Hi all, I could find the cause. It is the `-flto` in the compile and link flags of the libminimap2-dev package. LTO is introduced recently in the following commit on the [1]: 53883a7ff8c066c14c0ea4e42299ae9958feda6a
Removing `-flto` from CFLAGS and LDFLAGS, then building libminimap2-dev with pdebuild (sid), then building the nanopolish with pbuilder (sid), will succeed. I attached the patch which resolves the problem. It should be applied against [1]. The conclusion: The `-flto` behaves differently from the past maybe with the recent changes in the build tool-chain (maybe in GCC) and causes the problem. [1]:https://salsa.debian.org/med-team/minimap2.git Bests, Hamid Nassiby
From 5aa0491a6159895cdb0925617858cbca68c9e834 Mon Sep 17 00:00:00 2001 From: Hamid Nassiby <h.nass...@gmail.com> Date: Thu, 9 Apr 2020 23:01:48 +0430 Subject: [PATCH] Remove -flto flag --- debian/patches/addLTO.patch | 30 ------------------------------ debian/patches/series | 1 - 2 files changed, 31 deletions(-) delete mode 100644 debian/patches/addLTO.patch diff --git a/debian/patches/addLTO.patch b/debian/patches/addLTO.patch deleted file mode 100644 index 8dc0215..0000000 --- a/debian/patches/addLTO.patch +++ /dev/null @@ -1,30 +0,0 @@ -Author: Steffen Moeller -Last-Update: 2020-03-14 23:04:54 +0100 -Description: Add -flto flag - -Index: minimap2/Makefile -=================================================================== ---- minimap2.orig/Makefile -+++ minimap2/Makefile -@@ -1,10 +1,11 @@ --CFLAGS+= -g -Wall -O2 -Wc++-compat #-Wextra -+CFLAGS+= -g -Wall -O2 -Wc++-compat -flto #-Wextra - CPPFLAGS+= -DHAVE_KALLOC - INCLUDES= - OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o - PROG= minimap2 - PROG_EXTRA= sdust minimap2-lite - LIBS= -lm -lz -lpthread -+LDFLAGS+= -flto - - OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o - -@@ -29,7 +30,7 @@ all:$(PROG) - extra:all $(PROG_EXTRA) - - minimap2:main.o libminimap2.a -- $(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS) -+ $(CC) main.o -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS) - - minimap2-lite:example.o libminimap2.a - $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS) diff --git a/debian/patches/series b/debian/patches/series index 57c6966..65c2533 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,4 @@ hardening.patch do_not_use_natbib.bst.patch simde -addLTO.patch ar.patch -- 2.25.0