Hanspeter Niederstrasser | 16 Apr 14:17 2014

clustalo can't find omp.h on 10.9

Jack,

My Fink package clustalo has the ability to build using OpenMP.  When I 
set CC and CXX to mpicc and mpic++ on 10.7, the package builds fine and 
links to the openmpi and gcc48 libraries.  However, I have bug reports 
from two 10.9 users where omp.h is not found.  Here's the failed 
compiler command:

/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H 
-I. -I../../src   -I/sw/include -fopenmp  -O3 -g -O2 -MT ktuple_pair.lo 
-MD -MP -MF .deps/ktuple_pair.Tpo -c -o ktuple_pair.lo ktuple_pair.c
libtool: compile:  mpicc -DHAVE_CONFIG_H -I. -I../../src -I/sw/include 
-fopenmp -O3 -g -O2 -MT ktuple_pair.lo -MD -MP -MF .deps/ktuple_pair.Tpo 
-c ktuple_pair.c  -fno-common -DPIC -o .libs/ktuple_pair.o
clang: warning: argument unused during compilation: '-fopenmp'
ktuple_pair.c:41:10: fatal error: 'omp.h' file not found
#include <omp.h>
          ^
1 error generated.

And omp.h does exist for him:
$ ls -l /sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2/include/omp.h
-rw-r--r--  1 root  admin  3620 Oct 28 11:41 
/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2/include/omp.h

Debian has seen this failure in their clang build farm, which makes 
sense since clang can't do OpenMPI yet.

<http://clang.debian.net/logs/2013-07-14/clustalo_1.2.0-1_unstable_clang.log>

(Continue reading)

Andreas Bießmann | 13 Apr 14:33 2014

proj-4.8.0-3 broken with latest toolchain

Dear Kurt Schwehr,

I noticed that proj-4.8.0-3's info file contains the entry 'SetLDFLAGS:
-no-undefined'. Unfortunately this is the root cause for not compiling
that package on my box.

---8<---
configure:2850: gcc  -I/sw/include -no-undefined -L/sw/lib conftest.c  >&5
clang: error: unknown argument: '-no-undefined'
[-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a
warning) in the future
configure:2853: $? = 1
configure:2891: result:
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "PROJ.4 Projections"
| #define PACKAGE_TARNAME "proj"
| #define PACKAGE_VERSION "4.7.0"
| #define PACKAGE_STRING "PROJ.4 Projections 4.7.0"
| #define PACKAGE_BUGREPORT "warmerdam <at> pobox.com"
| #define PACKAGE "proj"
| #define VERSION "4.7.0"
| /* end confdefs.h.  */
|
| int
| main ()
| {
|
|   ;
(Continue reading)

Stephen J. Butler | 8 Apr 19:29 2014
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What's up with the vim info file?

Synced through CVS, and trying to update vim it's failing (404) to grab the source from:


Is that right? Been like this a couple days now.
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Derek Homeier | 5 Apr 22:06 2014
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version conflicts with sip-pyNN-bin

fink update sip-py33-bin                                                                                 
Information about 9023 packages read in 1 seconds.
The following package will be installed or updated:
 sip-py33-bin
Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/sip-py33-bin_4.15.5-1_darwin-x86_64.deb
Selecting previously deselected package sip-py33-bin.
(Reading database ... 463436 files and directories currently installed.)
Unpacking sip-py33-bin (from .../sip-py33-bin_4.15.5-1_darwin-x86_64.deb) ...
/sw/bin/dpkg: error processing
/sw/fink/dists/stable/main/binary-darwin-x86_64/languages/sip-py33-bin_4.15.5-1_darwin-x86_64.deb (--install):
 trying to overwrite `/sw/bin/sip', which is also in package sip-py32-bin
/sw/bin/dpkg-deb: subprocess paste killed by signal (Broken pipe: 13)

I think sip-py32-bin, sip-py33-bin, sip-py34-bin
have to be added to the
Conflicts:
and
Replaces:
fields?

						Derek
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Derek Homeier | 5 Apr 20:54 2014
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dateutil-py tests require sip-py to run

Hi,

found there is a missing

   TestDepends: six-py%type_pkg[python]

in dateutil-py-2.2-1.

Cheers,
					Derek

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Derek Homeier | 5 Apr 16:38 2014
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PyQt-mac/x11 source/md5sum error

Hi,

there seems to be some mixup of the source files and checksums for pyqt4:

The checksum of the file PyQt-mac-gpl-4.10.4.tar.gz of package pyqt4-py27-4.10.4-1 is incorrect. The
most likely cause
for this is a corrupted or incomplete download
Expected: 20940f6b2c957269cdd02d0efe537515
Actual: MD5(a1d33b15808993055931083813f5f399)
        SHA1(ef3bb2a05a5c8c3ab7578a0991ef5a4e17c314c0)
It is recommended that you download it again. How do you want to proceed?
...
The checksum of the file PyQt-mac-gpl-4.10.4.tar.gz of package pyqt4-mac-py27-4.10.4-1 is incorrect.
The most likely cause
for this is a corrupted or incomplete download
Expected: 20940f6b2c957269cdd02d0efe537515
Actual: MD5(a1d33b15808993055931083813f5f399)
        SHA1(ef3bb2a05a5c8c3ab7578a0991ef5a4e17c314c0)
It is recommended that you download it again. How do you want to proceed?

(1)	Give up
(2)	Delete it and download again
(3)	Assume it is a partial download and try to continue
(4)	Don't download, use existing file

Make your choice:  [2] 4

Sourceforge also gives the latter (actual) MD5, pyqt4-mac-py27 builds correctly with that;
but pyqt4-py27 fails in the patch phase; shouldn't it be using the PyQt-x11-gpl source?

Cheers,
						Derek

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Alexander Hansen | 2 Apr 23:00 2014
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New clang wrapper option available

It's the branch "refactor-compiler-wrapper" in fink's github:

https://github.com/fink/fink/tree/refactor-compiler-wrapper

Folks without an active git checkout can download an archive, e.g. via 
the "Download ZIP" button, and use "inject.pl" to install the update.

--

-- 
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/

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Kurt Schwehr | 30 Mar 23:18 2014
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fink dateutils py34 and 2.2 update -- return of the bad __pycache__

dmacks,

Mind if I do this update to dateutils?  I ran into trouble when installing in maintainer mode and added a -B to the python test line to nuke generated pyc files

    # -B prevents the test run from generating __pycache__ .pyc files.
    %p/bin/python%type_raw[python] -B test.py || exit 2

Also updated to dateutil 2.2 and switched download and url to pypi.

-kurt
(goatbar)
Attachment (dateutil-py.info): application/octet-stream, 1225 bytes
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Alexander Hansen | 29 Mar 01:48 2014
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Time for 10.6 to go EOL

We've reached the point where it appears that most maintainers don't 
have access to 10.6, and we're getting divergences between the trees. 
I've also found some packages that won't build as 32-bit.

Also, most of our efforts probably need to be concentrated on fixing the 
Xcode 5.1 build failures on 10.8 and 10.9.

I propose ending official project support for 10.6 at the end of April. 
  There are a couple of options:

1)  Move all of the package descriptions into a 10.6-EOL structure.
2)  Do nothing and just not update any of the base packages in the 10.4 
tree.

If somebody has an interest in keeping 10.6 going unofficially, they are 
certainly welcome to do that.
--

-- 
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/

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Daniel Macks | 20 Mar 07:13 2014

Killing python26

We've been dragging python26 along for years, since back when it was the latest thing. It's not. Python27
has been available in fink for many years, and even in the past several OS X versions. Upstream says "Python
itself has jumped to the 3.x series in 2008, with some major changes that may make upgrading non-trivial in
some cases, so it makes sense to keep "some" python2.x in fink (OS X still has python27 and maybe older
also). Upstream plans to keep 27 in maintenance mode for at least a while longer but gave up on even security
patches for 26 as I understand it. 

As of yesterday, the only dependencies on python26 are the -py26 suite of modules--there does not appear to
be anything outside of this self-contained tree. Is it time to chop down that tree? There are no -py26
modules that do not have a parallel -py27 variant. Ordinarily, I'd not object to keeping ancient versions
of things around and just stop bringing them forward when we roll the next Distribution, but python26 is
also the only package still using db48, another ancient version. I'd love to stop having to support
ancient versions of things that are not even getting security-support upstream altogether. 

dan

 --
Daniel Macks
dmacks <at> netspace.org

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Kurt Schwehr | 16 Mar 17:34 2014
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gnutls man-in-the-middle security vulnerability

Dave,

Are you aware of this?  http://www.gnutls.org/security.html#GNUTLS-SA-2014-2
http://lwn.net/Articles/589205/

I added a one line warning to the gnutls28.info file, but we definitely need to get a new version of gnutls into fink.  From the summary:

How to mitigate the attack?
  • Upgrade to the latest GnuTLS version (3.2.12 or 3.1.22), or apply the patch for GnuTLS 2.12.x.

-kurt
sf: goatbar
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