Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#36445 closed defect (fixed)

atlas @3.10.0+universal fails to install after apparently compiling

Reported by: jsalort (Julien Salort) Owned by: Veence (Vincent)
Priority: Normal Milestone:
Component: ports Version: 2.1.2
Keywords: Cc:
Port: atlas

Description (last modified by mf2k (Frank Schima))

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...

Attachments (2)

main.log (3.6 MB) - added by jsalort (Julien Salort) 12 years ago.
main.2.log (6.6 MB) - added by jsalort (Julien Salort) 12 years ago.
Log for i386 only

Change History (12)

Changed 12 years ago by jsalort (Julien Salort)

Attachment: main.log added

comment:1 Changed 12 years ago by jsalort (Julien Salort)

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.

Changed 12 years ago by jsalort (Julien Salort)

Attachment: main.2.log added

Log for i386 only

comment:2 Changed 12 years ago by Veence (Vincent)

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.

Last edited 12 years ago by Veence (Vincent) (previous) (diff)

comment:3 in reply to:  2 Changed 12 years ago by jsalort (Julien Salort)

Replying to 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...

comment:4 Changed 12 years ago by Veence (Vincent)

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.

comment:5 Changed 12 years ago by mf2k (Frank Schima)

Description: modified (diff)
Owner: changed from macports-tickets@… to vince@…
Port: atlas added

In the future, please use WikiFormatting, fill in the Port field and Cc the port maintainer(s).

comment:6 Changed 12 years ago by Veence (Vincent)

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.

comment:7 Changed 12 years ago by Veence (Vincent)

Should be fixed in r98544. Try again and tell me.

comment:8 Changed 12 years ago by Veence (Vincent)

Resolution: fixed
Status: newclosed

No response. I close the bug, please reopen it if anything is still wrong.

comment:9 in reply to:  7 Changed 12 years ago by jsalort (Julien Salort)

Replying to 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.

comment:10 Changed 12 years ago by Veence (Vincent)

Good news. Thanks for giving a try.

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