Package: fastp Version: 0.23.2+dfsg-1 Severity: normal Tags: ftbfs upstream patch User: [email protected] Usertags: riscv64
Dear maintainer, fastp currently fails to build from source on riscv64: | g++ ./obj/adaptertrimmer.o ./obj/basecorrector.o ./obj/duplicate.o ./obj/evaluator.o ./obj/fastareader.o ./obj/fastqreader.o ./obj/filter.o ./obj/filterresult.o ./obj/htmlreporter.o ./obj/jsonreporter.o ./obj/main.o ./obj/nucleotidetree.o ./obj/options.o ./obj/overlapanalysis.o ./obj/peprocessor.o ./obj/polyx.o ./obj/processor.o ./obj/read.o ./obj/readpool.o ./obj/seprocessor.o ./obj/sequence.o ./obj/stats.o ./obj/threadconfig.o ./obj/umiprocessor.o ./obj/unittest.o ./obj/writer.o ./obj/writerthread.o -o fastp -Wl,-z,relro -Wl,-z,now -lisal -ldeflate -lpthread | /usr/bin/ld: ./obj/duplicate.o: in function `Duplicate::applyBloomFilter(unsigned long*)': | ./src/duplicate.cpp:157: undefined reference to `__atomic_fetch_or_1' | /usr/bin/ld: ./obj/duplicate.o: in function `Duplicate::seq2intvector(char const*, int, unsigned long*, int)': | ./src/duplicate.cpp:110: undefined reference to `__atomic_fetch_or_1' | /usr/bin/ld: ./obj/duplicate.o: in function `std::__atomic_base<unsigned long>::fetch_add(unsigned long, std::memory_order)': | /usr/include/c++/11/bits/atomic_base.h:636: undefined reference to `__atomic_fetch_or_1' | collect2: error: ld returned 1 exit status | make[2]: *** [Makefile:26: fastp] Error 1 | make[2]: Leaving directory '/<<PKGBUILDDIR>>' | dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" returned exit code 2 | make[1]: *** [debian/rules:12: override_dh_auto_build] Error 25 | make[1]: Leaving directory '/<<PKGBUILDDIR>>' | make: *** [debian/rules:7: binary-arch] Error 2 | dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 The full build log is available there: https://buildd.debian.org/status/fetch.php?pkg=fastp&arch=riscv64&ver=0.23.2%2Bdfsg-1&stamp=1638916332&raw=0 The problem is that the linking is not done correctly, it uses -lpthread meaning linking with the pthread library, instead of -pthread which means enable thread support, and which brings libatomic.so on riscv64. BTW, bonus point for correctly passing -pthread for compiling individual source file, this is often forgotten. The attached patch updates the Makefile to link with -pthread instead of using -lpthread. Could you please include it in the next upload? Thanks, Aurelien
diff -Nru fastp-0.23.2+dfsg/debian/changelog fastp-0.23.2+dfsg/debian/changelog --- fastp-0.23.2+dfsg/debian/changelog 2021-12-07 22:34:23.000000000 +0100 +++ fastp-0.23.2+dfsg/debian/changelog 2021-12-11 11:29:12.000000000 +0100 @@ -1,3 +1,9 @@ +fastp (0.23.2+dfsg-1+riscv64) unreleased; urgency=medium + + * Fix build on riscv64. + + -- Aurelien Jarno <[email protected]> Sat, 11 Dec 2021 11:29:12 +0100 + fastp (0.23.2+dfsg-1) unstable; urgency=medium * New upstream version diff -Nru fastp-0.23.2+dfsg/debian/patches/fix-riscv64.patch- fastp-0.23.2+dfsg/debian/patches/fix-riscv64.patch- --- fastp-0.23.2+dfsg/debian/patches/fix-riscv64.patch- 1970-01-01 01:00:00.000000000 +0100 +++ fastp-0.23.2+dfsg/debian/patches/fix-riscv64.patch- 2021-12-11 11:29:12.000000000 +0100 @@ -0,0 +1,18 @@ +Description: Correctly link the binary with -pthread, to include -latomic when needed. +Author: Aurelien Jarno <[email protected]> +Last-Update: 2021-12-11 + +--- fastp-0.23.2+dfsg.orig/Makefile ++++ fastp-0.23.2+dfsg/Makefile +@@ -16,9 +16,9 @@ BIN_TARGET := ${TARGET} + + CXX ?= g++ + CXXFLAGS += -std=c++11 -pthread -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) +-LIBS := -lisal -ldeflate -lpthread ++LIBS := -lisal -ldeflate + STATIC_FLAGS := -static -Wl,--no-as-needed -pthread +-LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) ++LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) -pthread + STATIC_LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_FLAGS) $(LIBS) $(STATIC_LD_FLAGS) + + diff -Nru fastp-0.23.2+dfsg/debian/patches/series fastp-0.23.2+dfsg/debian/patches/series --- fastp-0.23.2+dfsg/debian/patches/series 2021-12-07 22:34:23.000000000 +0100 +++ fastp-0.23.2+dfsg/debian/patches/series 2021-12-11 11:29:12.000000000 +0100 @@ -1,2 +1,3 @@ makefile.patch fix-i386.patch +fix-riscv64.patch-
