Opened 5 years ago

Last modified 3 years ago

#34990 new defect

shogun: Undefined symbols: _drot_ _dswap_ __gfortran_concat_string _dgemm_ etc.

Reported by: noelia@… Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 2.1.1
Keywords: snowleopard Cc: ryandesign (Ryan Schmidt), trandu@…, kyunghee.kim@…, denis.peruzzo@…
Port: shogun

Description

The version of shogun on macports (0.9.3) came out before swig version 2.x.x. The source of the error is that configure does not check for the first digit in the version.

REQUEST: Update the shogun port to the current release

Attachments (1)

main.log (339.1 KB) - added by noelia@… 5 years ago.

Download all attachments as: .zip

Change History (15)

comment:1 Changed 5 years ago by noelia@…

  • Cc noelia@… added

Cc Me!

comment:2 Changed 5 years ago by ryandesign (Ryan Schmidt)

  • Cc ryandesign@… added; noelia@… removed
  • Keywords shogun removed
  • Owner changed from macports-tickets@… to jameskyle@…
  • Priority changed from High to Normal
  • Type changed from request to defect

The version of shogun on macports (0.9.3) came out before swig version 2.x.x. The source of the error is that configure does not check for the first digit in the version.

I'm unable to reproduce this problem. According to #25429 we already fixed this two years ago in r69300. Please "sudo port selfupdate", "sudo port clean shogun", and try again. If it still fails, attach the main.log file to this ticket.

REQUEST: Update the shogun port to the current release

This has already been requested in #33205.

Changed 5 years ago by noelia@…

comment:3 Changed 5 years ago by noelia@…

It still fails. I've attached the log file.

Thanks!

comment:4 Changed 5 years ago by ryandesign (Ryan Schmidt)

  • Summary changed from SHOGUN installation: Error: swig too old version 1.3.36 or later required to shogun: Undefined symbols: _drot_ _dswap_ __gfortran_concat_string _dgemm_ etc.

Ok, so the relevant error in the log seems to be:

:info:build Undefined symbols for architecture x86_64:
:info:build   "_drot_", referenced from:
:info:build       _dbdsqr_ in liblapack.a(dbdsqr.o)
:info:build   "_dswap_", referenced from:
:info:build       _dbdsqr_ in liblapack.a(dbdsqr.o)
:info:build       _dsteqr_ in liblapack.a(dsteqr.o)
:info:build      (maybe you meant: _ATL_dswap_xp0yp0aXbX)
:info:build   "__gfortran_concat_string", referenced from:
:info:build       _dgesvd_ in liblapack.a(dgesvd.o)
:info:build       _dormbr_ in liblapack.a(dormbr.o)
:info:build       _dormqr_ in liblapack.a(dormqr.o)
:info:build       _dormlq_ in liblapack.a(dormlq.o)
:info:build   "_dgemm_", referenced from:
:info:build       _dgesvd_ in liblapack.a(dgesvd.o)
:info:build       _dgebrd_ in liblapack.a(dgebrd.o)
:info:build   "_dgemv_", referenced from:
:info:build       _dlabrd_ in liblapack.a(dlabrd.o)
:info:build       _dlatrd_ in liblapack.a(dlatrd.o)
:info:build       _dlarf_ in liblapack.a(dlarf.o)
:info:build   "_dger_", referenced from:
:info:build       _dlarf_ in liblapack.a(dlarf.o)
:info:build      (maybe you meant: _ATL_dger_L1, _ATL_dger_L2 , _ATL_dger_OOC )
:info:build   "_dnrm2_", referenced from:
:info:build       _dlarfg_ in liblapack.a(dlarfg.o)
:info:build      (maybe you meant: _ATL_dnrm2_xp1yp0aXbX, _ATL_dnrm2_xp0yp0aXbX )
:info:build   "_dcopy_", referenced from:
:info:build       _dlasq1_ in liblapack.a(dlasq1.o)
:info:build      (maybe you meant: _ATL_dcopy_xp1yp1aXbX, _ATL_dcopy_xp0yp0aXbX )
:info:build   "_dsymv_", referenced from:
:info:build       _dlatrd_ in liblapack.a(dlatrd.o)
:info:build       _dsytd2_ in liblapack.a(dsytd2.o)
:info:build   "_ddot_", referenced from:
:info:build       _dlatrd_ in liblapack.a(dlatrd.o)
:info:build       _dsytd2_ in liblapack.a(dsytd2.o)
:info:build      (maybe you meant: _ATL_ddot_xp1yp1aXbX, _ATL_ddot_xp0yp0aXbX )
:info:build   "_daxpy_", referenced from:
:info:build       _dlatrd_ in liblapack.a(dlatrd.o)
:info:build       _dsytd2_ in liblapack.a(dsytd2.o)
:info:build      (maybe you meant: _ATL_daxpy_xp1yp1aXbX, _ATL_daxpy_xp0yp0aXbX )
:info:build   "_lsame_", referenced from:
:info:build       _dsyev_ in liblapack.a(dsyev.o)
:info:build       _dgesvd_ in liblapack.a(dgesvd.o)
:info:build       _dorgbr_ in liblapack.a(dorgbr.o)
:info:build       _dlange_ in liblapack.a(dlange.o)
:info:build       _dlaset_ in liblapack.a(dlaset.o)
:info:build       _dbdsqr_ in liblapack.a(dbdsqr.o)
:info:build       _dlacpy_ in liblapack.a(dlacpy.o)
:info:build       ...
:info:build   "_xerbla_", referenced from:
:info:build       _dsyev_ in liblapack.a(dsyev.o)
:info:build       _dgesvd_ in liblapack.a(dgesvd.o)
:info:build       _dgeqrf_ in liblapack.a(dgeqrf.o)
:info:build       _dorgqr_ in liblapack.a(dorgqr.o)
:info:build       _dgebrd_ in liblapack.a(dgebrd.o)
:info:build       _dorgbr_ in liblapack.a(dorgbr.o)
:info:build       _dgelqf_ in liblapack.a(dgelqf.o)
:info:build       ...
:info:build   "_dscal_", referenced from:
:info:build       _dsyev_ in liblapack.a(dsyev.o)
:info:build       _dbdsqr_ in liblapack.a(dbdsqr.o)
:info:build       _dlabrd_ in liblapack.a(dlabrd.o)
:info:build       _dorgl2_ in liblapack.a(dorgl2.o)
:info:build       _dorg2r_ in liblapack.a(dorg2r.o)
:info:build       _dlatrd_ in liblapack.a(dlatrd.o)
:info:build       _dlarfg_ in liblapack.a(dlarfg.o)
:info:build       ...
:info:build      (maybe you meant: _ATL_dscal_xp1yp0aXbX, _ATL_dscal_xp0yp0aXbX )
:info:build   "_dsyr2_", referenced from:
:info:build       _dsytd2_ in liblapack.a(dsytd2.o)
:info:build   "_dsyr2k_", referenced from:
:info:build       _dsytrd_ in liblapack.a(dsytrd.o)
:info:build   "__gfortran_compare_string", referenced from:
:info:build       _ilaenv_ in liblapack.a(ilaenv.o)
:info:build ld: symbol(s) not found for architecture x86_64

comment:5 Changed 5 years ago by noelia@…

Great! So what do I do about it?

comment:6 follow-up: Changed 5 years ago by ryandesign (Ryan Schmidt)

  • Cc trandu@… added

Has duplicate #35238.

comment:7 in reply to: ↑ 6 ; follow-up: Changed 5 years ago by kyunghee.kim@…

I am trying to install shogun now and have the same problem. Does anyone know how this problem has been fixed?

Error: Processing of port py26-pymvpa failed 
macports.org_release_ports_math_shogun/shogun/main.logar_macports_sources_rsync.m 

:info:build Undefined symbols for architecture x86_64:
:info:build   "_drot_", referenced from:
:info:build       _dbdsqr_ in liblapack.a(dbdsqr.o)
:info:build   "_dswap_", referenced from:
:info:build       _dbdsqr_ in liblapack.a(dbdsqr.o)
:info:build       _dsteqr_ in liblapack.a(dsteqr.o)
:info:build      (maybe you meant: _ATL_dswap_xp0yp0aXbX)
:info:build   "__gfortran_concat_string", referenced from:
:info:build       _dgesvd_ in liblapack.a(dgesvd.o)
:info:build       _dormbr_ in liblapack.a(dormbr.o)
:info:build       _dormqr_ in liblapack.a(dormqr.o)
:info:build       _dormlq_ in liblapack.a(dormlq.o)
:info:build   "_dgemm_", referenced from:  
:info:build       _dgesvd_ in liblapack.a(dgesvd.o)
:info:build       _dgebrd_ in liblapack.a(dgebrd.o)
:info:build   "_dgemv_", referenced from:
:info:build       _dlabrd_ in liblapack.a(dlabrd.o)
:info:build       _dlatrd_ in liblapack.a(dlatrd.o)
:info:build       _dlarf_ in liblapack.a(dlarf.o)
:info:build   "_dger_", referenced from:
:info:build       _dlarf_ in liblapack.a(dlarf.o)
:info:build      (maybe you meant: _ATL_dger_L1, _ATL_dger_L2 , _ATL_dger_OOC )
:info:build   "_dnrm2_", referenced from:
:info:build       _dlarfg_ in liblapack.a(dlarfg.o)
:info:build      (maybe you meant: _ATL_dnrm2_xp1yp0aXbX, _ATL_dnrm2_xp0yp0aXbX )
:info:build   "_dcopy_", referenced from:
:info:build       _dlasq1_ in liblapack.a(dlasq1.o)
:info:build      (maybe you meant: _ATL_dcopy_xp1yp1aXbX, _ATL_dcopy_xp0yp0aXbX )

Replying to ryandesign@…:

Has duplicate #35238.

Last edited 5 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:8 in reply to: ↑ 7 Changed 5 years ago by ryandesign (Ryan Schmidt)

  • Cc kyunghee.kim@… added

Replying to kyunghee.kim@…:

I am trying to install shogun now and have the same problem. Does anyone know how this problem has been fixed?

As you have seen, it has not been fixed; that is why this ticket is still open.

comment:9 Changed 5 years ago by ryandesign (Ryan Schmidt)

Has duplicate #38032.

comment:10 Changed 5 years ago by ryandesign (Ryan Schmidt)

Please check if this is still a problem with shogun 2.1.0.

comment:11 Changed 5 years ago by ryandesign (Ryan Schmidt)

According to the snowleopard buildbot, it's still a problem there. The lion and mountainlion buildbots had no problem.

comment:12 Changed 4 years ago by ryandesign (Ryan Schmidt)

  • Cc denis.peruzzo@… added

Has duplicates #39716, #40032.

comment:13 Changed 4 years ago by ryandesign (Ryan Schmidt)

  • Keywords snowleopard added

comment:14 Changed 3 years ago by mf2k (Frank Schima)

  • Owner changed from jameskyle@… to macports-tickets@…

jameskyle has retired. See #44641.

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