Pulling from the master is not reproducible. thanks

Where did you download the new 0.7.18? Thank you.

[RoanKanninga]

Can we please have a new 0.7.18 release?

[yifanfu01]

It's not only a useful solution for bwa package. Actually I solved another similar problems caused by higher version of GCC like svaba and delly package. thx alot.