October 2013 - macports-tickets - lists.macosforge.org

[MacPorts] #40689: R @3.0.2_0 +accelerate +cairo +gfortran48 +recommended +x11 Compile error
by MacPorts 09 Oct '13

09 Oct '13

#40689: R @3.0.2_0 +accelerate +cairo +gfortran48 +recommended +x11 Compile error -----------------------------+-------------------------------- Reporter: grischa.toedt@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Keywords: | Port: -----------------------------+-------------------------------- Hi, on my system i have: {{{ sh-3.2# port select --list gcc Available versions for gcc: llvm-gcc42 mp-gcc47 mp-gcc48 (active) none }}} after "port selfupdate", "port upgrade outdated", "port clean R" i try a "port install R +accelerate +cairo +gfortran48 +recommended +x11" and i get: {{{ ... :info:build f951: internal compiler error: Illegal instruction: 4 :info:build :info:build f951: internal compiler error: Abort trap: 6 :info:build /opt/local/bin/gfortran-mp-4.8 -fPIC -pipe -Os -m64 -c dposl.f -o dposl.o :info:build /opt/local/bin/gfortran-mp-4.8 -fPIC -pipe -Os -m64 -c dqrdc.f -o dqrdc.o :info:build f951: internal compiler error: Illegal instruction: 4 :info:build :info:build f951: internal compiler error: Abort trap: 6 :info:build gfortran-mp-4.8: internal compiler error: Abort trap: 6 (program f951) :info:build gfortran-mp-4.8: internal compiler error: Abort trap: 6 (program f951) :info:build make[3]: *** [dpofa.o] Abort trap: 6 :info:build make[3]: *** Deleting file `dpofa.o' :info:build make[3]: *** Waiting for unfinished jobs.... :info:build make[3]: *** [dqrdc.o] Abort trap: 6 :info:build make[3]: *** Deleting file `dqrdc.o' :info:build make[3]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_R/R/work/R-3.0.2/src/appl' :info:build make[2]: *** [R] Error 2 :info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_R/R/work/R-3.0.2/src/appl' :info:build make[1]: *** [R] Error 1 :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_R/R/work/R-3.0.2/src' :info:build make: *** [R] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_R/R/work/R-3.0.2' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_R/R/work/R-3.0.2" && /usr/bin/make -j2 -w all :info:build Exit code: 2 :error:build org.macports.build for port R returned: command execution failed :debug:build Error code: CHILDSTATUS 76211 2 :debug:build Backtrace: command execution failed }}} the full log is attached... Any suggestions? -- Ticket URL: <https://trac.macports.org/ticket/40689> MacPorts <http://www.macports.org/> Ports system for OS X

1 6

[MacPorts] #40709: "-fgnu89-inline" should not be used when building with clang
by MacPorts 09 Oct '13

09 Oct '13

#40709: "-fgnu89-inline" should not be used when building with clang --------------------+-------------------------------- Reporter: leo@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Keywords: | Port: flac --------------------+-------------------------------- This flag causes build error on Xcode 5.0.1 & OS X 10.9 GM seeds -- Ticket URL: <https://trac.macports.org/ticket/40709> MacPorts <http://www.macports.org/> Ports system for OS X

1 3

[MacPorts] #40717: apr-1.4.8_0 fails to install on Mavericks GM
by MacPorts 09 Oct '13

09 Oct '13

#40717: apr-1.4.8_0 fails to install on Mavericks GM ------------------------+-------------------------------- Reporter: gglittle@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Keywords: | Port: ------------------------+-------------------------------- With 2.2.0 installed and after running "selfupdate", "upgrade outdated" fails with the following message: ---> Attempting to fetch apr-1.4.8_0.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/apr ---> Fetching distfiles for apr ---> Verifying checksums for apr ---> Extracting apr Error: org.macports.extract for port apr returned: command execution failed Error: Failed to install apr -- Ticket URL: <https://trac.macports.org/ticket/40717> MacPorts <http://www.macports.org/> Ports system for OS X

1 1

[MacPorts] #40691: qgis @2.0.1: possible version issue with +grass variant
by MacPorts 09 Oct '13

09 Oct '13

#40691: qgis @2.0.1: possible version issue with +grass variant -----------------------------+-------------------------------- Reporter: Peter.Danecek@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: qgis -----------------------------+-------------------------------- This port hard-codes to grass version 6.4.2. {{{ variant grass description "Build Grass (6.42) plugin" { depends_lib-append port:grass configure.args-append \ "-DGRASS_PREFIX=${prefix}/share/grass-6.4.2" } }}} Now, grass is `grass @6.4.3 (gis)` and the respective path does not exist any more. Does this plugin work with 6.4.3 as well or does it really require version 6.4.2. The build itself would not fail, however I wonder I this might cause problems during runtime? -- Ticket URL: <https://trac.macports.org/ticket/40691> MacPorts <http://www.macports.org/> Ports system for OS X

1 5

[MacPorts] #39327: New portfile for ITSOL: ITerative linear SOLvers
by MacPorts 09 Oct '13

09 Oct '13

#39327: New portfile for ITSOL: ITerative linear SOLvers ---------------------------+-------------------------------- Reporter: kingcrimson@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: itsol-2.0.0 ---------------------------+-------------------------------- There is an ongoing GSoC project to integrate ITSOL in Octave So this library will soon become a dependence for octave and octave-devel. This is my first attempt at creating a portfile so please bear with me if it is not perfect. -- Ticket URL: <https://trac.macports.org/ticket/39327> MacPorts <http://www.macports.org/> Ports system for OS X

1 11

[MacPorts] #40715: Add Open MPI support to ParMETIS port
by MacPorts 09 Oct '13

09 Oct '13

#40715: Add Open MPI support to ParMETIS port -------------------------+-------------------------------- Reporter: jcverle@… | Owner: macports-tickets@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Keywords: | Port: -------------------------+-------------------------------- As it stands, the ParMETIS port can be compiled only with MPICH. I would like to use it with Open MPI. I will attach a suggested change in the form of a diff file. Note that I also added a license line, which is copied from the metis port. I would also be willing to help maintain the port, but I am a complete novice when it comes to portfiles. -- Ticket URL: <https://trac.macports.org/ticket/40715> MacPorts <http://www.macports.org/> Ports system for OS X

1 3

[MacPorts] #40670: errors installing and updating
by MacPorts 09 Oct '13

09 Oct '13

#40670: errors installing and updating -----------------------+-------------------------------- Reporter: cstring@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Keywords: | Port: -----------------------+-------------------------------- I recently tried to install valgrind using port, but ran into some errors in compiling part of it. So I then ran a selfupdate, but the selfupdate fails as well. The self update fails to make flock. I've looked for similar issues but I can't find a fix. I'll attach the debug results. Is there a fix outside of a clean install? -- Ticket URL: <https://trac.macports.org/ticket/40670> MacPorts <http://www.macports.org/> Ports system for OS X

1 5

[MacPorts] #40707: enable GSSAPI/Kerberos in serf1
by MacPorts 09 Oct '13

09 Oct '13

#40707: enable GSSAPI/Kerberos in serf1 -----------------------------+-------------------------------- Reporter: dogcow@… | Owner: macports-tickets@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Keywords: kerberos gssapi | Port: serf1 -----------------------------+-------------------------------- By default, serf-1.3.1 and prior (at very least) do not enable use of Kerberos and/or GSSAPI; they can be enabled by invoking scons as `scons GSSAPI=/path/to/kerb` - e.g. `scons GSSAPI=/usr` for the system libraries, `scons GSSAPI=${prefix}` for the macports-provided kerberos libraries, etc. It would be nice if it were enableable by default or as a variant. -- Ticket URL: <https://trac.macports.org/ticket/40707> MacPorts <http://www.macports.org/> Ports system for OS X

1 2

[MacPorts] #40711: cmake @2.8.11.2 - downstream software loses -O3 flag
by MacPorts 09 Oct '13

09 Oct '13

#40711: cmake @2.8.11.2 - downstream software loses -O3 flag -------------------------+-------------------------------- Reporter: johnsonsr@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Keywords: | Port: cmake -------------------------+-------------------------------- Any program newly compiled with the macports CMake '''will no longer use the -O3 flag''' when compiled as a "Release" code. This does not apply just to downstream macports installations but also to the user's custom installations that use the MacPorts-installed cmake. Basically, the CMake variable "CMAKE_CXX_FLAGS_RELEASE" is normally set to "-O3 -DNDEBUG" but an overzealous patch in the macports scripts changes this to " -DNDEBUG". Due to a change in revision 110069: {{{ eval reinplace "s|-O3||g" [glob ${worksrcpath}/Modules/{Compiler,Platform}/*.cmake] }}} the CMake flag variables are changed from {{{ ./Modules/Compiler/GNU.cmake:47: set(CMAKE_${lang}_FLAGS_RELEASE_INIT "-O3 -DNDEBUG") }}} to {{{ ./Modules/Compiler/GNU.cmake:47: set(CMAKE_${lang}_FLAGS_RELEASE_INIT " -DNDEBUG") }}} This has affected some of our scientific software that we benchmark regularly: the "Release" flag is no longer turning on optimization like it does for a standard CMake installation. This is a very subtle bug that must be fixed ASAP. -- Ticket URL: <https://trac.macports.org/ticket/40711> MacPorts <http://www.macports.org/> Ports system for OS X

1 2

[MacPorts] #40652: After selfupdate the list command fails
by MacPorts 09 Oct '13

09 Oct '13

#40652: After selfupdate the list command fails -------------------------------+-------------------------------- Reporter: feliks.kluzniak@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: base | Version: 2.2.0 Keywords: | Port: -------------------------------+-------------------------------- After today's "selfupdate" the basic "port" file has not changed, but apparently something got corrupted. Everything else seems to work well, but the command "list" gives an error, as show below. (Repeating selfupdate went without a hitch, but the problem persists.) If this is only on my machine, I'd appreciate a hint: How can I recover without reinstalling everything? {{{ > port list .... py25-pyprotocols @1.0a0dev-r2302 python/py-pyprotocols py26-pyprotocols @1.0a0dev-r2302 python/py-pyprotocols can't read "portinfo(version)": no such element in array while executing "format "%-30s @%-14s %s" $portinfo(name) $portinfo(version) $outdir" ("foreach" body line 8) invoked from within "foreach {name array} $res { array unset portinfo array set portinfo $array set outdir "" if {[info exi..." ("uplevel" body line 17) invoked from within "uplevel 1 $block" (procedure "foreachport" line 20) invoked from within "foreachport $portlist { if {$portname == "-all-"} { if {[catch {set res [mportlistall]} result]} { global errorInfo..." (procedure "action_list" line 10) invoked from within "$action_proc $action $portlist [array get global_options]" (procedure "process_cmd" line 93) invoked from within "process_cmd $remaining_args" invoked from within "if { [llength $remaining_args] > 0 } { # If there are remaining arguments, process those as a command set exit_status [process_cmd $remaining..." (file "/opt/local/bin/port" line 4857) > ll /opt/local/bin/port -r-xr-xr-x 1 root admin 167450 23 Jul 03:33 /opt/local/bin/port }}} -- Ticket URL: <https://trac.macports.org/ticket/40652> MacPorts <http://www.macports.org/> Ports system for OS X

1 4