[MacPorts] #47007: SuiteSparse @4.2.1_3 fails with undefined symbol
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol -------------------------+-------------------------------- Reporter: flatjunk1@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: SuiteSparse -------------------------+-------------------------------- Apparently same as ticket 45728, similar to ticket 39072 (SuiteSparse 4.1.0_0). Fixes proposed in latter did not work for me. Attempting to install octave (sudo port install octave +atlas+docs). Fails repeatedly despite cleaning SuiteSparse and updating ports. Occurred in Yosemite 10.10.1, and still in 10.10.2. Xcode 6.1.1. Logs and consoles attached. First attempt shown in console was to clean SuiteSparse then install octave. Second attempt follows directions per the "fix" of ticket 39072. Stymied. Solution MUCH appreciated. -- Ticket URL: <https://trac.macports.org/ticket/47007> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+-------------------------------- Reporter: flatjunk1@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+-------------------------------- Comment (by flatjunk1@…): Just realized the four attachments filenames may be confusing. They are in order and should be read as a)... b)... c)... d)... -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:1> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Changes (by ryandesign@…): * owner: macports-tickets@… => michaelld@… Old description:
Apparently same as ticket 45728, similar to ticket 39072 (SuiteSparse 4.1.0_0). Fixes proposed in latter did not work for me.
Attempting to install octave (sudo port install octave +atlas+docs). Fails repeatedly despite cleaning SuiteSparse and updating ports. Occurred in Yosemite 10.10.1, and still in 10.10.2. Xcode 6.1.1.
Logs and consoles attached. First attempt shown in console was to clean SuiteSparse then install octave. Second attempt follows directions per the "fix" of ticket 39072.
Stymied. Solution MUCH appreciated.
New description: Apparently same as ticket:45728, similar to ticket:39072 (SuiteSparse 4.1.0_0). Fixes proposed in latter did not work for me. Attempting to install octave (`sudo port install octave +atlas+docs`). Fails repeatedly despite cleaning SuiteSparse and updating ports. Occurred in Yosemite 10.10.1, and still in 10.10.2. Xcode 6.1.1. Logs and consoles attached. First attempt shown in console was to clean SuiteSparse then install octave. Second attempt follows directions per the "fix" of ticket:39072. Stymied. Solution MUCH appreciated. -- -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:2> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by sean@…): So, ATLAS seems to be throwing a wrench into this whole mess. I will need to recompile ATLAS ... which will probably take all night for me. If someone else can debug, that'd be great. -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:3> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by michaelld@…): Just out of curiosity, what do the following return: {{{ nm -a /opt/local/lib/libtatlas.dylib | grep dgemm lipo -info /opt/local/lib/libtatlas.dylib }}} -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:4> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by flatjunk1@…): Replying to [comment:4 michaelld@…]:
Just out of curiosity, what do the following return: {{{ nm -a /opt/local/lib/libtatlas.dylib | grep dgemm lipo -info /opt/local/lib/libtatlas.dylib }}}
Not sure what that's ''supposed'' to do, but no joy: {{{ kflaton% nm -a /opt/local/lib/libtatlas.dylib | grep dgemm nm: object: /opt/local/lib/libtatlas.dylib malformed object (unknown load command 9) }}} and {{{ kflaton% lipo -info /opt/local/lib/libtatlas.dylib Non-fat file: /opt/local/lib/libtatlas.dylib is architecture: x86_64 }}} -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:5> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by michaelld@…): OK; well that's the issue then: libtatlas is corrupt. So, let's go back a step & see if that issue can get fixed. What does "port installed atlas" return for you? -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:6> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by flatjunk1@…): Replying to [comment:6 michaelld@…]:
OK; well that's the issue then: libtatlas is corrupt. So, let's go back a step & see if that issue can get fixed. What does "port installed atlas" return for you?
I get: {{{ kflaton% port installed atlas The following ports are currently installed: atlas @3.10.2_1+clang+nofortran (active) }}} -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:7> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by flatjunk1@…): Replying to [comment:7 flatjunk1@…]:
Replying to [comment:6 michaelld@…]:
OK; well that's the issue then: libtatlas is corrupt. So, let's go back a step & see if that issue can get fixed. What does "port installed atlas" return for you?
I get: {{{ kflaton% port installed atlas The following ports are currently installed: atlas @3.10.2_1+clang+nofortran (active) }}}
FWIW, I did a clean install of MacPorts less than a week ago... -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:8> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by michaelld@…): So I'm thinking it's the +nofortran option that's the issue. Just a guess at this time without more testing / statistics. Can you do the following: {{{ sudo port clean suitesparse atlas octave sudo port selfupdate sudo port -f uninstall atlas @3.10.2_1+clang+nofortran sudo port install atlas sudo port install suitesparse +atlas }}} and see if that works. If so, then go forth with: {{{ sudo port install octave +atlas }}} and then if that works make sure octave executes as desired. -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:9> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by flatjunk1@…): Chokes on installing atlas: {{{ kflaton% sudo port install atlas ---> Fetching archive for atlas ---> Attempting to fetch atlas-3.10.2_1+clang.darwin_14.x86_64.tbz2 from http://packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.2_1+clang.darwin_14.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.2_1+clang.darwin_14.x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas ---> Fetching distfiles for atlas ---> Verifying checksums for atlas ---> Extracting atlas ---> Applying patches to atlas ---> Configuring atlas Selected C compiler: /usr/bin/clang Error: org.macports.configure for port atlas returned: Atlas could not detect any fortran compiler. If you really don’t need the fortran interface to be built, please use the +nofortran option, else install a fortran compiler (e.g. gcc4X) before building Atlas. Please see the log file for port atlas for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/atlas/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port atlas failed }}} and then again while installing SuiteSparse: {{{ kflaton% sudo port install suitesparse +atlas ---> Computing dependencies for SuiteSparse ---> Dependencies to be installed: atlas ---> Configuring atlas Selected C compiler: /usr/bin/clang Error: org.macports.configure for port atlas returned: Atlas could not detect any fortran compiler. If you really don’t need the fortran interface to be built, please use the +nofortran option, else install a fortran compiler (e.g. gcc4X) before building Atlas. Error: Failed to install atlas Please see the log file for port atlas for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/atlas/main.log Error: The following dependencies were not installed: atlas To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port suitesparse failed }}} (Thanks, btw.) -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:10> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by michaelld@…): Grr ... the atlas Portfile should handle this condition. How about: {{{ sudo port install gcc49 sudo port clean atlas suitesparse sudo port install atlas +gcc49 sudo port install suitesparse +atlas }}} and see if that works. -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:11> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by sean@…): Sigh, bitten again by the +nofortran variant. -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:12> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by michaelld@…): "again"? seems like this would be a good one to get fixed properly ;) -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:13> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by flatjunk1@…): Ok, that did it! Megathanks. You totally da man! -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:14> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by michaelld@…): On my system (OSX 10.8, Xcode 5.1.1), the +nofortran variant produces a library without the symbol "_dgemm_", so it won't work with suitesparse +atlas. I'm fixing suitesparse +atlas to check for +nofortran and bomb out when that happens so that we don't encounter this specific issue again (hopefully). -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:15> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: SuiteSparse | --------------------------+------------------------- Changes (by michaelld@…): * status: new => closed * resolution: => fixed Comment: Done in r133519. Thanks for bringing this to our attention! -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:16> MacPorts <https://www.macports.org/> Ports system for OS X
#47007: SuiteSparse @4.2.1_3 fails with undefined symbol --------------------------+------------------------- Reporter: flatjunk1@… | Owner: michaelld@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: SuiteSparse | --------------------------+------------------------- Comment (by sean@…): For future reference, by "again" I meant the ability to install atlas without a full lapack library (missing _dgemm_). Without removing the +nofortran variant or implement a 'lapack' port group, then each port that depends on atlas and needs a full lapack library needs to check for that variant. -- Ticket URL: <https://trac.macports.org/ticket/47007#comment:17> MacPorts <https://www.macports.org/> Ports system for OS X
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