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

[MacPorts] #49273: clang-mp-3.7 and MACOSX_DEPLOYMENT_TARGET=10.3 do not mix
by MacPorts 10 Aug '16

10 Aug '16

#49273: clang-mp-3.7 and MACOSX_DEPLOYMENT_TARGET=10.3 do not mix --------------------+-------------------------------- Reporter: jhi@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: clang --------------------+-------------------------------- I have the latest macports clang 3.7 on the latest Yosemite or 10.10 (not yet El Capitan or 10.11), and the XCode 7.0.1 Command Line Tools installed. Originally this failure came from trying to compile Perl, but I managed to reduce it to simply to the below-demonstrated problem, no Perl source needed: the macports clang doesn't work with the MACOSX_DEPLOYMENT_TARGET (https://developer.apple.com/library/mac/documentation/DeveloperTools/Concep…) as opposed to the system clang, or the macports clang with**OUT** the MACOSX_DEPLOYMENT_TARGET. I also show below the find outputs for the libgcc_s both in the XCode and under /opt/local/lib {{{ % cat main.c int main() { return 0; } % env MACOSX_DEPLOYMENT_TARGET=10.3 clang-mp-3.7 -o main main.c ld: library not found for -lgcc_s.10.4 clang: error: linker command failed with exit code 1 (use -v to see invocation) % env MACOSX_DEPLOYMENT_TARGET=10.3 /usr/bin/clang -o main main.c % env clang-mp-3.7 -o main main.c % clang-mp-3.7 -v clang version 3.7.0 (tags/RELEASE_370/final) Target: x86_64-apple-darwin14.5.0 % /usr/bin/clang -v Apple LLVM version 7.0.0 (clang-700.0.72) Target: x86_64-apple-darwin14.5.0 Thread model: posix % env MACOSX_DEPLOYMENT_TARGET=10.3 clang-mp-3.7 -v -o main main.c clang version 3.7.0 (tags/RELEASE_370/final) Target: x86_64-apple-darwin14.5.0 Thread model: posix "/opt/local/libexec/llvm-3.7/bin/clang" -cc1 -triple x86_64-apple- macosx10.3.0 -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name main.c -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 242 -v -dwarf-column-info -resource-dir /opt/local/libexec/llvm-3.7/bin/../lib/clang/3.7.0 -fdebug-compilation-dir /Users/jhi -ferror-limit 19 -fmessage-length 80 -mstackrealign -fblocks -fblocks-runtime-optional -fobjc-runtime=macosx-10.3.0 -fobjc-dispatch- method=non-legacy -fencode-extended-block-signature -fmax-type-align=16 -fdiagnostics-show-option -o /var/folders/yg/hdcrkqfx5cgc80b9zgbhnw_h0000gn/T/main-86350b.o -x c main.c clang -cc1 version 3.7.0 based upon LLVM 3.7.0 default target x86_64 -apple-darwin14.5.0 #include "..." search starts here: #include <...> search starts here: /usr/local/include /opt/local/libexec/llvm-3.7/bin/../lib/clang/3.7.0/include /usr/include /System/Library/Frameworks (framework directory) /Library/Frameworks (framework directory) End of search list. "/opt/local/libexec/llvm-3.7/bin/ld" -demangle -dynamic -arch x86_64 -macosx_version_min 10.3.0 -o main -lcrt1.o /var/folders/yg/hdcrkqfx5cgc80b9zgbhnw_h0000gn/T/main-86350b.o -lSystem -lgcc_s.10.4 /opt/local/libexec/llvm-3.7/bin/../lib/clang/3.7.0/lib/darwin/libclang_rt.10.4.a ld: library not found for -lgcc_s.10.4 clang: error: linker command failed with exit code 1 (use -v to see invocation) % find /Applications/Xcode.app -name 'libgcc_s*' /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/lib/libgcc_s.1.tbd /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/lib/libgcc_s.1.tbd /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/lib/libgcc_s.10.4.tbd /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/lib/libgcc_s.10.5.tbd % find /opt/local/lib -name 'libgcc_s*' /opt/local/lib/gcc43/libgcc_s.1.dylib /opt/local/lib/gcc43/libgcc_s.10.4.dylib /opt/local/lib/gcc43/libgcc_s.10.5.dylib /opt/local/lib/gcc43/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc43/libgcc_s_x86_64.1.dylib /opt/local/lib/gcc44/libgcc_s.1.dylib /opt/local/lib/gcc44/libgcc_s.10.4.dylib /opt/local/lib/gcc44/libgcc_s.10.5.dylib /opt/local/lib/gcc44/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc44/libgcc_s_x86_64.1.dylib /opt/local/lib/gcc45/libgcc_s.1.dylib /opt/local/lib/gcc45/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc45/libgcc_s_x86_64.1.dylib /opt/local/lib/gcc46/libgcc_s.1.dylib /opt/local/lib/gcc46/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc46/libgcc_s_x86_64.1.dylib /opt/local/lib/gcc47/libgcc_s.1.dylib /opt/local/lib/gcc47/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc47/libgcc_s_x86_64.1.dylib /opt/local/lib/gcc48/libgcc_s.1.dylib /opt/local/lib/gcc48/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc48/libgcc_s_x86_64.1.dylib /opt/local/lib/gcc49/libgcc_s.1.dylib /opt/local/lib/gcc49/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc49/libgcc_s_x86_64.1.dylib /opt/local/lib/gcc5/libgcc_s.1.dylib /opt/local/lib/gcc5/libgcc_s_ppc64.1.dylib /opt/local/lib/gcc5/libgcc_s_x86_64.1.dylib /opt/local/lib/libgcc/libgcc_s.1.dylib % }}} -- Ticket URL: <https://trac.macports.org/ticket/49273> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48486: lion buildslave registry damaged
by MacPorts 10 Aug '16

10 Aug '16

#48486: lion buildslave registry damaged ----------------------------+--------------------- Reporter: snc@… | Owner: admin@… Type: defect | Status: new Priority: Normal | Milestone: Component: server/hosting | Version: Keywords: | Port: ----------------------------+--------------------- I received build failures due to registry corruption. It seems all builds for Lion are failing: https://build.macports.org/builders/buildports-lion-x86_64 {{{ sqlite error: database disk image is malformed (11) while executing query: SELECT dependencies.id FROM ports port INNER JOIN dependencies USING(name) INNER JOIN ports dependent USING(id) WHERE port.id=27240 ORDER BY dependent.name,dependent.epoch, dependent.version, dependent.revision,dependent.variants while executing "$port dependents" (procedure "receipt_sqlite::list_dependents" line 16) invoked from within "${macports::registry.format}::list_dependents $name $version $revision $variants" (procedure "registry::list_dependents" line 3) invoked from within "registry::list_dependents $pvals(name)" (procedure "portlist_sortdependents" line 7) invoked from within "portlist_sortdependents $portlist" (procedure "action_deactivate" line 6) invoked from within "$action_proc $action $portlist [array get global_options]" (procedure "process_cmd" line 103) 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 5268) }}} -- Ticket URL: <https://trac.macports.org/ticket/48486> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #49808: update buildbot to 0.8.12
by MacPorts 10 Aug '16

10 Aug '16

#49808: update buildbot to 0.8.12 ----------------------------+--------------------- Reporter: ryandesign@… | Owner: admin@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: server/hosting | Version: Keywords: | Port: ----------------------------+--------------------- The buildbot software on the buildbot build slaves and the master should probably be updated to 0.8.12. -- Ticket URL: <https://trac.macports.org/ticket/49808> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51782: [Port Abandoned] Ports maintained by billitch
by MacPorts 09 Aug '16

09 Aug '16

#51782: [Port Abandoned] Ports maintained by billitch -------------------------+------------------------------------------------- Reporter: mf2k@… | Owner: billitch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: d-mode.el gtkglextmm php-mode.el | planner py-cssutils speex speex-devel uif2iso -------------------------+------------------------------------------------- [wiki:MacPortsDevelopers Macports committer] billitch has not been seen in [search:billitch@macports.org over 6 years] and has [query:owner=billitch@macports.org&status=assigned&status=new&status=reopened many open tickets]. -- Ticket URL: <https://trac.macports.org/ticket/51782> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51064: gtkglextmm port broken on OS X 10.11.4
by MacPorts 09 Aug '16

09 Aug '16

#51064: gtkglextmm port broken on OS X 10.11.4 --------------------------+-------------------------------- Reporter: sxpilot250@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: --------------------------+-------------------------------- Error: org.macports.build for port gtkglextmm returned: command execution failed Please see the log file for port gtkglextmm for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_devel_gtkglextmm/gtkglextmm/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port gtkglextmm failed -- Ticket URL: <https://trac.macports.org/ticket/51064> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51035: Error: Processing of port gtkglextmm failed
by MacPorts 09 Aug '16

09 Aug '16

#51035: Error: Processing of port gtkglextmm failed ----------------------+-------------------------------- Reporter: nay.oo@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: ----------------------+-------------------------------- Mac OS X El Capitan (Version 10.11.1) Port Version 2.3.4 Error: org.macports.build for port gtkglextmm returned: command execution failed -- Ticket URL: <https://trac.macports.org/ticket/51035> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51025: Metis won't build with Xcode 7.3
by MacPorts 09 Aug '16

09 Aug '16

#51025: Metis won't build with Xcode 7.3 ---------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: ---------------------+-------------------------------- Metis will not install from source with Xcode 7.3. It did build with Xcode 7.2.1 and it installs fine as a binary. I have attached a log file. The following two links suggest that it is actually a compiler bug in LLVM, but I don't know if they are correct or not: [https://github.com/Homebrew/homebrew-science/issues/3461] [https://llvm.org/bugs/show_bug.cgi?id=27059] [https://groups.google.com/forum/#!topic/spack/D9qt4BDv5yI] -- Ticket URL: <https://trac.macports.org/ticket/51025> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51592: xorg-libxcb: python clean-up
by MacPorts 09 Aug '16

09 Aug '16

#51592: xorg-libxcb: python clean-up -------------------------+------------------------- Reporter: mf2k@… | Owner: jeremyhu@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: xorg-libxcb -------------------------+------------------------- Like #51583, please clean-up and update the python variants in xorg-libxcb to add python35 and remove python25, python26, python31, python32 and python33. -- Ticket URL: <https://trac.macports.org/ticket/51592> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #51090: slepc @3.6.2_0 +arpack +mpich configure failure
by MacPorts 08 Aug '16

08 Aug '16

#51090: slepc @3.6.2_0 +arpack +mpich configure failure ------------------------+-------------------------------- Reporter: aeronova@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: slepc ------------------------+-------------------------------- Dear all, I've got the following configuration error when I tried to build slepc 3.6.2 w/ +arpack +mpich: {{{ ---> Configuring slepc Error: org.macports.configure for port slepc returned: configure failure: command execution failed Please see the log file for port slepc for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_slepc/slepc/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets }}} In the main.log file, the error has something to do with petsc: {{{ :info:configure ERROR: Unable to link with PETSc :info:configure ERROR: See "installed-arch- macports/lib/slepc/conf/configure.log" file for details :info:configure Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_slepc/slepc/work/v3.6.2" && ./configure --prefix=/opt/local --prefix=/opt/local/lib/slepc --with- arpack-dir=/opt/local --with-arpack-flags=-lparpack,-larpack :info:configure Exit code: 1 }}} In the configure.log file, I found that there are undefined symbols: {{{ Undefined symbols for architecture x86_64: "_get_rn_dbl_simple_mpi", referenced from: import-atom in libpetsc.dylib "_init_rng_simple_mpi", referenced from: import-atom in libpetsc.dylib ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) makefile:2: recipe for target 'checklink' failed gmake: *** [checklink] Error 1 ERROR: Unable to link with PETSc }}} I'd appreciate it if someone can help me fix this link error. FYI, the active port of petsc is the following: {{{ petsc @3.6.3_2+accelerate+debug+hdf5+hwloc+hypre+ml+mpich+mumps+netcdf+parmetis+sprng+suitesparse+sundials+yaml (active) }}} -- Ticket URL: <https://trac.macports.org/ticket/51090> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #47036: jython installation hardcodes JAVA_HOME such that jython will fail if a user upgrades the Java installation
by MacPorts 08 Aug '16

08 Aug '16

#47036: jython installation hardcodes JAVA_HOME such that jython will fail if a user upgrades the Java installation ---------------------+-------------------------------- Reporter: mtb19@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: jython ---------------------+-------------------------------- = To reproduce = * install an older version of Java (e.g., jdk1.7.0_67) * install jython * upgrade Java (e.g., to jdk1.7.0_75) * remove the older Java version * run `jython` * run `JAVA_HOME="$( /usr/libexec/java_home -v 1.7 )" jython` = Expected = Both `jython` and `JAVA_HOME="$( /usr/libexec/java_home -v 1.7 )" jython` should work. = Actual = Both fail, complaining that (e.g.) `/Library/Java/JavaVirtualMachines/jdk1.7.0_67.jdk/Contents/Home/bin/java` doesn't exist. = Additional Detail = An inspection of `cat $( which jython )` reveals: {{{ ... # This file was generated by the Jython installer # Created on ... JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.7.0_67.jdk/Contents/Home/jre" ... }}} These lines are not present in the [https://svn.code.sf.net/p/jython/svn/tags/Release_2_5_2/jython/src/shell/jy… original source file]. Setting `JAVA_HOME` in this manner: * a) may not be correct for very long; and * b) permanently overrides any external setting This leaves the user with hand-editing `$( which jython )` or reinstalling jython after every Java upgrade to get it to work, neither of which is ideal. -- Ticket URL: <https://trac.macports.org/ticket/47036> MacPorts <https://www.macports.org/> Ports system for OS X

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