[Debian-med-packaging] Bug#1104751: bedtools: FTBFS with GNUMAKEFLAGS=--shuffle=random

[Lucas Nussbaum]

Source: bedtools
Version: 2.31.1+dfsg-2
Severity: minor
Tags: patch

Hi,

GNU Make now has a --shuffle option that simulates non-deterministic 
ordering of dependencies. See 
https://trofi.github.io/posts/238-new-make-shuffle-mode.html and also 
previous work in Debian by Santiago Vila: 
https://people.debian.org/~sanvila/make-shuffle/

This package fails to build with GNUMAKEFLAGS=--shuffle=random.

I could also reproduce the failure with high number of parallelism (e.g.
dpkg-buildpackage -j100).

This patch fixes it.

--- bedtools-2.31.1+dfsg.orig/Makefile
+++ bedtools-2.31.1+dfsg/Makefile
@@ -177,6 +177,8 @@ include $(HTSDIR)/htslib.mk
 # but ignores the directory's timestamp, which changes every time a .o file is written.
 $(BUILT_OBJECTS): | $(OBJ_DIR)
 
+$(BUILT_OBJECTS): autoversion
+
 $(BIN_DIR)/bedtools: autoversion $(BUILT_OBJECTS) $(HTSDIR)/libhts.a | $(BIN_DIR)
        @echo "- Building main bedtools binary."
        $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_LDFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) $(HTSDIR)/libhts.a $(ALL_LIBS)

Best,

Lucas