[MacPorts] #47971: This is to introduce the new port gds
#47971: This is to introduce the new port gds ------------------------+-------------------------------- Reporter: ed.maros@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: gds ------------------------+-------------------------------- This package is used by scientist of LIGO Scientific Community. -- Ticket URL: <https://trac.macports.org/ticket/47971> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Changes (by ram@…): * cc: ram@… (removed) * owner: macports-tickets@… => ram@… * status: new => assigned -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:1> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ram@…): There's a large section of this commented out: {{{ 47 # EFM Done - FIXME: parallel build is currently broken 48 use_parallel_build yes 49 50 #set pythondir "${frameworks_dir}/Python.framework/Versions/2.7/lib/python2.7/site- packages" 51 #destroot.args-append \ 52 # pythondir="${pythondir}" \ 53 # pyexecdir="${pythondir}" \ 54 # pkgpythondir="${pythondir}/${name}" \ 55 # pkgpyexecdir="${pythondir}/${name}" 56 57 # FIXME: fails to build if previous version active 58 #conflicts_build ${name} }}} Can this be removed? -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:2> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ram@…): On Fri, Jun 5, 2015 at 4:32 PM, Edward Maros <emaros@ligo.caltech.edu> wrote:
It may be removed.
-- Ticket URL: <https://trac.macports.org/ticket/47971#comment:3> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ram@…): I think the modification of `pythondir` is needed as without it I can't import the python modules: {{{ [ram@hastur ~]$ python Python 2.7.10 (default, May 26 2015, 17:36:23) [GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import awg Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named awg
}}}
Whereas with the modification I can, but it fails: {{{ [ram@hastur ~]$ python Python 2.7.10 (default, May 26 2015, 17:36:23) [GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import awg Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named awg exit() [ram@hastur ~]$ python Python 2.7.10 (default, May 26 2015, 17:36:23) [GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin Type "help", "copyright", "credits" or "license" for more information. import awg Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/awg.py", line 35, in <module> import sys, numpy, awgbase File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/awgbase.py", line 20, in <module> libawg = CDLL('libawg.so') File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 365, in __init__ self._handle = _dlopen(self._name, mode) OSError: dlopen(libawg.so, 6): image not found
}}}
So this looks like missing dependency... Maybe we configure with the `--disable-python` option for the time being? -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:4> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ed.maros@…): OK. After listening to several people's feedback, I have corrected the Portfile to build the python extensions and install the necessary libraries required for the foton application. I have added the necessary patch files and the new Portfile. -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:5> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ram@…): There's no need to specify checksums for the patchfiles, these would only be needed if the patches were going to be downloaded but we'll add this to the repo so I've removed the checksums for the patches. Also there was a mixture of tabs and spaces so I've switched all these to spaces. It's building now... -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:6> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+-------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: gds | -------------------------+-------------------- Changes (by ram@…): * status: assigned => closed * resolution: => fixed Comment: r137318 -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:7> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Changes (by ram@…): * status: closed => reopened * resolution: fixed => Comment: This failed on all four build bots with what looks like the same error: {{{ libtool: link: /usr/bin/clang++ -O2 -pipe -Os -arch x86_64 -stdlib=libstdc++ "-DVCSID(x)=static const char* versionId[] = { versionId[1], x }" -o webview monweb.o webview.o ../../IO/web/.libs/libweb.a -L/opt/local/lib /opt/local/lib/libcurl.dylib ../.libs/libclient.a /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/IO/lmsg/.libs/liblmsg.a ../../IO/xsil/.libs/libxsil.a /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/Containers/.libs/libgdscntr.a /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/IO/lxr/.libs/liblxr.a /opt/local/lib/libmetaio.dylib ../../Containers/.libs/libgdscntr.a /opt/local/lib/libexpat.dylib ../../Base/.libs/libgdsbase.a ../../IO/sockutil/.libs/libsockutil.a ../../IO/lxr/.libs/liblxr.a ../../IO/lmsg/.libs/liblmsg.a /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/Base/.libs/libgdsbase.a /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/IO/sockutil/.libs/libsockutil.a -lz /opt/local/lib/libfftw3f_threads.dylib /opt/local/lib/libfftw3f.dylib /opt/local/lib/libfftw3_threads.dylib /opt/local/lib/libfftw3.dylib -lm -ldl -lpthread Undefined symbols for architecture x86_64: "void x86_vect::cvt<float, int>(float*, int const*, unsigned long) const", referenced from: DVecType<int>::getData(unsigned long, unsigned long, float*) const in libgdscntr.a(DVecType.o) "void x86_vect::cvt<int, float>(int*, float const*, unsigned long) const", referenced from: DVecType<float>::getData(unsigned long, unsigned long, int*) const in libgdscntr.a(DVecType.o) "void x86_vect::mul<basicplx<double> >(basicplx<double>*, basicplx<double> const*, unsigned long) const", referenced from: DVecType<basicplx<double> >::mpy(unsigned long, DVector const&, unsigned long, unsigned long) in libgdscntr.a(DVecType.o) "void x86_vect::mul<double>(double*, double, unsigned long) const", referenced from: DVecType<double>::scale(unsigned long, double, unsigned long) in libgdscntr.a(DVecType.o) DVecType<basicplx<double> >::scale(unsigned long, double, unsigned long) in libgdscntr.a(DVecType.o) "void x86_vect::muld<basicplx<double> >(basicplx<double>*, double const*, unsigned long) const", referenced from: DVecType<basicplx<double> >::mpy(unsigned long, DVector const&, unsigned long, unsigned long) in libgdscntr.a(DVecType.o) "void x86_vect::cmodsq<double>(double*, double const*, unsigned long) const", referenced from: dv_modsq(DVector const&) in libgdscntr.a(dv_function.o) "_global_x86_vect", referenced from: DVecType<float>::getData(unsigned long, unsigned long, int*) const in libgdscntr.a(DVecType.o) DVecType<int>::getData(unsigned long, unsigned long, float*) const in libgdscntr.a(DVecType.o) DVecType<basicplx<double> >::mpy(unsigned long, DVector const&, unsigned long, unsigned long) in libgdscntr.a(DVecType.o) DVecType<double>::scale(unsigned long, double, unsigned long) in libgdscntr.a(DVecType.o) DVecType<basicplx<double> >::scale(unsigned long, double, unsigned long) in libgdscntr.a(DVecType.o) dv_modsq(DVector const&) in libgdscntr.a(dv_function.o) ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) }}} Lion also had: {{{ /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/config/missing: line 52: aclocal-1.11: command not found WARNING: `aclocal-1.11' is missing on your system. You should only need it if you modified `acinclude.m4' or `configure.ac'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/config/missing --run autoconf cd . && /bin/sh /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/config/missing --run automake-1.11 --foreign /opt/local/var/macports/build/_opt_mports_dports_science_gds/gds/work/gds-2.17.1/config/missing: line 52: automake-1.11: command not found WARNING: `automake-1.11' is missing on your system. You should only need it if you modified `Makefile.am', `acinclude.m4' or `configure.ac'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. aclocal.m4:20: warning: this file was generated for autoconf 2.63. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically `autoreconf'. configure.ac:8: error: Autoconf version 2.62 or higher is required aclocal.m4:674: AM_INIT_AUTOMAKE is expanded from... configure.ac:8: the top level autom4te: /usr/bin/gm4 failed with exit status: 63 WARNING: `autoconf' is probably too old. You should only need it if you modified `configure.ac'. You might want to install the `Autoconf' and `GNU m4' packages. Grab them from any GNU archive site. /bin/sh ./config.status --recheck }}} You can take a look at the full logs here: https://build.macports.org/builders/buildports-lion-x86_64/builds/29394 \\ https://build.macports.org/builders/buildports-mtln-x86_64/builds/24054 \\ https://build.macports.org/builders/buildports-mavericks- x86_64/builds/13615 \\ https://build.macports.org/builders/buildports-yosemite-x86_64/builds/4373 \\ -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:8> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by larryv@…): You appear to be patching template files instead of the files that are generated from them. This is why Make is trying to run Autotools, and the configure script is being run a second time during the build phase. Preferably, you should patch the generated files instead of the source files; this would avoid the need to run Autotools at all. Failing that, you might have to add `use_autoreconf yes`. -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:9> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ed.maros@…): Replying to [comment:9 larryv@…]:
You appear to be patching template files instead of the files that are generated from them. This is why Make is trying to run Autotools, and the configure script is being run a second time during the build phase.
Preferably, you should patch the generated files instead of the source files; this would avoid the need to run Autotools at all. Failing that, you might have to add `use_autoreconf yes`. I have uploaded a modified Portfile which has replaced the patch /Users/efm/tmp/patch-config-ac_dmtoffline.m4.diff with /Users/efm/tmp /patch-configure.diff so only generated files are modified.
-- Ticket URL: <https://trac.macports.org/ticket/47971#comment:10> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ram@…): Replying to [comment:10 ed.maros@…]:
I have uploaded a modified Portfile which has replaced the patch /Users/efm/tmp/patch-config-ac_dmtoffline.m4.diff with /Users/efm/tmp /patch-configure.diff so only generated files are modified.
The new Portfile didn't take into account the changes I'd made when committing the port so I've applied them again. It's building now... -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:11> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ram@…): It's now failing for me with: {{{ Undefined symbols for architecture x86_64: "std::__1::basic_ios<char, std::__1::char_traits<char> >::widen(char) const", referenced from: table::tableIO_hdf::plan_data(table::Table const&) in tableIO_hdf.o table::tableIO_hdf::readTable(table::Table&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in tableIO_hdf.o table::tableIO_hdf::writeTable(table::Table const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in tableIO_hdf.o std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char>
(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in tableIO_hdf.o ld: symbol(s) not found for architecture x86_64 }}}
This is on Yosemite. -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:12> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+---------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: gds | -------------------------+---------------------- Comment (by ram@…): And this is building for me now, not sure why it didn't before... -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:13> MacPorts <https://www.macports.org/> Ports system for OS X
#47971: This is to introduce the new port gds -------------------------+-------------------- Reporter: ed.maros@… | Owner: ram@… Type: submission | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: gds | -------------------------+-------------------- Changes (by khindenburg@…): * status: reopened => closed * resolution: => fixed Comment: This was just updated to 2.17.3 which doesn't need any of the previous patches. -- Ticket URL: <https://trac.macports.org/ticket/47971#comment:15> MacPorts <https://www.macports.org/> Ports system for OS X
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