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From: Roland Smith <rsmith@xs4all.nl>
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Subject: Updating numpy port to use blaslapack
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After some experimentation I found that openblas can be significantly faster
than atlas (at least on AMD64). Combined with the recent introduction of
/usr/ports/Mk/Uses/blaslapack.mk it seemed a good idea to update the numpy
port to enable the use of openblas or atlas or netlib.

A patch to do that is given below. When using openblas, it uses the parallel
version.  I've tested it with atlas and openblas on 10.1-STABLE AMD64.
Portlint gives no errors.

Before I submit a PR, I'd like to ask volunteers for testing on other
releases/architectures as well as testing with the default netlib BLAS/LAPA=
CK.

----- numpy updated to build with blaslapack -----
diff -ruN py-numpy.orig/Makefile py-numpy/Makefile
--- py-numpy.orig/Makefile	2015-01-02 17:36:43.000000000 +0100
+++ py-numpy/Makefile	2015-02-08 17:17:34.000000000 +0100
@@ -3,7 +3,7 @@
=20
 PORTNAME=3D	numpy
 PORTVERSION=3D	1.9.1
-PORTREVISION=3D	1
+PORTREVISION=3D	2
 PORTEPOCH=3D	1
 CATEGORIES=3D	math python
 MASTER_SITES=3D	http://docs.scipy.org/doc/${PORTNAME}/:doc \
@@ -15,7 +15,7 @@
 EXTRACT_ONLY=3D	numpy-${PORTVERSION:S/r/rc/}${EXTRACT_SUFX}
=20
 MAINTAINER=3D	python@FreeBSD.org
-COMMENT=3D	The New Numeric Extension to Python
+COMMENT=3D	New Numeric Extension to Python
=20
 LICENSE=3D	BSD3CLAUSE
=20
@@ -25,9 +25,13 @@
 USE_PYTHON=3D	concurrent distutils py3kplist
 LDFLAGS+=3D	-shared
=20
-OPTIONS_DEFINE=3D		ATLAS SUITESPARSE DOCS
-OPTIONS_DEFAULT=3D	SUITESPARSE
-ATLAS_DESC=3D		Use optimized blas library
+OPTIONS_DEFINE=3D		SUITESPARSE DOCS
+OPTIONS_DEFAULT=3D	SUITESPARSE CBLAS
+OPTIONS_SINGLE=3D		BLAS
+OPTIONS_SINGLE_BLAS=3D	CBLAS OPENBLAS ATLAS
+CBLAS_DESC=3D		Use math/cblas as BLAS library
+OPENBLAS_DESC=3D		Use math/openblas as (optimized) BLAS library
+ATLAS_DESC=3D		Use math/atlas as (optimized) BLAS library
 SUITESPARSE_DESC=3D	Use AMD and UMFPACK in SuiteSparse
=20
 PYDISTUTILS_CONFIGUREARGS+=3D	--fcompiler=3Dgnu95
@@ -36,9 +40,9 @@
 PORTDOCS=3D	*
 WRKSRC=3D		${WRKDIR}/${DISTNAME:S/r/rc/}
=20
-ATLAS_LIB_DEPENDS=3D	libatlas.so:${PORTSDIR}/math/atlas
-ATLAS_LIB_DEPENDS_OFF=3D	libblas.so:${PORTSDIR}/math/blas \
-			liblapack.so:${PORTSDIR}/math/lapack
+ATLAS_USES=3D	blaslapack:atlas
+OPENBLAS_USES=3D	blaslapack:openblas
+CBLAS_USES=3D	blaslapack
 SUITESPARSE_LIB_DEPENDS=3Dlibumfpack.so:${PORTSDIR}/math/suitesparse
=20
 .include <bsd.port.pre.mk>
@@ -50,21 +54,21 @@
=20
 post-patch:
 	${REINPLACE_CMD} -e "s+%%FC%%+${FC}+" ${WRKSRC}/numpy/distutils/fcompiler=
/gnu.py
-	${CP} ${FILESDIR}/site.cfg ${WRKSRC}/site.cfg
-
-GCCLIBDIR_CMDS=3D	${FC} -print-file-name=3Dlibgfortran.so|${SED} -e s/libg=
fortran.so//
-
-pre-configure:
 .if ${PORT_OPTIONS:MATLAS}
-	@${REINPLACE_CMD} -e "s+%%ATLASLIBS%%+alapack, f77blas, cblas, atlas+" ${=
WRKSRC}/site.cfg
+	${CP} ${FILESDIR}/site.cfg.atlas ${WRKSRC}/site.cfg
+.elif ${PORT_OPTIONS:MOPENBLAS}
+	${CP} ${FILESDIR}/site.cfg.openblas ${WRKSRC}/site.cfg
 .else
-	@${REINPLACE_CMD} -e "s+%%ATLASLIBS%%+lapack, blas+" ${WRKSRC}/site.cfg
+	${CP} ${FILESDIR}/site.cfg.cblas ${WRKSRC}/site.cfg
 .endif
+GCCLIBDIR_CMDS=3D	${FC} -print-file-name=3Dlibgfortran.so|${SED} -e s/libg=
fortran.so//
+
+pre-configure:
 .if !${PORT_OPTIONS:MSUITESPARSE}
 	@${REINPLACE_CMD} -e "s+:%%LOCALBASE%%/include/suitesparse++" ${WRKSRC}/s=
ite.cfg
 .endif
 	@${REINPLACE_CMD} -e "s+%%GCCLIBDIR%%+$$(${GCCLIBDIR_CMDS})+" \
-	    -e "s+%%LOCALBASE%%+${LOCALBASE}+g" \
+		-e "s+%%LOCALBASE%%+${LOCALBASE}+g" \
 		${WRKSRC}/site.cfg
 	@${REINPLACE_CMD} -e "s+%%GCCLIBDIR%%+$$(${GCCLIBDIR_CMDS})+" ${WRKSRC}/n=
umpy/distutils/system_info.py
=20
diff -ruN py-numpy.orig/files/site.cfg py-numpy/files/site.cfg
--- py-numpy.orig/files/site.cfg	2015-01-02 17:36:43.000000000 +0100
+++ py-numpy/files/site.cfg	1970-01-01 01:00:00.000000000 +0100
@@ -1,10 +0,0 @@
-[DEFAULT]
-lapack_type=3Datlas
-library_dirs =3D /usr/lib:%%LOCALBASE%%/lib:%%GCCLIBDIR%%
-include_dirs =3D /usr/include:%%LOCALBASE%%/include:%%LOCALBASE%%/include/=
suitesparse
-src_dirs =3D %%LOCALBASE%%/src
-# search static libraries (.a) in preference to shared ones (.so)
-search_static_first =3D 0
-[atlas]
-library_dirs =3D %%LOCALBASE%%/lib:%%GCCLIBDIR%%
-atlas_libs =3D %%ATLASLIBS%%
diff -ruN py-numpy.orig/files/site.cfg.atlas py-numpy/files/site.cfg.atlas
--- py-numpy.orig/files/site.cfg.atlas	1970-01-01 01:00:00.000000000 +0100
+++ py-numpy/files/site.cfg.atlas	2015-02-08 17:19:17.000000000 +0100
@@ -0,0 +1,9 @@
+[DEFAULT]
+lapack_type=3Datlas
+library_dirs =3D /usr/lib:%%LOCALBASE%%/lib:%%GCCLIBDIR%%
+include_dirs =3D /usr/include:%%LOCALBASE%%/include:%%LOCALBASE%%/include/=
suitesparse
+src_dirs =3D %%LOCALBASE%%/src
+search_static_first =3D 0
+[atlas]
+library_dirs =3D %%LOCALBASE%%/lib:%%GCCLIBDIR%%
+atlas_libs =3D alapack, f77blas, cblas, atlas
diff -ruN py-numpy.orig/files/site.cfg.cblas py-numpy/files/site.cfg.cblas
--- py-numpy.orig/files/site.cfg.cblas	1970-01-01 01:00:00.000000000 +0100
+++ py-numpy/files/site.cfg.cblas	2015-02-08 17:19:30.000000000 +0100
@@ -0,0 +1,5 @@
+[DEFAULT]
+library_dirs =3D /usr/lib:%%LOCALBASE%%/lib:%%GCCLIBDIR%%
+include_dirs =3D /usr/include:%%LOCALBASE%%/include:%%LOCALBASE%%/include/=
suitesparse
+src_dirs =3D %%LOCALBASE%%/src
+search_static_first =3D 0
diff -ruN py-numpy.orig/files/site.cfg.openblas py-numpy/files/site.cfg.ope=
nblas
--- py-numpy.orig/files/site.cfg.openblas	1970-01-01 01:00:00.000000000 +01=
00
+++ py-numpy/files/site.cfg.openblas	2015-02-08 17:19:39.000000000 +0100
@@ -0,0 +1,9 @@
+[DEFAULT]
+lapack_type=3Dopenblas
+library_dirs =3D /usr/lib:%%LOCALBASE%%/lib:%%GCCLIBDIR%%
+include_dirs =3D /usr/include:%%LOCALBASE%%/include:%%LOCALBASE%%/include/=
suitesparse
+src_dirs =3D %%LOCALBASE%%/src
+search_static_first =3D 0
+[openblas]
+libraries =3D openblasp
+library_dirs =3D %%LOCALBASE%%/lib:%%GCCLIBDIR%%
----- numpy updated to build with blaslapack -----


--=20
R.F.Smith                                   http://rsmith.home.xs4all.nl/
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To view an individual PR, use:
  https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=(Bug Id).

The following is a listing of current problems submitted by FreeBSD users,
which need special attention. These represent problem reports covering
all versions including experimental development code and obsolete releases.

Status      |    Bug Id | Description
------------+-----------+---------------------------------------------------
Open        |    185884 | Miscellaneous ports fixes for Python 3            
Open        |    186316 | [NEW PORT] devel/spyder: Scientific PYthon Develo 
Open        |    196336 | security/py-fail2ban: Support Python 3            

3 problems total for which you should take action.

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Subject: [Bug 197078] devel/awscli: Update to 1.7.4
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197078

Brad Davis <brd@FreeBSD.org> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |brd@FreeBSD.org

--- Comment #4 from Brad Davis <brd@FreeBSD.org> ---
Created attachment 152818
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=152818&action=edit
regenerated patch with svn

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197078

--- Comment #5 from Brad Davis <brd@FreeBSD.org> ---
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poudriere build log

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197078

Brad Davis <brd@FreeBSD.org> changed:

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           Assignee|python@FreeBSD.org          |brd@FreeBSD.org

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Subject: [Bug 197523] devel/py-robotframework-selenium2library: Update to 1.6.0
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197523

Kubilay Kocak <koobs@FreeBSD.org> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
           Assignee|freebsd-ports-bugs@FreeBSD. |python@FreeBSD.org
                   |org                         |
            Summary|[Maintainer Update]         |devel/py-robotframework-sel
                   |devel/py-robotframework-sel |enium2library: Update to
                   |enium2library 1.5.0 ->      |1.6.0
                   |1.6.0                       |
           Keywords|                            |patch, patch-ready
             Status|New                         |Open

--- Comment #1 from Kubilay Kocak <koobs@FreeBSD.org> ---
Thanks Vladimir!

For future submissions, QA results/outputs are highly preferred as attachments,
as it means more than one set of eyes with the ability to detect potential
issues.

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197376

Kubilay Kocak <koobs@FreeBSD.org> changed:

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----------------------------------------------------------------------------
              Flags|maintainer-feedback?(python |maintainer-feedback+
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           Keywords|                            |needs-patch, needs-qa
             Status|New                         |Open

--- Comment #2 from Kubilay Kocak <koobs@FreeBSD.org> ---
Ed, 

Can you reproduce this in python33, python34 and against python upstream branch
default?

Please also provide uname -a output as attachment

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Subject: ctypes problem loading libc.so on FreeBSD current
From: Craig Rodrigues <rodrigc@FreeBSD.org>
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Hi,

I am looking at this blog post for loading libc with ctypes:

http://blogs.freebsdish.org/rpaulo/2008/11/30/sysctlbyname3-and-others-from-python/

I am using this version of python from ports:


Name           : python
Version        : 2.7_2,2
Installed on   : Mon Jan 12 22:10:27 PST 2015
Origin         : lang/python
Architecture   : freebsd:11:x86:64
Prefix         : /usr/local
Categories     : python lang ipv6
Licenses       :
Maintainer     : python@FreeBSD.org
WWW            : http://www.python.org/
Comment        : The "meta-port" for the default version of Python
interpreter
Annotations    :
    repo_type      : binary
    repository     : FreeBSD
Flat size      : 38.0B
Description    :
Python is an interpreted object-oriented programming language, and is
often compared to Tcl, Perl or Scheme.
This is a meta port to the Python interpreter and provides symbolic links
to bin/python, bin/pydoc, bin/idle and so on to allow compatibility with
version agnostic python scripts.

WWW: http://www.python.org/



I have this test program

import ctypes

mylib = ctypes.CDLL("libc.so")
print(mylib)

On FreeBSD 9, this program works, and I get a handle to libc.so.

On FreeBSD-CURRENT, I get this:

  File "a.py", line 3, in <module>
    mylib = ctypes.CDLL("libc.so")
  File "/usr/local/lib/python2.7/ctypes/__init__.py", line 365, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /usr/lib/libc.so: invalid file format


The problem seems to be that on FreeBSD 9,
/usr/lib/libc.so is a symlink to /lib/libc.so.7, while
on FreeBSD-CURRENT, /usr/lib/libc.so contains this:

/* $FreeBSD: head/lib/libc/libc.ldscript 258283 2013-11-17 22:52:17Z peter
$ */
GROUP ( /lib/libc.so.7 /usr/lib/libc_nonshared.a
/usr/lib/libssp_nonshared.a )


Any ideas what the problem is?
--
Craig

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Subject: [Bug 197061] sysutils/py-salt: Update to 2014.7.1
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197061

--- Comment #5 from christer.edwards@gmail.com ---
Apologies for the delay.. I just validated that the requirement for lsof
remains in this release. We should be able to remove it in the next feature
release, 2015.2.x.

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Subject: [Bug 197061] [MAINTAINER] sysutils/py-salt: Update to 2014.7.1
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197061

Kubilay Kocak <koobs@FreeBSD.org> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|sysutils/py-salt: Update to |[MAINTAINER]
                   |2014.7.1                    |sysutils/py-salt: Update to
                   |                            |2014.7.1

--- Comment #6 from Kubilay Kocak <koobs@FreeBSD.org> ---
Thanks Christer, can you attach QA (portlint / poudriere) results for the
attached please

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Subject: [Bug 197061] [MAINTAINER] sysutils/py-salt: Update to 2014.7.1
Date: Fri, 13 Feb 2015 03:56:18 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197061

--- Comment #7 from christer.edwards@gmail.com ---
I don't know that I've been asked to attach QA results for previous
submissions. Can you tell me more specifically what you're looking for? Do you
want the output of 'portlint -A' or 'poudriere testport -j 10amd64 -o
sysutils/py-salt-2014.7.1'?

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Subject: [Bug 197376] lang/python27: random module leaks file descriptor into
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Date: Fri, 13 Feb 2015 04:13:14 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197376

--- Comment #3 from Ed Maste <emaste@freebsd.org> ---
It is fixed in python 3.4.2 - see test result below. Looks like the fix[1] is
not in 2.x though. The fix is PEP 446 - issue 18571[2]

[1]
https://github.com/python/cpython/commit/621f57c094e7572bb4aa2734fe7264856921fc27
[2] http://bugs.python.org/issue18571

LLDB people do not see this issue on Linux; I do not yet know if they're using
Python 3 or if there's some other difference.

Also os.urandom() is sufficient to demonstrate the problem:

Python 2.7.9 (default, Jan  8 2015, 21:47:19) 
[GCC 4.2.1 Compatible FreeBSD Clang 3.3 (tags/RELEASE_33/final 183502)] on
freebsd10
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.urandom(1)
'8'
>>> os.system("./a.out")
File descriptor 3 is open.
512
>>> 
feynman% python3
Python 3.4.2 (default, Jan 28 2015, 05:38:04) 
[GCC 4.2.1 Compatible FreeBSD Clang 3.3 (tags/RELEASE_33/final 183502)] on
freebsd10
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.urandom(1)
b'\x00'
>>> os.system("./a.out")
0

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197061

--- Comment #8 from Kubilay Kocak <koobs@FreeBSD.org> ---
Christer,

They are not strictly compulsory, but issue reports with QA results tend
heavily to be triaged, prioritised and committed before others. 

Moving forward there will be more metadata attributes associated around, and
added to incentivizing high quality issue reports, with a view to making them
even more quickly discoverable to committers.

Regarding what constitutes QA:

1) portlint -AC, and
2) poudriere testport (or bulk -t)
3) software test suite / unit test output

With (1) and (2) being the minimum.

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On, Fri Feb 13, 2015, Craig Rodrigues wrote:

> Hi,
>
> I am looking at this blog post for loading libc with ctypes:
>
> http://blogs.freebsdish.org/rpaulo/2008/11/30/sysctlbyname3-and-others-from-python/
>
> I am using this version of python from ports:
>
>
> Name           : python
> Version        : 2.7_2,2
> Installed on   : Mon Jan 12 22:10:27 PST 2015
> Origin         : lang/python
> Architecture   : freebsd:11:x86:64
> Prefix         : /usr/local
> Categories     : python lang ipv6
> Licenses       :
> Maintainer     : python@FreeBSD.org
> WWW            : http://www.python.org/
> Comment        : The "meta-port" for the default version of Python
> interpreter
> Annotations    :
>     repo_type      : binary
>     repository     : FreeBSD
> Flat size      : 38.0B
> Description    :
> Python is an interpreted object-oriented programming language, and is
> often compared to Tcl, Perl or Scheme.
> This is a meta port to the Python interpreter and provides symbolic links
> to bin/python, bin/pydoc, bin/idle and so on to allow compatibility with
> version agnostic python scripts.
>
> WWW: http://www.python.org/
>
>
>
> I have this test program
>
> import ctypes
>
> mylib = ctypes.CDLL("libc.so")
> print(mylib)
>
> On FreeBSD 9, this program works, and I get a handle to libc.so.
>
> On FreeBSD-CURRENT, I get this:
>
>   File "a.py", line 3, in <module>
>     mylib = ctypes.CDLL("libc.so")
>   File "/usr/local/lib/python2.7/ctypes/__init__.py", line 365, in __init__
>     self._handle = _dlopen(self._name, mode)
> OSError: /usr/lib/libc.so: invalid file format
>
>
> The problem seems to be that on FreeBSD 9,
> /usr/lib/libc.so is a symlink to /lib/libc.so.7, while
> on FreeBSD-CURRENT, /usr/lib/libc.so contains this:
>
> /* $FreeBSD: head/lib/libc/libc.ldscript 258283 2013-11-17 22:52:17Z peter
> $ */
> GROUP ( /lib/libc.so.7 /usr/lib/libc_nonshared.a
> /usr/lib/libssp_nonshared.a )
>
>
> Any ideas what the problem is?

You described the problem above. ctypes is unable to load linker
scripts. The general advise is to use find_library():

>>> import ctypes
>>> import ctypes.util
>>> clib = ctypes.util.find_library("c")
>>> print clib
libc.so.7
>>> dll = ctypes.CDLL(clib)

Cheers
Marcus

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Subject: [Bug 197376] lang/python27: random module leaks file descriptor into
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197376

Kubilay Kocak <koobs@FreeBSD.org> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                URL|                            |http://bugs.python.org/issu
                   |                            |e23458

--- Comment #4 from Kubilay Kocak <koobs@FreeBSD.org> ---
Victor Stinner (haypo) @ Python has graciously created an issue with patch
upstream to take care of this.

Once merged I'll backport it to 2.7.9 (and other versions if applicable)

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197376

Kubilay Kocak <koobs@FreeBSD.org> changed:

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           Assignee|python@FreeBSD.org          |koobs@FreeBSD.org

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197061

--- Comment #9 from christer.edwards@gmail.com ---
Created attachment 152939
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=152939&action=edit
QA

portlint & testport output

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197061

Kubilay Kocak <koobs@FreeBSD.org> changed:

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              Flags|                            |

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Subject: Re: ctypes problem loading libc.so on FreeBSD current
From: Craig Rodrigues <rodrigc@FreeBSD.org>
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On Thu, Feb 12, 2015 at 11:42 PM, Marcus von Appen <mva@freebsd.org> wrote:

>
> You described the problem above. ctypes is unable to load linker
> scripts. The general advise is to use find_library():
>
> >>> import ctypes
> >>> import ctypes.util
> >>> clib = ctypes.util.find_library("c")
> >>> print clib
> libc.so.7
> >>> dll = ctypes.CDLL(clib)
>
> Cheers
> Marcus
>


That solves it.
Thanks!!

--
Craig