Control: tag -1 patch On Tue, Mar 12, 2024 at 06:31:20PM +0100, Andreas Tille wrote: > I can confirm that this bug also occures on amd64 thus removing the > arm-restriction from the title. Unfortunately I have no idea how to fix > this (except by possibly suppressing the -Werror=implicit-function-declaration > option). Thus tagging 'help'
Looks like bam_view1() and bam_sort_core() don't have prototypes in any header file in libbam-dev. Copying them from the actual .c files in samtools-legacy seems to work. Patch attached, this builds and passes the test suite for me. -- Niko
>From 3ddc905c9ceb635c6c876de1d372eedaa45de425 Mon Sep 17 00:00:00 2001 From: Niko Tyni <nt...@debian.org> Date: Tue, 12 Mar 2024 20:53:33 +0000 Subject: [PATCH] Lift prototypes of bam_view1 and bam_sort_core from bam.c in samtools-legacy This fixes builds with gcc -Werror=implicit-function-declaration . Bug-Debian: https://bugs.debian.org/1065759 --- lib/Bio/DB/Sam.xs | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs index 023f655..2231477 100644 --- a/lib/Bio/DB/Sam.xs +++ b/lib/Bio/DB/Sam.xs @@ -32,6 +32,11 @@ /* stolen from bam_aux.c */ #define MAX_REGION 1<<29 +/* stolen from bam.c */ +extern void bam_view1(const bam_header_t *header, const bam1_t *b); +/* stolen from bam_sort.c */ +extern void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem); + typedef tamFile Bio__DB__Tam; typedef faidx_t* Bio__DB__Sam__Fai; typedef bamFile Bio__DB__Bam; -- 2.43.0
