Trouble building from source

[mothur-westcott]

I am attempting to build on OSX 10.9.4. I ran the following:

sudo port install automake autoconf libtool
sudo port install  bzip2
git clone http://github.com/neufeld/pandaseq.git/
cd pandaseq
./autogen.sh && ./configure && make && sudo make install

I get the following error:

pandaseq sarahwestcott$ ./autogen.sh && ./configure && make && sudo make install
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 style of include used by make... GNU
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 dependency style of gcc... gcc3
checking for ar... ar
checking the archiver (ar) interface... ar
checking build system type... x86_64-apple-darwin13.3.0
checking host system type... x86_64-apple-darwin13.3.0
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
checking the name lister (/usr/bin/nm) 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-darwin13.3.0 file names to x86_64-apple-darwin13.3.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin13.3.0 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... no
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 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... darwin13.3.0 dyld
checking how to hardcode library paths into programs... immediate
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 windres... no
checking whether compiler accepts "-pedantic"... yes
checking for ANSI C header files... (cached) yes
checking whether make supports nested variables... (cached) yes
checking (non-cross) C compiler for building tools... gcc
checking for module flags...  -no-undefined -avoid-version -shared -flat_namespace
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking whether pthreads work with -pthreads... no
checking whether pthreads work with -mthreads... no
checking for the pthreads library -lpthread... yes
checking whether pthreads work with --thread-safe... no
checking whether pthreads work with -mt... no
checking for the pthreads library -lpthreadGC2... no
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking whether uname(2) is POSIX... yes
checking for sys/param.h... yes
checking for sys/sysctl.h... yes
./configure: line 13106: syntax error near unexpected token `Z,'
./configure: line 13106: `PKG_CHECK_MODULES(Z,  zlib )'

[apmasell]

Try installing pkgconfig from MacPorts.

[mothur-westcott]

Johns-iMac:pandaseq sarahwestcott$ sudo port install libtool
--->  Computing dependencies for libtool
--->  Cleaning libtool
--->  Scanning binaries for linking errors
--->  No broken files found.                             
Johns-iMac:pandaseq sarahwestcott$ ./autogen.sh && ./configure && make && sudo make install
...
checking for BZ2_bzDecompressInit in -lbz2... yes
checking ltdl.h usability... no
checking ltdl.h presence... no
checking for ltdl.h... no
configure: error: *** ltld required, install libtool library. 

[apmasell]

Odd. Can you verify that ltdl.h is available in /opt/local/include? If it is present, it is not being found by the C compiler. Have a check in config.log to see the specific error. Try setting export CFLAGS=-I/opt/local/include LDFLAGS=-L/opt/local/lib.

[mothur-westcott]

Thanks for your help with this!

cd /opt/local/include
Johns-iMac:include sarahwestcott$ ls
X11         cursesf.h       db46            expat.h         gdbm.h          libintl.h       ltdl.h   ...

The export CFLAGS=-I/opt/local/include LDFLAGS=-L/opt/local/lib fixed it.