[MacPorts] #28549: py26-h5py @1.3.1 Configure error - build failure
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- I am running Mac OS 10.6.6 on a fresh macports installation. I have installed hdf5-18 as follows: {{{ sudo port installed hdf5-18 The following ports are currently installed: hdf5-18 @1.8.6_1+gcc45 (active) }}} Here is my output of the build fail: {{{
sudo port -v install py26-h5py ---> Computing dependencies for py26-h5py. ---> Fetching py26-h5py ---> Verifying checksum(s) for py26-h5py ---> Checksumming h5py-1.3.1.tar.gz ---> Extracting py26-h5py ---> Extracting h5py-1.3.1.tar.gz ---> Configuring py26-h5py Undefined symbols: "_inflateEnd", referenced from: _H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o) _H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o) _H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o) "_SZ_encoder_enabled", referenced from: _H5Z_init_interface in libhdf5.a(H5Z.o) "_compress2", referenced from: _H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o) "_inflateInit_", referenced from: _H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o) "_SZ_BufftoBuffDecompress", referenced from: _H5Z_filter_szip in libhdf5.a(H5Zszip.o) "_SZ_BufftoBuffCompress", referenced from: _H5Z_filter_szip in libhdf5.a(H5Zszip.o) "_inflate", referenced from: _H5Z_filter_deflate in libhdf5.a(H5Zdeflate.o) ld: symbol(s) not found collect2: ld returned 1 exit status
Configure: Autodetecting HDF5 settings... Custom HDF5 dir: /opt/local Custom API level: (1, 8) Failed to compile HDF5 test program. Please check to make sure: * You have a C compiler installed * A development version of Python is installed (including header files) * A development version of HDF5 is installed (including header files) * If HDF5 is not in a default location, supply the argument --hdf5=<path> ****************************************** error: command 'cc' failed with exit status 1 shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py26-h5py/work/h5py-1.3.1" && /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 setup.py configure --api=18 --hdf5=/opt/local " returned error 1 Error: Target org.macports.configure returned: configure failure: shell command failed (see log for details) Warning: the following items did not execute (for py26-h5py): org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install Log for py26-h5py is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py26-h5py/main.log Error: Status 1 encountered during processing. To report a bug, see <http://guide.macports.org/#project.tickets> }}} I have attached the full log file. -- Ticket URL: <https://trac.macports.org/ticket/28549> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- Comment(by bobby.mendoza@…): I just noticed that on the [http://code.google.com/p/h5py/downloads/list h5py homepage], h5py-1.3.1 is only applicable for hdf5 versions 1.6.5-1.8.5, yet the latest macports build of hdf5 is 1.8.6. -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: eborisch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- Changes (by jmr@…): * owner: macports-tickets@… => eborisch@… Comment: Please remember to cc the maintainer. -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: eborisch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- Comment(by eborisch@…): Could you send the output of these commands? {{{ file /opt/local/lib/libsz.dylib file /opt/local/lib/libz.dylib file /opt/local/lib/libhdf5.dylib }}} I think there might be some architecture issues... I see some i386 references but it's building with -arch=x86_64 -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: eborisch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- Comment(by bobby.mendoza@…): Replying to [comment:3 eborisch@…]:
Could you send the output of these commands?
{{{ file /opt/local/lib/libsz.dylib file /opt/local/lib/libz.dylib file /opt/local/lib/libhdf5.dylib }}}
I think there might be some architecture issues... I see some i386 references but it's building with -arch=x86_64 Here you go: {{{ ~ > file /opt/local/lib/libz.dylib /opt/local/lib/libz.dylib: Mach-O universal binary with 2 architectures /opt/local/lib/libz.dylib (for architecture x86_64): Mach-O 64-bit dynamically linked shared library x86_64 /opt/local/lib/libz.dylib (for architecture i386): Mach-O dynamically linked shared library i386
~> file /opt/local/lib/libsz.dylib /opt/local/lib/libsz.dylib: Mach-O 64-bit dynamically linked shared library x86_64 ~> file /opt/local/lib/libhdf5.dylib /opt/local/lib/libhdf5.dylib: cannot open `/opt/local/lib/libhdf5.dylib' (No such file or directory) }}} There is no /opt/local/lib/libhdf5.dylib file, but I do have /opt/local/lib/libhdf5.a {{{ ~> file /opt/local/lib/libhdf5.a /opt/local/lib/libhdf5.a: current ar archive random library ~> ls /opt/local/lib/libhdf5* /opt/local/lib/libhdf5.a /opt/local/lib/libhdf5_fortran.a /opt/local/lib/libhdf5_hl_cpp.la* /opt/local/lib/libhdf5.la* /opt/local/lib/libhdf5_fortran.la* /opt/local/lib/libhdf5hl_fortran.a /opt/local/lib/libhdf5.settings /opt/local/lib/libhdf5_hl.a /opt/local/lib/libhdf5hl_fortran.la* /opt/local/lib/libhdf5_cpp.a /opt/local/lib/libhdf5_hl.la* /opt/local/lib/libhdf5_cpp.la* /opt/local/lib/libhdf5_hl_cpp.a }}} -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: eborisch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- Comment(by eborisch@…): The missing hdf5.dylib is the issue -- hdf5-18 with fortran (+gcc4x variants) doesn't support shared libs; h5py needs the shared lib version of hdf5-18. If you don't need fortran support, uninstall hdf5-18+gcc45 and install hdf5-18 (no gcc variants) and try py27-h5py again. Perhaps some of the other port maintainers can suggest a way to catch this... Please let me know if this fixes the problem for you so I can update the ticket. -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:5> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: eborisch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- Comment(by eborisch@…): I think I have a fix to enable static fortran and shared (c/c++ libs) for hdf5-18. I'll post a reference here once I've submitted it. -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:6> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure -------------------------------------+-------------------------------------- Reporter: bobby.mendoza@… | Owner: eborisch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: py26-h5py -------------------------------------+-------------------------------------- Comment(by eborisch@…): See #28554 for possible changes to hdf5-18 to support +gccXX (and therefore fortran) and shared c/c++ libs. -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:7> MacPorts <http://www.macports.org/> Ports system for Mac OS
#28549: py26-h5py @1.3.1 Configure error - build failure --------------------------------------+------------------------------------- Reporter: bobby.mendoza@… | Owner: eborisch@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Resolution: fixed | Keywords: Port: py26-h5py | --------------------------------------+------------------------------------- Changes (by eborisch@…): * status: new => closed * resolution: => fixed Comment: r76521 to hdf5-18 applies the patches from #28554, and should fix this (lack of shared c/c++ hdf5 libs) problem. Self-update and upgrade outdated and then try installing py26-h5py again. Closing -- please comment here if this hasn't fixed things. -- Ticket URL: <https://trac.macports.org/ticket/28549#comment:8> MacPorts <http://www.macports.org/> Ports system for Mac OS
participants (1)
-
MacPorts