[MacPorts] #36445: atlas @3.10.0+universal fails to install after apparently compiling
#36445: atlas @3.10.0+universal fails to install after apparently compiling ---------------------+-------------------------------- Reporter: lists@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Keywords: | Port: ---------------------+-------------------------------- Installing atlas for x86_64 worked. However, I want a universal version. So I did: % sudo port install atlas +universal Password: ---> Computing dependencies for atlas ---> Fetching archive for atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://packages.macports.org/atlas ---> Fetching distfiles for atlas Warning: GCC compilers on OS X do not support AVX instructions. ---> Verifying checksum(s) for atlas ---> Extracting atlas ---> Applying patches to atlas ---> Configuring atlas ---> Building atlas Error: reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory Error: org.macports.build for port atlas returned: reinplace sed(1) failed Please see the log file for port atlas for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_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 The log file says: :info:build ATLAS install complete. Examine :info:build ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details. :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build /usr/bin/make clean :info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build rm -rf *.dSYM :info:build rm -rf *.o x* config?.out *core* :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :debug:build Executing proc-post-org.macports.build-build-0 :debug:build Executing reinplace: /usr/bin/sed {s|^LIBTOOL=.*$|LIBTOOL=$(GCC) $(GCCFLAGS)|} < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile
@ file10 :debug:build couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory while executing "exec /usr/bin/sed {s|^LIBTOOL=.*$|LIBTOOL=$(GCC) $(GCCFLAGS)|} < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_rele..." ("eval" body line 1) invoked from within "eval exec $cmdline" :error:build reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory :error:build org.macports.build for port atlas returned: reinplace sed(1) failed :debug:build Error code: NONE :debug:build Backtrace: reinplace sed(1) failed
(full log file attached) So it seems that the actual compilation went fine... -- Ticket URL: <https://trac.macports.org/ticket/36445> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+-------------------------------- Reporter: lists@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: | ----------------------+-------------------------------- Comment (by lists@…): Additionnally, if I build for i386 only, I get another error, in relation with gfortran: {{{ :info:build cd RCW_tMp ; /opt/local/bin/gcc-mp-4.5 -fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2 -msse3 -fPIC -m32 -fPIC -dynamiclib -o ../libsatlas.dylib \ :info:build -install_name /opt/local/lib/libsatlas.dylib -current_version 3.10.0 \ :info:build -compatibility_version 3.10.0 *.o -lpthread -lm /opt/local/lib/gcc45/libgfortran.dylib :info:build ld: warning: ignoring file /opt/local/lib/gcc45/libgfortran.dylib, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 6 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): /opt/local/lib/gcc45/libgfortran.dylib :info:build Undefined symbols for architecture i386: :info:build "__gfortran_compare_string", referenced from: :info:build _ilaenv_ in ilaenv.o :info:build "__gfortran_concat_string", referenced from: :info:build _cgesvd_ in cgesvd.o :info:build _chseqr_ in chseqr.o :info:build _cunmbr_ in cunmbr.o :info:build _cunmhr_ in cunmhr.o :info:build _cunmlq_ in cunmlq.o :info:build _cunmql_ in cunmql.o :info:build _cunmqr_ in cunmqr.o :info:build ... :info:build "__gfortran_pow_i4_i4", referenced from: :info:build _claed0_ in claed0.o :info:build _claed7_ in claed7.o :info:build _clalsa_ in clalsa.o :info:build _cstedc_ in cstedc.o :info:build _dlaed0_ in dlaed0.o :info:build _dlaed7_ in dlaed7.o :info:build _dlaeda_ in dlaeda.o :info:build ... :info:build "__gfortran_st_write", referenced from: :info:build _xerbla_ in xerbla.o :info:build "__gfortran_st_write_done", referenced from: :info:build _xerbla_ in xerbla.o :info:build "__gfortran_stop_numeric", referenced from: :info:build _xerbla_ in xerbla.o :info:build "__gfortran_transfer_character", referenced from: :info:build _xerbla_ in xerbla.o :info:build "__gfortran_transfer_integer", referenced from: :info:build _xerbla_ in xerbla.o :info:build ld: symbol(s) not found for architecture i386 :info:build collect2: ld returned 1 exit status :info:build make[1]: *** [dylib] Error 1 :info:build make: *** [shared_all] Error 2 }}} Full log attached. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+-------------------------------- Reporter: lists@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: | ----------------------+-------------------------------- Comment (by vince@…): Your gcc has not been compiled with the universal flag set, which triggers the multilib option. In other word, your gfortran library is x86_64 only, wherefore you cannot build an i386 version. You must rebuild gcc. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+-------------------------------- Reporter: lists@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: | ----------------------+-------------------------------- Comment (by lists@…): Replying to [comment:2 vince@…]:
Your gcc has not been compiled with the universal flag set, which triggers the multilib option. In other words, your gfortran library is x86_64 only, wherefore you cannot build an i386 version. You must rebuild gcc.
I have compiled gcc45 with the universal variant: {{{ port installed gcc* The following ports are currently installed: gcc45 @4.5.4_6+universal (active) gcc47 @4.7.2_1+universal (active) gcc_select @0.1_7 (active) gccmakedep @1.0.2_3 (active) }}} And I have this: {{{ ls /opt/local/lib/gcc45/i386/*gfortran* /opt/local/lib/gcc45/i386/libgfortran.3.dylib /opt/local/lib/gcc45/i386/libgfortran.a /opt/local/lib/gcc45/i386/libgfortran.dylib /opt/local/lib/gcc45/i386/libgfortran.la }}} Therefore, I don't think this is the answer... -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+-------------------------------- Reporter: lists@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: | ----------------------+-------------------------------- Comment (by vince@…): Hmmm… Pretty weird. There was some patch committed recently by someone else, I have to find out if this issue does not proceed from this. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+--------------------- Reporter: lists@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: atlas | ----------------------+--------------------- Changes (by macsforever2000@…): * owner: macports-tickets@… => vince@… * port: => atlas Old description:
Installing atlas for x86_64 worked. However, I want a universal version. So I did: % sudo port install atlas +universal Password: ---> Computing dependencies for atlas ---> Fetching archive for atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://packages.macports.org/atlas ---> Fetching distfiles for atlas Warning: GCC compilers on OS X do not support AVX instructions. ---> Verifying checksum(s) for atlas ---> Extracting atlas ---> Applying patches to atlas ---> Configuring atlas ---> Building atlas Error: reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory Error: org.macports.build for port atlas returned: reinplace sed(1) failed Please see the log file for port atlas for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_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
The log file says:
:info:build ATLAS install complete. Examine :info:build ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details. :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build /usr/bin/make clean :info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build rm -rf *.dSYM :info:build rm -rf *.o x* config?.out *core* :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :debug:build Executing proc-post-org.macports.build-build-0 :debug:build Executing reinplace: /usr/bin/sed {s|^LIBTOOL=.*$|LIBTOOL=$(GCC) $(GCCFLAGS)|} < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile
@ file10 :debug:build couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory while executing "exec /usr/bin/sed {s|^LIBTOOL=.*$|LIBTOOL=$(GCC) $(GCCFLAGS)|} < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_rele..." ("eval" body line 1) invoked from within "eval exec $cmdline" :error:build reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory :error:build org.macports.build for port atlas returned: reinplace sed(1) failed :debug:build Error code: NONE :debug:build Backtrace: reinplace sed(1) failed
(full log file attached)
So it seems that the actual compilation went fine...
New description: Installing atlas for x86_64 worked. However, I want a universal version. So I did: {{{ % sudo port install atlas +universal Password: ---> Computing dependencies for atlas ---> Fetching archive for atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/atlas ---> Attempting to fetch atlas-3.10.0_0+gcc45+universal.darwin_12.i386-x86_64.tbz2 from http://packages.macports.org/atlas ---> Fetching distfiles for atlas Warning: GCC compilers on OS X do not support AVX instructions. ---> Verifying checksum(s) for atlas ---> Extracting atlas ---> Applying patches to atlas ---> Configuring atlas ---> Building atlas Error: reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory Error: org.macports.build for port atlas returned: reinplace sed(1) failed Please see the log file for port atlas for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_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 }}} The log file says: {{{ :info:build ATLAS install complete. Examine :info:build ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details. :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build /usr/bin/make clean :info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build rm -rf *.dSYM :info:build rm -rf *.o x* config?.out *core* :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0-i386/build' :debug:build Executing proc-post-org.macports.build-build-0 :debug:build Executing reinplace: /usr/bin/sed {s|^LIBTOOL=.*$|LIBTOOL=$(GCC) $(GCCFLAGS)|} < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile
@ file10 :debug:build couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory while executing "exec /usr/bin/sed {s|^LIBTOOL=.*$|LIBTOOL=$(GCC) $(GCCFLAGS)|} < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_rele..." ("eval" body line 1) invoked from within "eval exec $cmdline" :error:build reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.0/build/lib/Makefile": no such file or directory :error:build org.macports.build for port atlas returned: reinplace sed(1) failed :debug:build Error code: NONE :debug:build Backtrace: reinplace sed(1) failed }}}
(full log file attached) So it seems that the actual compilation went fine... -- Comment: In the future, please use WikiFormatting, fill in the Port field and Cc the port maintainer(s). -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:5> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+--------------------- Reporter: lists@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: atlas | ----------------------+--------------------- Comment (by vince@…): It is definitely tied to the patch that was committed a while ago. I’m diving into it, but it takes more time than I expected: since I had no time to work on Macports during the last few weeks, I have to catch up and it takes a while. I hope to be able to get something neat tonight. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:6> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+--------------------- Reporter: lists@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: atlas | ----------------------+--------------------- Comment (by vince@…): Should be fixed in r98544. Try again and tell me. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:7> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+--------------------- Reporter: lists@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: fixed | Keywords: Port: atlas | ----------------------+--------------------- Changes (by vince@…): * status: new => closed * resolution: => fixed Comment: No response. I close the bug, please reopen it if anything is still wrong. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:8> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+--------------------- Reporter: lists@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: fixed | Keywords: Port: atlas | ----------------------+--------------------- Comment (by lists@…): Replying to [comment:7 vince@…]:
Should be fixed in r98544. Try again and tell me.
Sorry for the delay. I couldn't try before today. It seems fixed for me now. Thank you. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:9> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36445: atlas @3.10.0+universal fails to install after apparently compiling ----------------------+--------------------- Reporter: lists@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: fixed | Keywords: Port: atlas | ----------------------+--------------------- Comment (by vince@…): Good news. Thanks for giving a try. -- Ticket URL: <https://trac.macports.org/ticket/36445#comment:10> MacPorts <http://www.macports.org/> Ports system for Mac OS
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