Jacques Bloch | 18 Dec 09:23 2014
Picon

ppl9

I get the following error when fink makes ppl9:

g++ -DHAVE_CONFIG_H -I. -I../../src -I..  -I.. -I../../src  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/include -I/sw/include  -Winvalid-pch -g -O2  -g -O2 -pipe -fpch-preprocess -fPIC -W -Wall -xc++-header -DPIC -o ppl.hh.gch ppl.hh
ppl.hh:14386:15: error: flexible array member 'vec_' of type 'Coefficient []' with non-trivial destruction
  Coefficient vec_[
              ^
ppl.hh:31483:10: warning: class 'RAII_Temporary_Real_Relaxation' was previously declared as a struct [-Wmismatched-tags]
  friend class RAII_Temporary_Real_Relaxation;
         ^
ppl.hh:31468:10: note: previous use is here
  struct RAII_Temporary_Real_Relaxation {
         ^
ppl.hh:31483:10: note: did you mean struct here?
  friend class RAII_Temporary_Real_Relaxation;
         ^~~~~
         struct
ppl.hh:33972:64: warning: unused parameter 'to' [-Wunused-parameter]
diff_restriction(Interval_Restriction_Integer_Modulo<T, Base>& to,
                                                               ^
ppl.hh:33973:17: warning: unused parameter 'x' [-Wunused-parameter]
                 const From1& x, const From2& y) {
                              ^
ppl.hh:33973:33: warning: unused parameter 'y' [-Wunused-parameter]
                 const From1& x, const From2& y) {
                                              ^
ppl.hh:34514:54: warning: unused parameter 's' [-Wunused-parameter]
Interval_Info_Null<Policy>::ascii_dump(std::ostream& s) const {
                                                     ^
ppl.hh:34519:54: warning: unused parameter 's' [-Wunused-parameter]
Interval_Info_Null<Policy>::ascii_load(std::istream& s) {
                                                     ^
ppl.hh:35923:14: warning: unused variable 'ru' [-Wunused-variable]
      Result ru = Boundary_NS::assign(UPPER, upper(), info(),
             ^
ppl.hh:35933:14: warning: unused variable 'ru' [-Wunused-variable]
      Result ru = Boundary_NS::assign(UPPER, upper(), info(),
             ^
ppl.hh:35943:14: warning: unused variable 'rl' [-Wunused-variable]
      Result rl = Boundary_NS::assign(LOWER, lower(), info(),
             ^
ppl.hh:35953:14: warning: unused variable 'rl' [-Wunused-variable]
      Result rl = Boundary_NS::assign(LOWER, lower(), info(),
             ^
ppl.hh:54188:12: warning: unused variable 'vars_end' [-Wunused-variable]
           vars_end = vars.end(); i != vars.end(); ++i) {
           ^
11 warnings and 1 error generated.
make: *** [ppl.hh.gch] Error 1
### execution of /tmp/fink.jt3OM failed, exit code 2
### execution of /tmp/fink.kRoXD failed, exit code 2
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-ppl9-0.11.2-5
(Reading database ... 196503 files and directories currently installed.)
Removing fink-buildlock-ppl9-0.11.2-5 ...
Failed: phase compiling: ppl9-0.11.2-5 failed

Before reporting any errors, please run "fink selfupdate" and try again.
Also try using "fink configure" to set your maximum build jobs to 1 and
attempt to build the package again.
If you continue to have issues, please check to see if the FAQ on Fink's
website solves the problem.  If not, ask on one (not both, please) of
these mailing lists:

The Fink Users List <fink-users <at> lists.sourceforge.net>
The Fink Beginners List <fink-beginners <at> lists.sourceforge.net>,

with a carbon copy to the maintainer:

David Fang <fangism <at> users.sourceforge.net>

Note that this is preferable to emailing just the maintainer directly,
since most fink package maintainers do not have access to all possible
hardware and software configurations.

Please try to include the complete error message in your report.  This
generally consists of a compiler line starting with e.g. "gcc" or "g++"
followed by the actual error output from the compiler.

Also include the following system information:
Package manager version: 0.38.3
Distribution version: selfupdate-rsync Thu Dec 18 09:14:14 2014, 10.10, x86_64
Trees: local/main stable/main local/injected
Xcode.app: 6.1.1
Xcode command-line tools: 6.1.1.0.1.1416017670
Max. Fink build jobs:  8


---
Dr. Jacques C.R. Bloch
Institute for Theoretical Physics
University of Regensburg
93040 Regensburg, Germany
tel: +49 941 943-2018
fax: +49 941 943-3887
email: jacques.bloch <at> ur.de
web: http://homepages.uni-regensburg.de/~blj05290



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Hanspeter Niederstrasser | 18 Dec 03:56 2014

pythonmods with no Distribution field and py32 and py33 variants

OS X 10.10 only has python27 and py34 available.  The following packages 
all have py32 or py33 variants, but don't have a Distribution: field to 
restrict the 32 and 33 variants to 10.7-10.9.  The solution can be 
something as simple as the following field (please verify it meets the 
specific needs for your package):

Distribution: <<
	(%type_pkg[python] = 32) 10.7,
	(%type_pkg[python] = 32) 10.8,
	(%type_pkg[python] = 32) 10.9,
	(%type_pkg[python] = 33) 10.7,
	(%type_pkg[python] = 33) 10.8,
	(%type_pkg[python] = 33) 10.9
<<

List of packages (with maintainer):

database/psycopg2-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
database/sqlalchemy-migrate-py.info: Charles Lepple <clepple+fink <at> ghz.cc>
database/sqlalchemy-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
devel/astng-py.info: Kurt Schwehr <goatbar <at> users.sf.net>
devel/logilab-common-py.info: Kurt Schwehr <goatbar <at> users.sf.net>
languages/pip-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
languages/setuptools-tng-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pexpect-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
libs/pythonmods/anyjson-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pythonmods/appscript-py.info: Tristan Thiede <fink <at> thetiredsaint.com>
libs/pythonmods/astropy-py.info: Derek Homeier <dhomeie <at> gwdg.de>
libs/pythonmods/beaker-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
libs/pythonmods/biplist-py.info: Jack Howarth <howarth.at.fink <at> gmail.com>
libs/pythonmods/bitvector-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pythonmods/bottleneck-py.info: Derek Homeier <dhomeie <at> gwdg.de>
libs/pythonmods/configobj-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pythonmods/coverage-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pythonmods/jdcal-py.info: Derek Homeier <dhomeie <at> gwdg.de>
libs/pythonmods/jinja2-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
libs/pythonmods/mako-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
libs/pythonmods/markupsafe-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pythonmods/mock-py.info: Charles Lepple <clepple+fink <at> ghz.cc>
libs/pythonmods/mox-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
libs/pythonmods/nose-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
libs/pythonmods/ntplib-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
libs/pythonmods/openpyxl-py-1.8.6.info: Derek Homeier <dhomeie <at> gwdg.de>
libs/pythonmods/openpyxl-py.info: Derek Homeier <dhomeie <at> gwdg.de>
libs/pythonmods/pygments-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pythonmods/pytz-py.info: Daniel Macks <dmacks <at> netspace.org>
libs/pythonmods/tempita-py.info: Charles Lepple <clepple+fink <at> ghz.cc>
libs/pythonmods/virtualenv-py.info: Kurt Schwehr 
<goatbar <at> users.sourceforge.net>
libs/pythonmods/yaml-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
net/zmq-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
sci/h5py-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
sci/numexpr-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
sci/pyfits-py.info: Derek Homeier <dhomeie <at> gwdg.de>
sci/pyproj-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
sci/pytables-py.info: Derek Homeier <dhomeie <at> gwdg.de>
sci/qgis20-py.info: BABA Yoshihiko <babayoshihiko <at> mac.com>
sci/qgis22-py.info: BABA Yoshihiko <babayoshihiko <at> mac.com>
text/docutils-py.info: Charles Lepple <clepple+fink <at> ghz.cc>
text/lxml-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
web/django-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>
web/tornado-py.info: Kurt Schwehr <goatbar <at> users.sourceforge.net>

Hanspeter

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Xiaoguang Xue | 17 Dec 22:46 2014
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libxml2.2.dylib is incompatible with pymol-py27

Dear All


I got an error after I install pymol-py27 through the latest fink.


My system is OS X Yosemite 10.10.1


Traceback (most recent call last):

  File "/sw/lib/python2.7/site-packages/pymol/__init__.py", line 71, in <module>

    import pymol

  File "/sw/lib/python2.7/site-packages/pymol/__init__.py", line 533, in <module>

    import pymol._cmd

ImportError: dlopen(/sw/lib/python2.7/site-packages/pymol/_cmd.so, 2): Library not loaded: /sw/lib/libxml2.2.dylib

  Referenced from: /sw/lib/python2.7/site-packages/pymol/_cmd.so

  Reason: Incompatible library version: _cmd.so requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0


Does anyone have idea about how to fix it?

Thanks!

--
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Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383
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Jack Howarth | 13 Dec 02:51 2014
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glew-1.11.0-1

Benjamin,
      Could you update the glew package to the latest 1.11.0 release?
                   Jack

Index: glew.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/graphics/glew.info,v
retrieving revision 1.4
diff -r1.4 glew.info
2c2
< Version: 1.10.0
---
> Version: 1.11.0
19c19
< Source-MD5: 2f09e5e6cb1b9f3611bcac79bc9c2d5d
---
> Source-MD5: f6d72c7426a5f66580ad09e50816450a
56c56
< Shlibs: %p/lib/libGLEW.1.dylib 1.10.0 %n (>= 1.10.0-1)
---
> Shlibs: %p/lib/libGLEW.1.dylib 1.11.0 %n (>= 1.11.0-1)

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Remko Scharroo | 8 Dec 13:00 2014

Phasing out HDF5.8?

I've noticed the HFD5.9 is making inroads into Fink. For example, the gdal package now requires hdf5.9.
What are the plans for phasing out hdf5.8?
I see that cdo, grads, netcdf-c7 and octave382 are still using hdf5.8.

Remko
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Frava | 4 Dec 19:00 2014
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refmac 5.7.0032-5 doesn't compile due to missing dependency

Hello everyone,

refmac fails to compile on a fresh Fink installation (on Yosemite) with an error message stating that it doesn't find the FFTW(2) libraries.

Doing a "fink install fftw" before the "fink install refmac" fixes the problem, so I guess there is just a missing dependency in the refmac.info.

Cheers,
Rafael Navaza.
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Jack Howarth | 30 Nov 00:25 2014
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flawed os version tests

   The failure of the inkscape-0.48.5-4 build exposed the fact that
the commonly used conditional...

        if [[ $(sw_vers -productVersion | cut -d. -f1-2) > 10.8 ]]; then

is failing on 10.10 and needs to be replaced with...

        if [ $(sw_vers -productVersion | cut -d. -f2) > 8 ]; then

This conditional is used in the following packages...

% grep -R "f1-2" * | grep info | grep sw_vers
database/postgresql90.info: if [[ $(sw_vers -productVersion | cut -d.
-f1-2) > 10.6 ]]; then
database/postgresql91.info: if [[ $(sw_vers -productVersion | cut -d.
-f1-2) > 10.6 ]]; then
database/postgresql92.info: if [[ $(sw_vers -productVersion | cut -d.
-f1-2) > 10.6 ]]; then
database/postgresql93.info: if [[ $(sw_vers -productVersion | cut -d.
-f1-2) > 10.6 ]]; then
graphics/glew.info: if [[ $(sw_vers -productVersion | cut -d. -f1-2) >
10.6 ]]; then
graphics/inkscape.info: if [[ $(sw_vers -productVersion | cut -d.
-f1-2) > 10.8 ]]; then
languages/lua51.info: if [ `/usr/bin/sw_vers -productVersion | cut
-d'.' -f1-2` == 10.3 ]; then
languages/lua51.info: if [ `/usr/bin/sw_vers -productVersion | cut
-d'.' -f1-2` == 10.3 ]; then
libs/gmm.info: case `sw_vers -productVersion | cut -d. -f1-2` in
libs/jicmp.info: if [[ $(sw_vers -productVersion | cut -d. -f1-2) >
10.6 ]]; then
libs/jicmp6.info: if [[ $(sw_vers -productVersion | cut -d. -f1-2) >
10.6 ]]; then
libs/libxine1.info: if [[ $(sw_vers -productVersion | cut -d. -f1-2) =
10.6 ]]; then
libs/osxfuse.info:osxversion=`sw_vers -productVersion | cut -d. -f1-2`
libs/qt4-base-x11.info: if [[ $(sw_vers -productVersion | cut -d.
-f1-2) > 10.6 ]]; then
sci/gdl.info:  if [[ $(sw_vers -productVersion | cut -d. -f1-2) > 10.8 ]]; then
sci/pywavelets-py.info: export PYTHONPATH=%b/build/lib.macosx-`sw_vers
-productVersion | cut -d. -f1-2`-%m-%type_raw[python]:$PYTHONPATH
sound/jack.info: if [[ $(sw_vers -productVersion | cut -d. -f1-2) >
10.7 ]]; then
web/linkchecker.info: if [[ $(sw_vers -productVersion | cut -d. -f1-2)
> 10.8 ]]; then

and perhaps more which aren't being captured by that regex.
              Jack

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Alexander Hansen | 19 Nov 19:20 2014
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bowtie2 giving help2man warnings(?) on Yosemite with exporter-pm installed

Hi.  I saw this when building bowtie2 on Yosemite with exporter-pm-5.68-1 installed:


make install PREFIX=/sw DESTDIR=/sw/src/fink.build/root-bowtie2-2.2.4-1
help2man --name="wrapper for bowtie2-align" --no-info \
`pwd`/bowtie2 > bowtie2.1
Constant subroutine main::LC_ALL redefined at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.
Prototype mismatch: sub main::LC_ALL () vs none at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.
help2man --name="building a colorspace index for bowtie2" --no-info \
`pwd`/bowtie2-build > bowtie2-build.1
Constant subroutine main::LC_ALL redefined at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.
Prototype mismatch: sub main::LC_ALL () vs none at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.
help2man --name="extracts information from a bowtie2 index" --no-info \
`pwd`/bowtie2-inspect > bowtie2-inspect.1
Constant subroutine main::LC_ALL redefined at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.
Prototype mismatch: sub main::LC_ALL () vs none at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.
help2man --name="ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences" --no-info \
    `pwd`/bowtie2-align-s> bowtie2-align.1
Constant subroutine main::LC_ALL redefined at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.
Prototype mismatch: sub main::LC_ALL () vs none at /sw/lib/perl5/Exporter.pm line 66.
 at /sw/bin/help2man line 28.

It may be harmless.  I was just a bit unsettled to see the Perl functions in the output. :-)
-- 
Alexander Hansen, Ph.D.
Fink User Liaison

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Jack Howarth | 18 Nov 01:33 2014
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xvfb-run oddity

Daniel,
     Is it expected that invoking xvfb-run is insufficient to trigger the launching of Xquartz (even after the application has been run once in an account)? I was very surprised by this behavior as every other X windows program that I have run manages to trigger the launch of Xquartz. In the case of xvfb-run, if Xquartz isn't already running, one gets the error…

Xvfb failed to start


          Jack

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Alexander Hansen | 13 Nov 19:35 2014
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Updating mirrors

I’m in the process of refreshing the fink-mirrors package as a prelude to releasing fink-0.38.3—a
bootstrap goes more smoothly when fink starts out with a current mirror set.  I’m thinking that since
distfiles.sjc.ca.us doesn’t seem to be updating either source packages or its .info collection, we
should remove it from the mirror list (at least temporarily), unless we can get a hold of the
administrator. 

Any objections to that?
--

-- 
Alexander Hansen, Ph.D.
Fink User Liaison

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Alexander Hansen | 13 Nov 19:16 2014
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Some perlmods to be Yosemified

I’m installing the perlmods needed for the mirror validation script in the fink-mirrors source, and the
following modules didn’t have pm5182 variants yet:

html-form-pm (Daniel J.)
http-response-encoding-pm (Daniel M.)

I’ve got updated packaging which just adds pm5182 variants to the existing packages, and I can add that to
the distro if there are no objections (these are in the dep chain for www-mechanize-pm).
--

-- 
Alexander Hansen, Ph.D.
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