From 158f5e9c4a2c2f0a3e88b8cf07d54946506c9f9c Mon Sep 17 00:00:00 2001 From: David Engster Date: Thu, 30 Sep 2021 11:01:22 +0200 Subject: [PATCH] Always build htslib without the libdeflate library If libdeflate is installed on the host, the configure script for htslib will pick it up and link with it, leading to undefined symbols in the final link since -ldeflate is missing from PKG_LIBS. We also cannot simply add it to PKG_LIBS, since then we would get an error on hosts where libdeflate is unavailable, so just configure htslib without libdeflate support. --- src/Makevars | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makevars b/src/Makevars index 01689c2..10ca19b 100644 --- a/src/Makevars +++ b/src/Makevars @@ -28,7 +28,7 @@ $(HTSDIR)/Makefile: wget -O "htslib-$(HSTLIB_VERSION).tar.bz2" "https://github.com/samtools/htslib/releases/download/$(HSTLIB_VERSION)/htslib-$(HSTLIB_VERSION).tar.bz2" tar xfj htslib-$(HSTLIB_VERSION).tar.bz2 mv "htslib-$(HSTLIB_VERSION)" "$(HTSDIR)" - (cd $(HTSDIR) && ./configure && sed -i '/^CFLAGS/s/$$/ -fPIC/' config.mk) || rm $@ + (cd $(HTSDIR) && ./configure --without-libdeflate && sed -i '/^CFLAGS/s/$$/ -fPIC/' config.mk) || rm $@ clean: rm -f librbcf.so