CODEWITHSUNDEEP
c++linuxmakefilezlib
Paramar
Paramar

Reputation: 307

zlib.h:34:19: fatal error: zconf.h: No such file or directory #include "zconf.h"

There are quite some posts about this error, but I was not able to solve it, I hope you can come up with the solution. I am on a Ubuntu machine.

~/graphmap2$

In this folder, I downloaded zlib. You can see the picture

image

After some Googling, I also noticed that there is no -lz parameter, so I also added that manually as you can see below

image

However, I still get the same error as when none of the above were done.

Might it be that the path to zlib is not clear for the compiler? However, I installed it in this same folder.

The make file looks like the below:

BIN = ./bin/graphmap2
BIN_DEBUG = ./bin/graphmap-debug
BIN_LINUX = ./bin/Linux-x64/graphmap2
BIN_MAC = ./bin/Mac/graphmap
OBJ_TESTING = ./obj_test
OBJ_TESTING_EXT = ./obj_testext
OBJ_DEBUG = ./obj_debug
OBJ_LINUX = ./obj_linux
OBJ_EXTCIGAR = ./obj_extcigar
OBJ_MAC = ./obj_mac
SOURCE = src
CODEBASE = codebase
# This finds all 'src' folders at maximum depth 2 (level one inside each submodule's folder).
CODEBASE_SRC_FOLDERS = $(shell find $(CODEBASE) -maxdepth 2 -type d -name "src" -exec echo "-I"{} \;)
# $(shell find $(CODEBASE) -maxdepth 3 -type d -name "libs" -exec echo "-I"{} \;)
# $(shell find $(CODEBASE) -maxdepth 2 -type d -name "src" -exec echo "-I"{}"/*/" \;)

# ? allows override by user using env var
GCC ?= g++
# define variables for GCC version check here
GCC_MAJOR_VERSION_GE_4 := $(shell expr `$(GCC) -dumpversion | cut -f1 -d.` \>= 4)
GCC_MINOR_VERSION_GE_7 := $(shell expr `$(GCC) -dumpversion | cut -f2 -d.` \>= 7)
GCC_MAC ?= g++


# CPP_FILES := $(wildcard $(SOURCE)/*/*.cpp) $(wildcard $(SOURCE)/*.cpp) $(wildcard $(SOURCE)/libs/*/*.cpp)
# CC_FILES := $(wildcard $(SOURCE)/*/*.cc) $(wildcard $(SOURCE)/*.cc) $(wildcard $(SOURCE)/libs/*/*.cc)
# H_FILES := $(wildcard $(SOURCE)/*/*.h) $(wildcard $(SOURCE)/*.h) $(wildcard $(SOURCE)/libs/*/*.h)
CPP_FILES :=  $(wildcard $(CODEBASE)/*/src/*.cpp) $(wildcard $(CODEBASE)/*/src/libs/*/*.cpp) $(wildcard $(CODEBASE)/*/src/*/*.cpp) $(wildcard $(SOURCE)/*/*.cpp) $(wildcard $(SOURCE)/*.cpp) $(wildcard $(SOURCE)/libs/*/*.cpp)
CC_FILES :=  $(wildcard $(CODEBASE)/*/src/*.cc) $(wildcard $(CODEBASE)/*/src/libs/*/*.cc) $(wildcard $(CODEBASE)/*/src/*/*.cc) $(wildcard $(SOURCE)/*/*.cc) $(wildcard $(SOURCE)/*.cc) $(wildcard $(SOURCE)/libs/*/*.cc)
H_FILES := $(wildcard $(CODEBASE)/*/src/*.h) $(wildcard $(CODEBASE)/*/src/libs/*/*.h) $(wildcard $(CODEBASE)/*/src/*/*.h) $(wildcard $(SOURCE)/*/*.h) $(wildcard $(SOURCE)/*.h) $(wildcard $(CODEBASE)/*/src/*.hpp) $(wildcard $(CODEBASE)/*$
OBJ_FILES := $(CPP_FILES:.cpp=.o) $(CC_FILES:.cc=.o)
OBJ_FILES_FOLDER_TESTING := $(addprefix $(OBJ_TESTING)/,$(OBJ_FILES))
OBJ_FILES_FOLDER_TESTING_EXT := $(addprefix $(OBJ_TESTING_EXT)/,$(OBJ_FILES))
OBJ_FILES_FOLDER_DEBUG := $(addprefix $(OBJ_DEBUG)/,$(OBJ_FILES))
OBJ_FILES_FOLDER_LINUX := $(addprefix $(OBJ_LINUX)/,$(OBJ_FILES))
OBJ_FILES_FOLDER_EXTCIGAR := $(addprefix $(OBJ_EXTCIGAR)/,$(OBJ_FILES))
OBJ_FILES_FOLDER_MAC := $(addprefix $(OBJ_MAC)/,$(OBJ_FILES))

LIB_DIRS = -L"/usr/local/lib"
CC_LIBS = -static-libgcc -static-libstdc++ -D__cplusplus=201103L
# INCLUDE = -I"./src/" -I"/usr/include/" -I"libs/libdivsufsort-2.0.1/build/include" -I"libs/seqan-library-1.4.2/include"
# INCLUDE = -I"./src/" -I"/usr/include/" -I"src/libs/seqan-library-1.4.2/include"
INCLUDE = -I"./src/" -I"/usr/include/" -I"$(CODEBASE)/seqlib/src/libs/seqan-library-2.0.1/include" -I"$(CODEBASE)/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" $(CODEBASE_SRC_FOLDERS)

CC_FLAGS_DEBUG = -O3 -g -rdynamic -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -lz
CC_FLAGS_RELEASE = -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -lz # -march=native
CC_FLAGS_EXTCIGAR = -DRELEASE_VERSION -DUSE_EXTENDED_CIGAR_FORMAT -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -lz
CC_FLAGS_NOT_RELEASE = -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -lz
CC_FLAGS_NOT_RELEASE_EXT = -g -O3 -DUSE_EXTENDED_CIGAR_FORMAT -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -lz               LD_FLAGS = -static-libgcc -static-libstdc++ -m64 -ffreestanding -lz
# LD_LIBS = -lpthread -lgomp -lm -lz -ldivsufsort64
LD_LIBS = -lpthread -lgomp -lm -lz



all: gcc_version_check linux

install: /usr/bin/graphmap

/usr/bin/graphmap: bin/Linux-x64/graphmap
        cp bin/Linux-x64/graphmap /usr/bin/graphmap

modules:
        git submodule update --init --recursive
        # git submodule foreach git pull origin master

testing: $(OBJ_FILES_FOLDER_TESTING)
        mkdir -p $(dir $(BIN))
        $(GCC) $(LD_FLAGS) $(LIB_DIRS) -o $(BIN) $(OBJ_FILES_FOLDER_TESTING) $(LD_LIBS)

obj_test/%.o: %.cc $(H_FILES)
        mkdir -p $(dir $@)
        $(GCC) $(CC_LIBS) $(INCLUDE) $(CC_FLAGS_NOT_RELEASE) -o $@ $<
obj_test/%.o: %.cpp $(H_FILES)
        mkdir -p $(dir $@)
        $(GCC) $(CC_LIBS) $(INCLUDE) $(CC_FLAGS_NOT_RELEASE) -o $@ $<

testingext: $(OBJ_FILES_FOLDER_TESTING_EXT)
        mkdir -p $(dir $(BIN))                                                                                                                                                                                                                       $(GCC) $(LD_FLAGS) $(LIB_DIRS) -o $(BIN) $(OBJ_FILES_FOLDER_TESTING_EXT) $(LD_LIBS)

obj_testext/%.o: %.cc $(H_FILES)
        mkdir -p $(dir $@)
        $(GCC) $(CC_LIBS) $(INCLUDE) $(CC_FLAGS_NOT_RELEASE_EXT) -o $@ $<

obj_testext/%.o: %.cpp $(H_FILES)
        mkdir -p $(dir $@)
        $(GCC) $(CC_LIBS) $(INCLUDE) $(CC_FLAGS_NOT_RELEASE_EXT) -o $@ $<



gcc_version_check:
ifneq ($(GCC_MAJOR_VERSION_GE_4), 1)
        $(warning "*** WARNING $(GCC) major version <4 ***")
endif
ifneq ($(GCC_MINOR_VERSION_GE_7), 1)
        $(warning "*** WARNING $(GCC) minor version <7 ***")
endif

Any ideas?

Upvotes: 2

Views: 9060

Answers (2)

Paramar
Paramar

Reputation: 307

Just for future reference, what Altaf mentioned is correct. More than that, you can continue adding things that are not in the appropriate place exactly like this. Locate them and then add them manually.

If the makefile is not very big this will eventually be ok. It doesn't scale on the general case however, and maybe changing the makefile in a more radical way should be done.

Upvotes: 0

Altaf
Altaf

Reputation: 3076

Seems compiler is not able to find the file in the includes path you mentioned.
First check if zconf.h file is available on your machine and get that location. If the file is available then just give the path of the file to the compiler using -I option. 

INCLUDE = -I"<YourPath>" -I"./src/" -I"/usr/include/" -I"$(CODEBASE)/seqlib/src/libs/seqan-library-2.0.1/include" -I"$(CODEBASE)/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" $(CODEBASE_SRC_FOLDERS)

If the file itself is missing, then you would need to install it

sudo apt-get install libz-dev

Based on information shared by @Knud Larsen :
The Ubuntu package name is zlib1g-dev from where you can get the missing file. /usr/include/zconf.h
https://packages.ubuntu.com/focal-updates/amd64/zlib1g-dev/filelist

Upvotes: 6

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