Re: [Hdf-forum] build problems with hdf51.8.10-pre1 on macOS

Fri, 26 Oct 2012 15:02:08 -0700 

Hi Scott,

"make clean" only removes all compiled files (*.o, a.out).
It does not purge the Makefile and testh5ump.sh, etc.
This is true at least for the autotools configure side.
I don't know enough of cmake to say for sure but the left over Makefile from one 
system (configure) likely interferes with the other system (cmake).
You can try "make distclean" to purge the Makefile's and other files generated by configure and try cmake again. If that does not clear up the problems, your 
best bet is to start from scratch again.

-Albert

On 10/26/12 3:48 PM, Scott Sides wrote:

I'm having a problem even building the hdf5 1.8.10 pre-1 version now.
I was having a problem with the binaries, but now I see this.
I'm not entirely sure what changed... but maybe this is a clue to some
larger problems? One thing that changed was that I tried both the autotools 
configure and the cmake configure in the same build directory. I've done
make clean in between the different methods, but I thought I'd mention it. 

Scott
[ 70%] Building C object fortran/src/CMakeFiles/hdf5_f90cstub.dir/H5f90kit.c.o cd /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/fortran/src && /usr/bin/gcc -D_BSD_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -DH5_BUILT_AS_STATIC_LIB -DPIC -DNDEBUG -pipe -fPIC -std=c99 -fomit-frame-pointer -finline-functions -fno-common -fmessage-length=0 -O3 -DNDEBUG -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/src -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/bin -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/fortran -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/bin/fortran -o CMakeFiles/hdf5_f90cstub.dir/H5f90kit.c.o -c /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90kit.c In file included from /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90.h:23, from /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90kit.c:29: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:99: error: ‘H5_FC_FUNC_’ declared as function returning a function /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:99: warning: parameter names (without types) in function declaration /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:100: error: ‘H5_FC_FUNC_’ declared as function returning a function /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:100: warning: parameter names (without types) in function declaration /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:101: error: ‘H5_FC_FUNC_’ declared as function returning a function /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:101: warning: parameter names (without types) in function declaration /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:102: error: ‘H5_FC_FUNC_’ declared as function returning a function /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:102: warning: parameter names (without types) in function declaration /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:103: error: ‘H5_FC_FUNC_’ declared as function returning a function /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:103: warning: parameter names (without types) in function declaration /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/fortran/src/H5f90proto.h:104: error: ‘H5_FC_FUNC_’ declared as function returning a function 


My compilers are:

polymer:ser swsides$ gcc --version ; g++ --version ; gfortran --version
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00) 
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00) 
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 

GNU Fortran (GCC) 4.6.2 20111019 (prerelease)
Copyright (C) 2011 Free Software Foundation, Inc.
Darwin polymer.txcorp.com 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 


And my cmake configure script is the following:

#!/bin/bash

# Clear cmake cache to ensure a clean configure.
rm -rf CMakeFiles CMakeCache.txt

'/Users/swsides/contrib/cmake/bin/cmake' \
-DCMAKE_INSTALL_PREFIX:PATH=/Users/swsides/contrib/hdf5-1.8.10-pre1-ser \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DCMAKE_COLOR_MAKEFILE:BOOL=FALSE \
-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
-DCMAKE_C_COMPILER:FILEPATH='/usr/bin/gcc' \
-DCMAKE_CXX_COMPILER:FILEPATH='/usr/bin/g++' \
-DCMAKE_Fortran_COMPILER:FILEPATH='/usr/local/bin/gfortran' \
-DCMAKE_C_FLAGS:STRING='-pipe -fPIC' \
-DCMAKE_CXX_FLAGS:STRING='-pipe -fPIC' \
-DCMAKE_Fortran_FLAGS:STRING='-fPIC' \
-DHDF5_BUILD_TOOLS:BOOL=ON \
-DHDF5_BUILD_HL_LIB:BOOL=ON \
-DHDF5_BUILD_FORTRAN:BOOL=ON \
/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1


For just the make h5dump target I get the following:


[ 98%] Built target hdf5_tools
make -f tools/h5dump/CMakeFiles/h5dump.dir/build.make tools/h5dump/CMakeFiles/h5dump.dir/depend cd /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser && /Users/swsides/contrib/cmake-2.8.9-ser/bin/cmake -E cmake_depends "Unix Makefiles" /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1 /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/tools/h5dump /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/tools/h5dump/CMakeFiles/h5dump.dir/DependInfo.cmake make -f tools/h5dump/CMakeFiles/h5dump.dir/build.make tools/h5dump/CMakeFiles/h5dump.dir/build /Users/swsides/contrib/cmake-2.8.9-ser/bin/cmake -E cmake_progress_report /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/CMakeFiles 
[ 98%] Building C object tools/h5dump/CMakeFiles/h5dump.dir/h5dump.c.o
cd /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/tools/h5dump && /usr/bin/gcc -D_BSD_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -DH5_BUILT_AS_STATIC_LIB -DPIC -DNDEBUG -D_POSIX_C_SOURCE=199506L -pipe -fPIC -std=c99 -fomit-frame-pointer -finline-functions -fno-common -fmessage-length=0 -O3 -DNDEBUG -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/src -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/bin -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/lib -o CMakeFiles/h5dump.dir/h5dump.c.o -c /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c: In function ‘parse_command_line’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1068: warning: implicit declaration of function ‘strdup’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1068: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1080: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1097: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1109: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1121: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c: In function ‘main’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1490: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump.c:1572: warning: assignment makes pointer from integer without a cast /Users/swsides/contrib/cmake-2.8.9-ser/bin/cmake -E cmake_progress_report /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/CMakeFiles [ 98%] Building C object tools/h5dump/CMakeFiles/h5dump.dir/h5dump_ddl.c.o cd /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/tools/h5dump && /usr/bin/gcc -D_BSD_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -DH5_BUILT_AS_STATIC_LIB -DPIC -DNDEBUG -D_POSIX_C_SOURCE=199506L -pipe -fPIC -std=c99 -fomit-frame-pointer -finline-functions -fno-common -fmessage-length=0 -O3 -DNDEBUG -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/src -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/bin -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/lib -o CMakeFiles/h5dump.dir/h5dump_ddl.c.o -c /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c: In function ‘dump_all_cb’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c:238: warning: implicit declaration of function ‘strdup’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c:238: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c: In function ‘dump_group’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c:831: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘haddr_t’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c: In function ‘handle_datatypes’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_ddl.c:1762: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘haddr_t’ /Users/swsides/contrib/cmake-2.8.9-ser/bin/cmake -E cmake_progress_report /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/CMakeFiles 6 [100%] Building C object tools/h5dump/CMakeFiles/h5dump.dir/h5dump_xml.c.o cd /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/tools/h5dump && /usr/bin/gcc -D_BSD_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -DH5_BUILT_AS_STATIC_LIB -DPIC -DNDEBUG -D_POSIX_C_SOURCE=199506L -pipe -fPIC -std=c99 -fomit-frame-pointer -finline-functions -fno-common -fmessage-length=0 -O3 -DNDEBUG -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/src -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/bin -I/Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/lib -o CMakeFiles/h5dump.dir/h5dump_xml.c.o -c /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c: In function ‘xml_dump_all_cb’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:130: warning: implicit declaration of function ‘strdup’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:130: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c: In function ‘xml_name_to_XID’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:511: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘haddr_t’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:522: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘haddr_t’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:531: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘haddr_t’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c: In function ‘xml_escape_the_name’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:594: warning: return makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c: In function ‘xml_dump_group’: /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:2565: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:2570: warning: assignment makes pointer from integer without a cast /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:2722: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘haddr_t’ /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/tools/h5dump/h5dump_xml.c:2805: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘haddr_t’ 
Linking C executable ../../bin/h5dump
cd /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1/ser/tools/h5dump && /Users/swsides/contrib/cmake-2.8.9-ser/bin/cmake -E cmake_link_script CMakeFiles/h5dump.dir/link.txt --verbose=1 /usr/bin/gcc -pipe -fPIC -std=c99 -fomit-frame-pointer -finline-functions -fno-common -fmessage-length=0 -O3 -DNDEBUG -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/h5dump.dir/h5dump.c.o CMakeFiles/h5dump.dir/h5dump_ddl.c.o CMakeFiles/h5dump.dir/h5dump_xml.c.o -o ../../bin/h5dump ../../bin/libhdf5_tools.a ../../bin/libhdf5.a -lm 
Undefined symbols for architecture x86_64:
"_inflateInit_", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.c.o)
"_inflate", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.c.o)
"_inflateEnd", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.c.o)
"_compress2", referenced from:
_H5Z_filter_deflate in libhdf5.a(H5Zdeflate.c.o)
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[3]: *** [bin/h5dump] Error 1
make[2]: *** [tools/h5dump/CMakeFiles/h5dump.dir/all] Error 2
make[1]: *** [tools/h5dump/CMakeFiles/h5dump.dir/rule] Error 2






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