May 2016 - macports-tickets - lists.macosforge.org

[MacPorts] #50705: Please add a port for mlpack
by MacPorts 03 May '16

03 May '16

#50705: Please add a port for mlpack ---------------------+-------------------------------- Reporter: subs@… | Owner: macports-tickets@… Type: request | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: mlpack ---------------------+-------------------------------- MLPack is a machine learning library available at: https://github.com/mlpack/mlpack -- Ticket URL: <https://trac.macports.org/ticket/50705> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51147: gnutls @3.3.22_0: update to 3.4.11
by MacPorts 03 May '16

03 May '16

#51147: gnutls @3.3.22_0: update to 3.4.11 ---------------------------------+-------------------------------- Reporter: mschamschula@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: haspatch maintainer | Port: gnutls ---------------------------------+-------------------------------- The gnutls stable branch has moved to 3.4.x as of version 3.4.7, with the current release being version 3.4.11. See http://www.gnutls.org/news.html for all the news items. '''Note''': Here is a list of ports that will likely need a revision bump: aqbanking5 aria2 bitlbee claws-mail emacs-app emacs-mac-app empathy ffmpeg ffmpeg-devel FileZilla pidgin gloox gnomint gnustep-gui gstreamer1-gst- plugins-bad gwenhywfar4 iksemel libinfinity libmicrohttpd pianobar libprelude pidgin libvirt libvmime LibVNCServer loudmouth mod_gnutls mpop msmtp ncdc net6 nzbget octave-parallel openconnect openconnect-gui openvas-libraries pan2 pianobar pianod postal prelude-manager qemu samba4 squid3 task telepathy-gabble telepathy-salut tigervnc vino VLC VLC-devel vte weechat wget wine wine-crossover wine-devel wireshark2 wput xmlsec yaz -- Ticket URL: <https://trac.macports.org/ticket/51147> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51089: hdf5 netcdf version problem
by MacPorts 03 May '16

03 May '16

#51089: hdf5 netcdf version problem -------------------------------+-------------------------------- Reporter: barry.j.mcinnes@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: hdf5 netcdf | Port: hdf5 netcdf-c -------------------------------+-------------------------------- Can netcdf 4.4.0 be put back as an option to install as well as hdf5 1.8.16 as an option to select. When we use the latest updates we get for a fortran program netid, reading from 0 /Projects/Reforecast2/netcdf/refcstv2_precip_ccpav3_012_to_024.nc netcdf error NetCDF: HDF error For ncdump, we get the same errors for the latest versions. When we go back to previous macports install of previous version the program and ncdump then works. There is also this problem https://github.com/Unidata/netcdf4-python/issues/549 -- Ticket URL: <https://trac.macports.org/ticket/51089> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #50815: dolfin @1.6.0_0: add vtk6 variant
by MacPorts 03 May '16

03 May '16

#50815: dolfin @1.6.0_0: add vtk6 variant ----------------------------+-------------------------------- Reporter: mschamschula@… | Owner: macports-tickets@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: haspatch | Port: dolfin ----------------------------+-------------------------------- Apparently dolfin fails to build under El Capitan since vtk5 currently cannot be installed. However, vtk6 a.k.a. vtk does properly install. See http://www.mail-archive.com/macports- users(a)lists.macosforge.org/msg39781.html I added a vtk6 variant (only test built it under Yosemite, as I don't have access to my El Cap build machine from home). -- Ticket URL: <https://trac.macports.org/ticket/50815> MacPorts <https://www.macports.org/> Ports system for OS X

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Re: [MacPorts] #44698: py-gwpy @0.1a10 new port submission
by MacPorts 03 May '16

03 May '16

#44698: py-gwpy @0.1a10 new port submission -------------------------------+-------------------------------- Reporter: duncanmmacleod@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: py-gwpy | -------------------------------+-------------------------------- Comment (by aronnax@…): Adam, why is it glue and not py-glue? -- Ticket URL: <https://trac.macports.org/ticket/44698#comment:22> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51292: tardiff: CVE-2015-0857, CVE-2015-0858 and other bugs
by MacPorts 03 May '16

03 May '16

#51292: tardiff: CVE-2015-0857, CVE-2015-0858 and other bugs -------------------------------+-------------------------- Reporter: raimue@… | Owner: ryandesign@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: security haspatch | Port: tardiff -------------------------------+-------------------------- I am attaching a patch to update tardiff with patches created by Debian to fix security bugs. In order to apply these patches without re-editing, other fixes should be applied first. I stripped the path prefix from the patches to apply them with -p0 and retained the explicit `gnutar`. Details are published in Debian's security advisory: https://www.debian.org/security/2016/dsa-3562 The patch is meant to be applied using `svn patch`. -- Ticket URL: <https://trac.macports.org/ticket/51292> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51294: Failed to build doxygen while installing gnuradio
by MacPorts 03 May '16

03 May '16

#51294: Failed to build doxygen while installing gnuradio ---------------------------------+-------------------------------- Reporter: red.carpet.guitar@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: gnuradio, doxygen | Port: gnuradio ---------------------------------+-------------------------------- Hi using a yosemite on mid 2012 macbook pro. While installing gnuradio saw the following error: Error: org.macports.build for port doxygen returned: command execution failed Error: Failed to install doxygen i tried cleaning the gnuradio port by using following command: sudo port clean gnuradio but still see the same problem while installing gnuradio. I have attached the main.log for further debugging. -- Ticket URL: <https://trac.macports.org/ticket/51294> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51277: hdf5-18 +cxx+hl+openmpi+szip does not compile
by MacPorts 03 May '16

03 May '16

#51277: hdf5-18 +cxx+hl+openmpi+szip does not compile -----------------------+-------------------------------- Reporter: smasson@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: hdf5-18 -----------------------+-------------------------------- hdf5-18 is not compiling because of the option +openmpi. [[BR]] In this case, it looks that configure is not able to find the compiler that is wrapped into openmpi. [[BR]] There is my main.log file: {{{ version:1 :msg:clean ---> Computing dependencies for netcdf:info:clean .:debug:clean netcdf has no conflicts :debug:clean Searching for dependency: cmake :debug:clean Found Dependency: receipt exists for cmake :debug:clean Searching for dependency: gcc48 :debug:clean Found Dependency: receipt exists for gcc48 :debug:clean Searching for dependency: libgcc :debug:clean Found Dependency: receipt exists for libgcc :debug:clean Searching for dependency: openmpi-gcc48 :debug:clean Found Dependency: receipt exists for openmpi-gcc48 :debug:clean Searching for dependency: hdf5-18 :debug:clean Found Dependency: receipt exists for hdf5-18 :debug:clean Searching for dependency: curl :debug:clean Found Dependency: receipt exists for curl :msg:clean :debug:main Executing org.macports.main (netcdf) :debug:main changing euid/egid - current euid: 0 - current egid: 0 :debug:main egid changed to: 501 :debug:main euid changed to: 503 :debug:main Skipping completed org.macports.archivefetch (netcdf) :debug:main Privilege de-escalation not attempted as not running as root. :debug:fetch fetch phase started at Fri Apr 29 16:01:34 PDT 2016 :notice:fetch ---> Fetching distfiles for netcdf :debug:fetch Executing proc-pre-org.macports.fetch-fetch-0 :debug:fetch compilers.enforce_c list: :debug:fetch compilers.enforce_fortran list: :debug:fetch compilers.enforce_some_fortran list: :debug:fetch Executing proc-pre-org.macports.fetch-fetch-1 :debug:fetch openmpi-gcc48 is installed with the following variants: +fortran :debug:fetch required: fortran, forbidden: :debug:fetch accepted :debug:fetch Executing proc-pre-org.macports.fetch-fetch-2 :debug:fetch mpi.enforce_variant list: hdf5-18 :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: , forbidden: :debug:fetch accepted :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: mpich, forbidden: :debug:fetch rejected, because required variant mpich is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: mpich_devel, forbidden: :debug:fetch rejected, because required variant mpich_devel is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: openmpi, forbidden: :debug:fetch accepted :debug:fetch compilers.enforce_c list: hdf5-18 :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: , forbidden: :debug:fetch accepted :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: clang33, forbidden: :debug:fetch rejected, because required variant clang33 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: clang34, forbidden: :debug:fetch rejected, because required variant clang34 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: clang35, forbidden: :debug:fetch rejected, because required variant clang35 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: clang36, forbidden: :debug:fetch rejected, because required variant clang36 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: clang37, forbidden: :debug:fetch rejected, because required variant clang37 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: clang38, forbidden: :debug:fetch rejected, because required variant clang38 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: dragonegg33, forbidden: :debug:fetch rejected, because required variant dragonegg33 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: dragonegg34, forbidden: :debug:fetch rejected, because required variant dragonegg34 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc44, forbidden: :debug:fetch rejected, because required variant gcc44 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc45, forbidden: :debug:fetch rejected, because required variant gcc45 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc46, forbidden: :debug:fetch rejected, because required variant gcc46 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc47, forbidden: :debug:fetch rejected, because required variant gcc47 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc48, forbidden: :debug:fetch rejected, because required variant gcc48 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc49, forbidden: :debug:fetch rejected, because required variant gcc49 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc5, forbidden: :debug:fetch rejected, because required variant gcc5 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: gcc6, forbidden: :debug:fetch rejected, because required variant gcc6 is missing :debug:fetch hdf5-18 is installed with the following variants: +cxx+hl+openmpi+szip :debug:fetch required: llvm, forbidden: :debug:fetch rejected, because required variant llvm is missing :error:fetch Install hdf5-18 +gcc48 :error:fetch org.macports.fetch for port netcdf returned: hdf5-18 +gcc48 not installed :debug:fetch Error code: NONE :debug:fetch Backtrace: hdf5-18 +gcc48 not installed while executing "proc-pre-org.macports.fetch-fetch-2 org.macports.fetch" ("eval" body line 1) invoked from within "eval $pre $targetname" :info:fetch Warning: targets not executed for netcdf: org.macports.install org.macports.fetch org.macports.checksum org.macports.extract org.macports.patch org.macports.configure org.macports.build org.macports.destroot :notice:fetch Please see the log file for port netcdf for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/main.log }}} -- Ticket URL: <https://trac.macports.org/ticket/51277> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51242: lapack error
by MacPorts 03 May '16

03 May '16

#51242: lapack error -------------------------------+-------------------------------- Reporter: barry.j.mcinnes@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: lapack | Port: lapack -------------------------------+-------------------------------- A clean install of lapack library gives the following error The first issue is that it does not like the liblapack version installed on Mac89. Undefined symbols for architecture x86_64: "_ATL_dger", referenced from: _ATL_dgetf2 in liblapack.a(ATL_dgetf2.o) "_ATL_xerbla", referenced from: _atl_f77wrap_dgetrf_ in liblapack.a(ATL_f77wrap_dgetrf.o) _atl_f77wrap_dgetri_ in liblapack.a(ATL_f77wrap_dgetri.o) ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make: *** [bin/pamtra] Error 1 The same makefile except specifying the Mac library in /usr/lib works fine, as does using the liblapack_ncl.a. Mac 10.11.4 latest install macports versions rw-r--r-- 1 root admin 10092720 Jan 30 03:21 /opt/local/lib/liblapack.a -rw-r--r-- 1 root admin 5588232 Apr 25 13:23 /opt/local/lib/liblapack_ncl.a -- Ticket URL: <https://trac.macports.org/ticket/51242> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51228: libemos fails to install
by MacPorts 03 May '16

03 May '16

#51228: libemos fails to install -------------------------------+-------------------------------- Reporter: barry.j.mcinnes@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: libemos | Port: libemos -------------------------------+-------------------------------- libemos fails from a clean install of macports,fftw-3 and gcc5 are installed, but not gcc48 and gcc49. debug file is attached. thanks for your macports support work, we could not exists without macports -- Ticket URL: <https://trac.macports.org/ticket/51228> MacPorts <https://www.macports.org/> Ports system for OS X

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