May 2014 - macports-tickets - lists.macosforge.org

[MacPorts] #35992: Gate 6.2 (new port)
by MacPorts 13 May '14

13 May '14

#35992: Gate 6.2 (new port) --------------------------------------------+------------------------------- Reporter: mojca.miklavec.lists@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: gate --------------------------------------------+------------------------------- I would like to see Gate 6.2 included in MacPorts. This is slightly related to Geant4 (#32716). Gate needs version 9.5.p01. I have written a preliminary Portfile here which needs a bit of help from experts to get linker flags work properly (and of course an updated Geant4). I'll post updates here as I proceed. {{{ PortSystem 1.0 PortGroup cmake 1.0 name gate version 6.2 categories science maintainers gmail.com:mojca.miklavec.lists license TODO description GATE description long_description GATE is dedicated to numerical simulations in medical imaging and radiotherapy. \ It currently supports simulations of Emission Tomography (PET and SPECT), \ Computed Tomography (CT) and Radiotherapy experiments. homepage http://www.opengatecollaboration.org platforms darwin distfiles gate_v6_2_tar_gz_15277.gz master_sites http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/… checksums rmd160 3fb8ec0fc7b78761e9eb0f39605ef84f1c485d42 \ sha256 d8c0dcbb74e734a60bae868ba1ce4d334919695e2b59099d87933ec425c7f98a patchfiles patch-compileerrors.diff worksrcdir gate_v${version} configure.dir ${workpath}/build build.dir ${configure.dir} post-extract { file mkdir ${configure.dir} } configure.post_args ${worksrcpath} depends_lib port:geant4 \ port:clhep # clhep implied with geant4 configure.args-append -DGATE_USE_OWN_CLHEP=OFF }}} {{{ --- source/digits_hits/include/GateMaps.hh.orig +++ source/digits_hits/include/GateMaps.hh @@ -117,7 +117,7 @@ inline GateMap<Tkey,Tvalue>::GateMap(size_t n, GateMap<Tkey,Tvalue> *mapArray[]) for (size_t i=0; i<n ; i++){ GateMap<Tkey,Tvalue>* mapElement = mapArray[i]; for (iterator iter = mapElement->begin(); iter != mapElement->end(); iter++) - insert(*iter); + this->insert(*iter); } } --- source/general/include/GateUIcmdWithAVector.hh.orig +++ source/general/include/GateUIcmdWithAVector.hh @@ -118,14 +118,14 @@ template<typename vContentType> G4String GateUIcmdWithAVector<vContentType>::ConvertToString (std::vector<vContentType> vec) { - char st[100]; + //char st[100]; //LF //std::ostrstream os(st,100); - std::ostringstream os(st,100); + std::ostringstream os; //LF for (G4int i=0; i<vec.size(); i++) os << vec[i] << " "; os << '\0'; - G4String vl = st; + G4String vl = os.str(); G4cout << "GateUIcmdWithAVector::ConvertToString : " << vl << G4endl; return vl; } }}} Compilation currently fails with {{{ Undefined symbols for architecture x86_64: "vtable for CLHEP::HepVector", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o NOTE: a missing vtable usually means the first non-inline virtual member function has no definition. "vtable for CLHEP::HepSymMatrix", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o NOTE: a missing vtable usually means the first non-inline virtual member function has no definition. "CLHEP::HepVector::HepVector(int)", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o "CLHEP::HepVector::operator=(CLHEP::HepVector const&)", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o "CLHEP::HepVector::~HepVector()", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o GateSourcePencilBeam::~GateSourcePencilBeam() in GateSourcePencilBeam.cc.o GateSourcePencilBeam::GenerateVertex(G4Event*) in GateSourcePencilBeam.cc.o "CLHEP::HepSymMatrix::HepSymMatrix(int, int)", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o "CLHEP::HepSymMatrix::operator=(CLHEP::HepSymMatrix const&)", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o "CLHEP::HepSymMatrix::~HepSymMatrix()", referenced from: GateSourcePencilBeam::GateSourcePencilBeam(G4String) in GateSourcePencilBeam.cc.o GateSourcePencilBeam::~GateSourcePencilBeam() in GateSourcePencilBeam.cc.o "CLHEP::RandMultiGauss::fire()", referenced from: GateSourcePencilBeam::GenerateVertex(G4Event*) in GateSourcePencilBeam.cc.o "CLHEP::RandMultiGauss::RandMultiGauss(CLHEP::HepRandomEngine*, CLHEP::HepVector const&, CLHEP::HepSymMatrix const&)", referenced from: GateSourcePencilBeam::GenerateVertex(G4Event*) in GateSourcePencilBeam.cc.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [Gate] Error 1 }}} -- Ticket URL: <https://trac.macports.org/ticket/35992> MacPorts <http://www.macports.org/> Ports system for Mac OS

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[MacPorts] #43685: gnuradio or grc command not fount
by MacPorts 13 May '14

13 May '14

#43685: gnuradio or grc command not fount -------------------------------------------------+------------------------- Reporter: briansullivan2@… | Owner: macports- Type: defect | tickets@… Priority: Normal | Status: new Component: ports | Milestone: Keywords: command not found, environment | Version: 2.2.1 variables, bashrc, | Port: gnuradio, | gr-osmosdr, -------------------------------------------------+------------------------- I had GQRX installed and working fine as well GNU Radio Companion, both installed from a .pkg(not using Macports) for a while I wanted to use the Osmosdr block in Gunuradio Companion and the only way to do this was via macports. I installed the gr-osmosdr port. Foolishly I made some other change regarding what I think was the environmental variables according to the instructions before conforming the new port installed and worked okay. Before the macports install all I need to do to open GNURadio Companion was to type grc in terminal. Now I get "command not found" I don't know what changes I made exactly but I can tell you that env command gives me: {{{..TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/_m/nwgn502d0zzf2xvy_frt8gqc0000gp/T/ Apple_PubSub_Socket_Render=/tmp/launch-W0grD9/Render TERM_PROGRAM_VERSION=303.2 TERM_SESSION_ID=F4D140BD-3910-4C14-8B82-84E71A1DAF1D USER=programming COMMAND_MODE=unix2003 SSH_AUTH_SOCK=/tmp/launch-5lkR7I/Listeners Apple_Ubiquity_Message=/tmp/launch-t9vkeh/Apple_Ubiquity_Message __CF_USER_TEXT_ENCODING=0x1F6:0:0 PATH=/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/X11/bin:/usr/local/git/bin:/opt/local/bin PWD=/Users/programming DBUS_LAUNCHD_SESSION_BUS_SOCKET=/tmp/launch-1bOS9C/unix_domain_listener EDITOR=/user/bin/pico LANG=en_US.UTF-8 HOME=/Users/programming SHLVL=1 LOGNAME=programming DISPLAY=/tmp/launch-uvktbH/org.macosforge.xquartz:0 _=/usr/bin/env OLDPWD=/usr/libexec.}}} It's not the same as what the example in the instructions show, but I'm a bit of a NOOB and not sure how to interoperate this. This is what I have done so far to try to remedy the problem: install GNU Radio via macports, thinking that the gr-osomsdr port could not "talk" to GNU stuff installed via binary (osx traditional method) THEN uninstalled GQRX by dragging to the trash. THEN I tried uninstalling and reinstalling gnu radio with some different variants. have tried this on three different macs iMac os x 10.7.5 MBP 10.9.2 and an MBA os x10.6.8(this last one was an effort on a clean os without Macports or gnu prior) Your guidance is much appreciated. Brian -- Ticket URL: <https://trac.macports.org/ticket/43685> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #42825: Update libtasn1 to @3.4
by MacPorts 12 May '14

12 May '14

#42825: Update libtasn1 to @3.4 ----------------------------+-------------------------------- Reporter: mschamschula@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: libtasn1 ----------------------------+-------------------------------- libtasn1 has been updated several times upstream. the current version is @3.4. -- Ticket URL: <https://trac.macports.org/ticket/42825> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #42970: wannier90: Needs to use compilers portgroup
by MacPorts 12 May '14

12 May '14

#42970: wannier90: Needs to use compilers portgroup -------------------------------+------------------------ Reporter: macsforever2000@… | Owner: dstrubbe@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: wannier90 -------------------------------+------------------------ wannier90 needs to use the new compilers portgroup so it can be built with newer compilers like gcc48. -- Ticket URL: <https://trac.macports.org/ticket/42970> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #42962: [Port Abandonement] gradle
by MacPorts 12 May '14

12 May '14

#42962: [Port Abandonement] gradle ----------------------------+-------------------------------- Reporter: poldwusmokow@… | Owner: macports-tickets@… Type: request | Status: new Priority: Normal | Milestone: MacPorts 2.3.0 Component: ports | Version: 2.2.1 Keywords: | Port: ----------------------------+-------------------------------- Based on version history gradle port hasn't been maintained for 4 months now. There have been problems with it in the past, I remember creating patch before (https://trac.macports.org/ticket/39104) Ticket regarding portfile upgrade to most recent gradle version: https://trac.macports.org/ticket/42898 After creating this ticket I'm going to link it to the gradle forums, hopefully someone actively using macports and gradle will step up to maintain the port. -- Ticket URL: <https://trac.macports.org/ticket/42962> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #42888: Upgrade of netcdf-fortran fails staging into destroot
by MacPorts 12 May '14

12 May '14

#42888: Upgrade of netcdf-fortran fails staging into destroot ------------------------------+-------------------------------- Reporter: david.w.watson@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: netcdf-fortran ------------------------------+-------------------------------- See log. -- Ticket URL: <https://trac.macports.org/ticket/42888> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #43402: clang-3.3 upgrade fails
by MacPorts 12 May '14

12 May '14

#43402: clang-3.3 upgrade fails ------------------------------+-------------------------------- Reporter: david.w.watson@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: clang-3.3 ------------------------------+-------------------------------- It's the error: invalid version number in '-mmacosx-version-min='. -- Ticket URL: <https://trac.macports.org/ticket/43402> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #42376: maxima upgrade fails after sbcl upgrade to 1.1.15_0
by MacPorts 12 May '14

12 May '14

#42376: maxima upgrade fails after sbcl upgrade to 1.1.15_0 ------------------------------+-------------------------------- Reporter: david.w.watson@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: maxima ------------------------------+-------------------------------- See log -- Ticket URL: <https://trac.macports.org/ticket/42376> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #43687: [port abandoned] gerbv
by MacPorts 12 May '14

12 May '14

#43687: [port abandoned] gerbv --------------------+--------------------------- Reporter: mf2k@… | Owner: darwinports@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: gerbv --------------------+--------------------------- The maintainer of gerbv has never responded to tickets including: #19340, #22424, #24725, #36454, and #42882. -- Ticket URL: <https://trac.macports.org/ticket/43687> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #42882: Add quartz variant to gerbv
by MacPorts 12 May '14

12 May '14

#42882: Add quartz variant to gerbv ----------------------+-------------------------------- Reporter: darius@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: ----------------------+-------------------------------- If GTK is built in Quartz mode gerbv won't build, this patch lets you turn Quartz mode on. -- Ticket URL: <https://trac.macports.org/ticket/42882> MacPorts <http://www.macports.org/> Ports system for OS X

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