How can I set .h and linker data to compiler using autotools? - c

Question

Problem
Compilation process throws me messages that some .h file was not found.
I am trying to compile my own library.
These commands I use to build in a script called compile.sh (just for make easy):
echo "=====AUTORECONF=====" && autoreconf -fvi && \
echo "=====CONFIGURE=====" && ./configure --prefix="$HOME/local" && \
echo "=====COMPILE=====" && make && \
echo "=====CHECK=====" && make check && \
echo "=====INSTALL=====" && make install
After run this script I get (sorry because of large logs, I added them to be clear and explicit):
=====AUTORECONF=====
autoreconf: Entering directory `.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force -I m4
autoreconf: configure.ac: tracing
autoreconf: running: glibtoolize --copy --force
glibtoolize: putting auxiliary files in '.'.
glibtoolize: copying file './ltmain.sh'
glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
glibtoolize: copying file 'm4/libtool.m4'
glibtoolize: copying file 'm4/ltoptions.m4'
glibtoolize: copying file 'm4/ltsugar.m4'
glibtoolize: copying file 'm4/ltversion.m4'
glibtoolize: copying file 'm4/lt~obsolete.m4'
glibtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT'
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force
autoreconf: running: automake --add-missing --copy --force-missing
configure.ac:10: installing './compile'
configure.ac:6: installing './missing'
Makefile.am: installing './depcomp'
autoreconf: Leaving directory `.'
=====CONFIGURE=====
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for ar... ar
checking the archiver (ar) interface... ar
configure: WARNING: Libtool does not cope well with whitespace in `pwd`
checking build system type... x86_64-apple-darwin16.6.0
checking host system type... x86_64-apple-darwin16.6.0
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin16.6.0 file names to x86_64-apple-darwin16.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin16.6.0 file names to toolchain format... func_convert_file_noop
checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver #FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin16.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for csv_init in -lcsv... no
checking for CU_add_test in -lcunit... no
checking for sodium_init in -lsodium... no
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking sodium.h usability... no
checking sodium.h presence... no
checking for sodium.h... no
checking csv.h usability... no
checking csv.h presence... no
checking for csv.h... no
checking CUnit/CUnit.h usability... no
checking CUnit/CUnit.h presence... no
checking for CUnit/CUnit.h... no
checking CUnit/Basic.h usability... no
checking CUnit/Basic.h presence... no
checking for CUnit/Basic.h... no
checking for size_t... yes
checking for ssize_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for strerror... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=====COMPILE=====
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
depbase=`echo src/fseq4c.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2 -MT src/fseq4c.lo -MD -MP -MF $depbase.Tpo -c -o src/fseq4c.lo src/fseq4c.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT src/fseq4c.lo -MD -MP -MF src/.deps/fseq4c.Tpo -c src/fseq4c.c -fno-common -DPIC -o src/.libs/fseq4c.o
src/fseq4c.c:17:10: fatal error: 'sodium.h' file not found
#include <sodium.h>
^
1 error generated.
make[1]: *** [src/fseq4c.lo] Error 1
make: *** [all] Error 2
Questions
What should I modify in Makefile.am or configure.ac to solve this compiler error src/fseq4c.c:17:10: fatal error: 'sodium.h' file not found?
Are #sodium_CFLAGS# and #sodium_LIBS# the right way to set headers and linker data for build process? Note that in configure.ac is set these lines: AC_CHECK_LIB([cunit],[CU_add_test]) and AC_CHECK_LIB([sodium],[sodium_init]). I do not want to hardcode paths.
Stage
I have this file structure (keep in mind that I hide some files which can be autogenerated by autotools and only leave sources):
```
.
├── Doxyfile
├── Makefile.am
├── configure.ac
├── lib
│   └── fseq4c.o
└── src
   ├── fseq4c.c
   ├── fseq4c.h
   ├── lab
   │   ├── lab_gen_rand_fs.c
   │   └── lab_rand.c
   ├── test
   │   └── test_fseq4c.c
   └── utils
   ├── is_fsequence.c
   ├── is_fsequence.h
   └── parse_csv.c
My Makefile.am looks like this:
AUTOMAKE_OPTIONS = subdir-objects
ACLOCAL_AMFLAGS = -I m4
lib_LTLIBRARIES = libfseq4c.la
libfseq4c_la_SOURCES = src/fseq4c.c src/fseq4c.h
libfseq4c_la_CXXFLAGS = #sodium_CFLAGS#
libfseq4c_la_LIBS = #sodium_LIBS#
libfseq4c_la_LDFLAGS = -version-info 0:1:0
bin_PROGRAMS = is_fsequence lab_gen_rand_fs lab_rand parse_csv
is_fsequence_SOURCES = src/utils/is_fsequence.c src/utils/is_fsequence.h src/fseq4c.h
is_fsequence_DEPENDENCIES = libfseq4c.la
is_fsequence_LDADD = "-dlopen" libfseq4c.la
lab_gen_rand_fs_SOURCES = src/lab/lab_gen_rand_fs.c
lab_gen_rand_fs_DEPENDENCIES = libfseq4c.la
lab_gen_rand_fs_LDADD = "-dlopen" libfseq4c.la
lab_rand_SOURCES = src/lab/lab_rand.c
lab_rand_DEPENDENCIES = libfseq4c.la
parse_csv_SOURCES = src/utils/parse_csv.c
parse_csv_DEPENDENCIES = libfseq4c.la
parse_csv_LDADD = "-dlopen" libfseq4c.la
TESTS = testfseq4c
check_PROGRAMS = testfseq4c
testfseq4c_SOURCES = src/test/test_fseq4c.c
testfseq4c_DEPENDENCIES = libfseq4c.la
testfseq4c_LDADD = libfseq4c.la
My configure.ac looks like this:
AC_PREREQ([2.68])
AC_INIT([libfseq4c], [0.0.1])
AC_CONFIG_SRCDIR([src])
AC_CONFIG_HEADERS([config.h])
AC_CONFIG_MACRO_DIR([m4])
AM_INIT_AUTOMAKE([-Wall foreign dist-bzip2])
AC_LANG_C
# Checks for programs.
AC_PROG_CC
AM_PROG_AR
# Libtool
LT_PREREQ([2.4.6])
LT_INIT([dlopen])
# Checks for libraries.
AC_CHECK_LIB([csv],[csv_init])
AC_CHECK_LIB([cunit],[CU_add_test])
AC_CHECK_LIB([sodium],[sodium_init])
# Checks for header files.
AC_CHECK_HEADERS([stdlib.h string.h stdint.h unistd.h])
AC_CHECK_HEADERS([sodium.h])
AC_CHECK_HEADERS([csv.h])
AC_CHECK_HEADERS([CUnit/CUnit.h CUnit/Basic.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_TYPE_SIZE_T
AC_TYPE_SSIZE_T
AC_TYPE_UINT32_T
AC_TYPE_UINT8_T
# Checks for library functions.
AC_FUNC_MALLOC
AC_CHECK_FUNCS([strerror strtol])
AC_CONFIG_FILES([Makefile])
AC_OUTPUT
As you can see I use CUnit, libsodium, and libcsv as external libraries.