Makefile enhancements

[outpaddling]

The patch below adds DESTDIR support and an install-strip target. This will facilitate installing fastp via package managers, most of which can use these features by default.

Also suggesting a slightly cleaner way to amend CXXFLAGS, but it works for me either way.

It was pretty easy already, though - thanks for making fastp simple and portable to begin with!

--- Makefile.orig	2019-04-17 03:23:22 UTC
+++ Makefile
@@ -3,9 +3,11 @@ DIR_SRC := ./src
 DIR_OBJ := ./obj
 
 PREFIX ?= /usr/local
+DESTDIR ?=
 BINDIR ?= $(PREFIX)/bin
 INCLUDE_DIRS ?=
 LIBRARY_DIRS ?=
+STRIP_CMD ?= strip
 
 SRC := $(wildcard ${DIR_SRC}/*.cpp)
 OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
@@ -15,7 +17,8 @@ TARGET := fastp
 BIN_TARGET := ${TARGET}
 
 CXX ?= g++
-CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+CXXFLAGS ?= -g -O3
+CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
 LIBS := -lz -lpthread
 LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
 
@@ -38,5 +41,8 @@ make_obj_dir:
 	fi
 
 install:
-	install $(TARGET) $(BINDIR)/$(TARGET)
+	install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
 	@echo "Installed."
+
+install-strip: install
+	$(STRIP_CMD) $(DESTDIR)$(BINDIR)/$(TARGET)

[outpaddling]

Patches improved and updated for 0.23.1:

--- Makefile.orig       2021-10-19 02:19:29 UTC
+++ Makefile
@@ -2,11 +2,13 @@ DIR_INC := ./inc
 DIR_SRC := ./src
 DIR_OBJ := ./obj
 
-PREFIX ?= /usr/local
-BINDIR ?= $(PREFIX)/bin
-INCLUDE_DIRS ?=
-LIBRARY_DIRS ?=
+PREFIX ?= /usr/local
+BINDIR ?= $(PREFIX)/bin
+INCLUDE_DIRS   ?=
+LIBRARY_DIRS   ?=
 
+STRIP  ?= strip
+
 SRC := $(wildcard ${DIR_SRC}/*.cpp)
 OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
 
@@ -15,15 +17,19 @@ TARGET := fastp
 BIN_TARGET := ${TARGET}
 
 CXX ?= g++
-CXXFLAGS := -std=c++11 -pthread -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+# Optional flags that the user can override by setting CXXFLAGS in the
+# env or make argument
+CXXFLAGS ?= -g -O3
+# Required flags
+CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
 LIBS := -lisal -ldeflate -lpthread
 STATIC_FLAGS := -static -Wl,--no-as-needed -pthread
-LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
+# Append required flags to standard LDFLAGS from env
+LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS)
 STATIC_LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_FLAGS) $(LIBS) $(STATIC_LD_FLAGS)
 
-
 ${BIN_TARGET}:${OBJ}
-       $(CXX) $(OBJ) -o $@ $(LD_FLAGS)
+       $(CXX) $(OBJ) -o $@ $(LDFLAGS)
 
 static:${OBJ}
        $(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS)
@@ -49,6 +55,11 @@ make_obj_dir:
                mkdir $(DIR_OBJ) ; \
        fi
 
+# Respect DESTDIR for staged installs (used by most package managers)
 install:
-       install $(TARGET) $(BINDIR)/$(TARGET)
+       install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
        @echo "Installed."
+
+# Many package managers use install-strip target if debugging is not enabled
+install-strip: install
+       $(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET)
--- src/main.cpp.orig   2021-10-19 02:19:29 UTC
+++ src/main.cpp
@@ -1,4 +1,5 @@
 #include <stdio.h>
+#include <sysexits.h>
 #include "fastqreader.h"
 #include "unittest.h"
 #include <time.h>
@@ -18,7 +19,7 @@ int main(int argc, char* argv[]){
     if(argc == 1) {
         cerr << "fastp: an ultra-fast all-in-one FASTQ preprocessor" << endl << "version " << FASTP_VER << endl;
         //cerr << "fastp --help to see the help"<<endl;
-        //return 0;
+        return EX_USAGE;
     }
     if (argc == 2 && strcmp(argv[1], "test")==0){
         UnitTest tester;

[joesphbeller]

Fix for Compiling fastp on Apple Silicon (M1/M2/M4)

Hello,

I’m aware this is an older thread, but I wanted to share another Makefile improvement that helped me successfully compile fastp from source on an Apple Silicon M4 chip.

Problem

Compilation failed with architecture mismatch when linking to Intel-only (x86_64) versions of libdeflate and isa-l:

ld: warning: ignoring file '/usr/local/lib/libdeflate.dylib': found architecture 'x86_64', required architecture 'arm64'
ld: warning: ignoring file '/usr/local/lib/libisal.dylib': found architecture 'x86_64', required architecture 'arm64'
Undefined symbols for architecture arm64:
"_isal_gzip_header_init", referenced from: ...
"_libdeflate_gzip_compress", referenced from: ...
...
ld: symbol(s) not found for architecture arm64
clang++: error: linker command failed with exit code 1
make: *** [fastp] Error 1

Solution

1. Make sure you are using Homebrew for Arm64.
   You can verify and set up the correct installation by following the discussion here:
   https://github.com/orgs/Homebrew/discussions/3223

2. Edit the Makefile in the fastp directory.

Replace lines 5–8 with the following:

PREFIX ?= /opt/homebrew
BINDIR ?= $(PREFIX)/bin
INCLUDE_DIRS ?= /opt/homebrew/include
LIBRARY_DIRS ?= /opt/homebrew/lib

After saving those changes, run a make clean and continue following the instructions,

make clean
make -j
sudo make install

This compiled successfully and installed the fastp binary linked against the correct native Arm64 libraries.

I hope this helps other Apple Silicon users trying to build fastp from source!

[outpaddling]

PREFIX ?= /opt/homebrew
BINDIR ?= $(PREFIX)/bin
INCLUDE_DIRS ?= /opt/homebrew/include
LIBRARY_DIRS ?= /opt/homebrew/lib

Are you compiling outside of homebrew, using homebrew-installed libraries? If so, you should be able to set PREFIX, etc. on the command-line using make arguments, e.g.

make -j PREFIX=/opt/homebrew ...

This will override the PREFIX set with ?=.

[outpaddling]

This issue is obsoleted by #619.