Opened 12 years ago

Last modified 16 months 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 Carsten 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@… 12 years ago.

Download all attachments as: .zip

Change History (16)

comment:1 Changed 12 years ago by noelia@…

Cc: noelia@… added

Cc Me!

comment:2 Changed 12 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: ryandesign@… added; noelia@… removed
Keywords: shogun removed
Owner: changed from macports-tickets@… to jameskyle@…
Priority: High → Normal
Type: request → 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 12 years ago by noelia@…

Attachment: main.log​ added

comment:3 Changed 12 years ago by noelia@…

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

Thanks!

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

Summary: SHOGUN installation: Error: swig too old version 1.3.36 or later required → 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 12 years ago by noelia@…

Great! So what do I do about it?

comment:6 Changed 12 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: trandu@… added

Has duplicate #35238.

comment:7 in reply to:  6 ; Changed 11 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 11 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:8 in reply to:  7 Changed 11 years ago by ryandesign (Ryan Carsten 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 11 years ago by ryandesign (Ryan Carsten Schmidt)

Has duplicate #38032.

comment:10 Changed 11 years ago by ryandesign (Ryan Carsten Schmidt)

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

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

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

comment:12 Changed 11 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: denis.peruzzo@… added

Has duplicates #39716, #40032.

comment:13 Changed 11 years ago by ryandesign (Ryan Carsten Schmidt)

Keywords: snowleopard added

comment:14 Changed 10 years ago by mf2k (Frank Schima)

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

jameskyle has retired. See #44641.

comment:15 Changed 16 months ago by barracuda156

Got undefined _lsame_ error with another port on 10.6.8. Any solution to that so far?

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