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Message-Id: <201403041045.s24AjPFO042584@mech-cluster241.men.bris.ac.uk>
Date: Tue, 04 Mar 2014 02:45:27 -0800 (PST)
From: Anton Shterenlikht <mexas@bris.ac.uk>
Sender: Anton Shterenlikht <mexas@bristol.ac.uk>
Reply-To: Anton Shterenlikht <mexas@bris.ac.uk>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: science/hdf5-18: ia64 11-current: build failure: /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
X-Send-Pr-Version: 3.114
X-GNATS-Notify:

>Number:         187252
>Category:       ports
>Synopsis:       science/hdf5-18: ia64 11-current: build failure: /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
>Confidential:   no
>Severity:       serious
>Priority:       medium
>Responsible:    sunpoet
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          sw-bug
>Submitter-Id:   current-users
>Arrival-Date:   Tue Mar 04 10:50:00 UTC 2014
>Closed-Date:    Thu Mar 06 14:22:06 UTC 2014
>Last-Modified:  Fri Mar  7 17:40:01 UTC 2014
>Originator:     Anton Shterenlikht
>Release:        FreeBSD 11.0-CURRENT ia64
>Organization:
University of Bristol	
>Environment:
System: FreeBSD mech-cluster241.men.bris.ac.uk 11.0-CURRENT FreeBSD 11.0-CURRENT #11 r260914: Fri Feb 7 13:43:53 GMT 2014 root@mech-cluster241.men.bris.ac.uk:/usr/obj/usr/src/sys/TZAV ia64


	
>Description:

Building in a poudriere ia64 jail at r262690.
The ports tree is at r347001.

The error:

H5Ztrans.c:1539: warning: will never be executed
  CCLD     libhdf5.la
/usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
*** Error code 1

The full build log:

http://eis.bris.ac.uk/~mexas/logs/hdf5-18-1.8.10.log

	
>How-To-Repeat:
	
>Fix:

	


>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->sunpoet 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Tue Mar 4 10:50:09 UTC 2014 
Responsible-Changed-Why:  
Over to maintainer (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=187252 

From: Anton Shterenlikht <mexas@bris.ac.uk>
To: bug-followup@freebsd.org
Cc:  
Subject: ports/187252: science/hdf5-18: ia64 11-current: build failure: /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
Date: Thu, 06 Mar 2014 03:11:00 -0800 (PST)

 fixed in r347176:
 
 http://eis.bris.ac.uk/~mexas/logs/hdf5-18-1.8.10.log
 
 Please close this PR.
 
 Thanks
State-Changed-From-To: open->closed 
State-Changed-By: eadler 
State-Changed-When: Thu Mar 6 14:22:05 UTC 2014 
State-Changed-Why:  
Per submitter request 

http://www.freebsd.org/cgi/query-pr.cgi?pr=187252 

From: Tijl Coosemans <tijl@FreeBSD.org>
To: bug-followup@FreeBSD.org, mexas@bris.ac.uk
Cc:  
Subject: Re: ports/187252: science/hdf5-18: ia64 11-current: build failure:
 /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong
 format
Date: Thu, 6 Mar 2014 18:36:16 +0100

 Hi Anton,
 
 Can you test this port with the FORTRAN option enabled.  I suspect this
 is still a valid PR.

From: Anton Shterenlikht <mexas@bris.ac.uk>
To: bug-followup@FreeBSD.org, mexas@bris.ac.uk, tijl@FreeBSD.org
Cc:  
Subject: Re: ports/187252: science/hdf5-18: ia64 11-current: build failure: /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
Date: Fri, 07 Mar 2014 03:21:45 -0800 (PST)

 >From tijl@freebsd.org Thu Mar  6 18:15:44 2014
 >
 >Hi Anton,
 >
 >Can you test this port with the FORTRAN option enabled.  I suspect this
 >is still a valid PR.
 >
 
 Tijl,
 
 You are right:
 
 LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-rpath=/usr/local/lib/gcc46  -L/usr/local/lib/gcc46 -B/ur/local/bin |                   sed -e 's/-L/:/g' -e 's/ //g'`"                                 ./Hdetect > H5Tinit.c  ||                                (test $HDF5_Make_Ignore && echo "*** Error igored") ||           (rm -f H5Tinit.c ; exit 1)
 --- H5lib_settings.c ---
 LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-rpath=/usr/local/lib/gcc46  -L/usr/local/lib/gcc46 -B/ur/local/bin |                   sed -e 's/-L/:/g' -e 's/ //g'`"                                 ./Hmake_libsettings > H5lib_settings.c  ||                                (test $HDF5_Make_Ignore && eho "*** Error ignored") ||           (rm -f H5lib_settings.c ; exit 1)
 --- H5Tinit.lo ---
   CC       H5Tinit.lo
 H5Tinit.c: In function 'H5TN_init_interface':
 H5Tinit.c:958: warning: will never be executed
 --- H5lib_settings.lo ---
   CC       H5lib_settings.lo
 --- libhdf5.la ---
   CCLD     libhdf5.la
 /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
 *** [libhdf5.la] Error code 1
 
 make[4]: stopped in /usr/ports/science/hdf5-18/work/hdf5-1.8.10-patch1/src
 1 error
 
 Also, you fixed math/fftw in r347124,
 and closed my PR on it,
 but I still get the same error,
 with ports tree at 347176:
 
 /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
 
 http://eis.bris.ac.uk/~mexas/logs/fftw-2.1.5_8.log
 
 Shall I reopen the fftw PR?
 
 Finally, note a very similar error in french/med:
 
 /usr/local/lib/gcc46/libgfortran.so: could not read symbols: File in wrong format
 
 http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/187345
 
 Many thanks
 
 Anton

From: Tijl Coosemans <tijl@FreeBSD.org>
To: mexas@bris.ac.uk
Cc: bug-followup@FreeBSD.org
Subject: Re: ports/187252: science/hdf5-18: ia64 11-current: build failure:
 /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong
 format
Date: Fri, 7 Mar 2014 18:39:30 +0100

 On Fri, 07 Mar 2014 03:21:45 -0800 (PST) Anton Shterenlikht wrote:
 > >From tijl@freebsd.org Thu Mar  6 18:15:44 2014
 > >
 > >Hi Anton,
 > >
 > >Can you test this port with the FORTRAN option enabled.  I suspect this
 > >is still a valid PR.
 > >
 > 
 > Tijl,
 > 
 > You are right:
 > 
 > LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-rpath=/usr/local/lib/gcc46  -L/usr/local/lib/gcc46 -B/ur/local/bin |                   sed -e 's/-L/:/g' -e 's/ //g'`"                                 ./Hdetect > H5Tinit.c  ||                                (test $HDF5_Make_Ignore && echo "*** Error igored") ||           (rm -f H5Tinit.c ; exit 1)
 > --- H5lib_settings.c ---
 > LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-rpath=/usr/local/lib/gcc46  -L/usr/local/lib/gcc46 -B/ur/local/bin |                   sed -e 's/-L/:/g' -e 's/ //g'`"                                 ./Hmake_libsettings > H5lib_settings.c  ||                                (test $HDF5_Make_Ignore && eho "*** Error ignored") ||           (rm -f H5lib_settings.c ; exit 1)
 > --- H5Tinit.lo ---
 >   CC       H5Tinit.lo
 > H5Tinit.c: In function 'H5TN_init_interface':
 > H5Tinit.c:958: warning: will never be executed
 > --- H5lib_settings.lo ---
 >   CC       H5lib_settings.lo
 > --- libhdf5.la ---
 >   CCLD     libhdf5.la
 > /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
 > *** [libhdf5.la] Error code 1
 > 
 > make[4]: stopped in /usr/ports/science/hdf5-18/work/hdf5-1.8.10-patch1/src
 > 1 error
 
 This should work now as of r347410.
 
 > Also, you fixed math/fftw in r347124,
 > and closed my PR on it,
 > but I still get the same error,
 > with ports tree at 347176:
 > 
 > /usr/local/lib/gcc46/libgcc_s.so: could not read symbols: File in wrong format
 > 
 > http://eis.bris.ac.uk/~mexas/logs/fftw-2.1.5_8.log
 > 
 > Shall I reopen the fftw PR?
 
 I committed a fix, so now it should really work.
 
 > Finally, note a very similar error in french/med:
 > 
 > /usr/local/lib/gcc46/libgfortran.so: could not read symbols: File in wrong format
 > 
 > http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/187345
 
 Still have to look into this.

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/187252: commit references a PR
Date: Fri,  7 Mar 2014 17:36:13 +0000 (UTC)

 Author: tijl
 Date: Fri Mar  7 17:36:05 2014
 New Revision: 347410
 URL: http://svnweb.freebsd.org/changeset/ports/347410
 QAT: https://qat.redports.org/buildarchive/r347410/
 
 Log:
   Add USES=libtool to fix a linker problem when the FORTRAN option is enabled
   on versions of FreeBSD where the base system binutils is too old to link
   object files generated by lang/gcc (gfortran).
   
   PR:		ports/187252
 
 Modified:
   head/science/hdf5-18/Makefile
   head/science/hdf5-18/pkg-plist
 
 Modified: head/science/hdf5-18/Makefile
 ==============================================================================
 --- head/science/hdf5-18/Makefile	Fri Mar  7 17:29:28 2014	(r347409)
 +++ head/science/hdf5-18/Makefile	Fri Mar  7 17:36:05 2014	(r347410)
 @@ -3,6 +3,7 @@
  
  PORTNAME=	hdf5
  PORTVERSION=	1.8.10
 +PORTREVISION=	1
  CATEGORIES=	science archivers graphics
  MASTER_SITES=	http://www.hdfgroup.org/ftp/HDF5/current/src/ \
  		ftp://ftp.hdfgroup.org/HDF5/current/src/ \
 @@ -18,6 +19,7 @@ OPTIONS_DEFINE=	DEBUG EXAMPLES FORTRAN S
  
  CONFLICTS_INSTALL=	hdf-4.[0-9]* hdf5-1.6.[0-9]*
  
 +USES=		libtool
  USE_BZIP2=	yes
  USE_LDCONFIG=	yes
  GNU_CONFIGURE=	yes
 
 Modified: head/science/hdf5-18/pkg-plist
 ==============================================================================
 --- head/science/hdf5-18/pkg-plist	Fri Mar  7 17:29:28 2014	(r347409)
 +++ head/science/hdf5-18/pkg-plist	Fri Mar  7 17:36:05 2014	(r347410)
 @@ -126,26 +126,32 @@ lib/libhdf5.la
  lib/libhdf5.settings
  lib/libhdf5.so
  lib/libhdf5.so.7
 +lib/libhdf5.so.7.0.4
  lib/libhdf5_cpp.a
  lib/libhdf5_cpp.la
  lib/libhdf5_cpp.so
  lib/libhdf5_cpp.so.7
 +lib/libhdf5_cpp.so.7.0.4
  %%FORTRAN%%lib/libhdf5_fortran.a
  %%FORTRAN%%lib/libhdf5_fortran.la
  %%FORTRAN%%lib/libhdf5_fortran.so
  %%FORTRAN%%lib/libhdf5_fortran.so.7
 +%%FORTRAN%%lib/libhdf5_fortran.so.7.0.4
  lib/libhdf5_hl.a
  lib/libhdf5_hl.la
  lib/libhdf5_hl.so
  lib/libhdf5_hl.so.7
 +lib/libhdf5_hl.so.7.0.4
  lib/libhdf5_hl_cpp.a
  lib/libhdf5_hl_cpp.la
  lib/libhdf5_hl_cpp.so
  lib/libhdf5_hl_cpp.so.7
 +lib/libhdf5_hl_cpp.so.7.0.4
  %%FORTRAN%%lib/libhdf5hl_fortran.a
  %%FORTRAN%%lib/libhdf5hl_fortran.la
  %%FORTRAN%%lib/libhdf5hl_fortran.so
  %%FORTRAN%%lib/libhdf5hl_fortran.so.7
 +%%FORTRAN%%lib/libhdf5hl_fortran.so.7.0.4
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/chunks.cpp
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/compound.cpp
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>Unformatted:
