BTW, BLT still compiles fine on my 10.11.6 machine at work. I haven’t had a
chance to test on anything with 10.12 and my home internet has been down since
the orange coup.
William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry
t
> upgrades gdk-gl-glue.c to use the modern equivalents of those deprecated
> functions. Wonder why your package is getting as far as compiling that source
> file without the patch seeming to be applied...
> dan
>
> --
> Daniel Macks
> dma...@netspace.org
>
I can’t reproduce
Hi folks:
I’ve been using fink for well over 10 years now, but am having problems for the
first time that I just can’t seem to get around. This has happened several
times now, typically after a power failure due to the crumbling neglected
University of California, albeit Santa Cruz
On Oct 7, 2013, at 9:27 AM, Alexander Hansen alexanderk.han...@gmail.com
wrote:
It seems to me like there's a missing dependency on numpy-py27.
Indeed, that is the problem.
Thanks, Alexander, yet again!
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
In Code/GraphMol/CMakeLists.txt, there is a conditional
if(RDK_BUILD_SLN_SUPPORT AND NOT CMAKE_COMPILER_IS_CLANG)
add_subdirectory(SLNParse)
endif()
In my case, it appears that CMAKE_COMPILER_IS_CLANG is false. Indeed, I see
in build/CMakeCache.txt
email:wgsc...@ucsc.edu
On Sep 7, 2013, at 5:28 AM, Martin Costabel costa...@wanadoo.fr wrote:
On 7/09/13 05:06, William G. Scott wrote:
On Sep 6, 2013, at 5:59 PM, Dmitry Rodionov d.rodio...@gmail.com wrote:
Hi Bill,
I get the following error when trying to update rdkit:
Just
On Sep 6, 2013, at 5:59 PM, Dmitry Rodionov d.rodio...@gmail.com wrote:
Hi Bill,
I get the following error when trying to update rdkit:
Just to keep it surreal, yesterday it built for me; today on the same computer
it does not. I will idiot-fix it, and then must go and ponder.
Sorry.
Dear Jon:
I can't reproduce it, having tried on three 10.8.4 computers and one 10.6.8.
Are you running something else (10.7 maybe)?
The only thing that changed is a newer compiler (gcc4.8 vs. 4.7).
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center
Thanks for checking. Briefly, I have no idea why this happened, but will try
to fix it. cctbx builds its own as far as I am aware. Nothing I can find in
CCP4 links to it.
On Feb 13, 2013, at 11:30 AM, Dmitry Rodionov d.rodio...@gmail.com wrote:
Yes, fftw3 was installed. I tried
This is my fault. I'm testing now before I commit it to cvs.
Sorry.
Bill
On Jan 13, 2013, at 6:35 AM, Collins, Edward J edward_coll...@med.unc.edu
wrote:
Hi folks,
Sorry to add to the noise of emails on a weekend. I was updating my fink
distribution and ran across this error. A
It needs guile18-gtk-shlibs
which should have been installed as a dependency of guile18-gtk-dev, which in
turn is required for building coot, so I am not sure what went wrong.
Maybe (re)install guile18-gtk-shlibs
Sorry.
Bill
William G. Scott
Professor
Department of Chemistry
OK, I have it fixed.
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459
?
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax
OK, that makes sense. I will add it to the dependencies, although the two
header files are the same, so presumably both would have to be absent if the
build fails?
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228
I'm getting this failure with both 32 and 64 bit fink on 10.6
libtool: link: gcc -Os -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include
-I/sw/include/libmpd-1.0/ -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include
-I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/gtk-2.0
If you issue the command
fink list x11-dev
do you get this output?
Information about 3226 packages read in 8 seconds.
p x11-dev [virtual package]
x11-dev is a placeholder package that fink uses to keep track of whether the
Xcode X11 header files
Thanks. I am testing this now, and will commit the fix as soon as I verify it
indeed
solves the problem (the tar ball also got changed upstream, so I don't have a
proper
experimental control).
Yes. fink-0.31.2 has introduced using multiple threads to build
packages by default. Some
On Sep 30, 2011, at 6:47 PM, Alexander Hansen wrote:
Yes. fink-0.31.2 has introduced using multiple threads to build
packages by default. Some packages aren't compatible with this, and
it appears that ccp4 is one of them.
OK, this seems to have fixed it (at least on my computer), so I have
Could you please have a look at the attached file to help me? This
would be very much appreciated to install these important programs!
Thanks a lot in advance for your help
Best wishes,
helge
Ironically, I couldn't compile your tex file.
But it looks like there are multile
Hi Frank:
I think you need to make sure that unstable is being used and then issue the
commands
fink selfupdate-cvs
fink update-all
fink install pymol-py27
I have to confess I have never used fink commander, so I don't know what the
equivalent commands are from the GUI.
Bill
On Sep 2,
Hi Frank:
It looks like you have an old version. 1.4 is what is current (rev. 8 for 10.7
and rev. 4 for the rest).
http://pdb.finkproject.org/pdb/package.php/pymol-py27
I probably need to update all of them to 1.4-8 for consistency, but 1.4-4
should compile ok.
I'm not sure what is going
On Jul 23, 2011, at 5:06 AM, Hanspeter Niederstrasser wrote:
Hi,
I tried to build gromacs-4.5.3-2 on 10.5/i386 and had a validation error.
Thanks. I will fix it.
Bill
--
Storage Efficiency Calculator
This
Dear Natasha:
I'm afraid I haven't tried to compile this on 10.4 since 10.5 was released, as
I don't have access to it any more. I'll change the package to reflect that it
should only be in 10.5 and 10.6 distributions. I'm afraid I don't have any way
to debug this.
Bill
On Dec 8, 2010, at
Apologies for a question that is likely off-topic: Is there a unix
command (fink package or otherwise) to read/write the sampling
frequency for an audio output device that one normally sets in the
Audi MIDI Setup GUI?
Many thanks in advance.
Bill Scott
On Jun 7, 2010, at 7:49 AM, Robert Wyatt wrote:
On 10.6.3 64-bit, I have the following error while updating coot. Happy to
try suggestions. --Robert
checking for GtkGLExt - version = 1.0.0... no
*** Could not run GtkGLExt test program, checking why...
*** The test program compiled, but
Thanks Bill,
While fink reinstall did not work, fink rebuild gtkglext1 gtkglext1-shlibs
did work.
Thanks. I'll put a note to this effect in the info file.
--
ThinkGeek and WIRED's GeekDad team up for the
On Apr 20, 2010, at 11:44 AM, Alexander Hansen wrote:
You might try running the commands from
/sw64/var/lib/dpkg/info/dbus.postrm manually to see what's failing--
that
way we can see what is griping.
I've now tried every script in that directory in which the string
*dbus* appears, to no
I found, after the install failure, issuing
fink remove --recursive scipy-core-py26
and then reinstalling anything else recursively removed that you want to keep
sorted everything out with minimal pain.
--
Download
They must have changed something, but in checking I just realized they
officially released 6.1.3 in December (although their front web page makes no
mention of this). I have the update files on a home computer that I cannot
access for a few more hours, but as soon as I double-check everything
On Dec 30, 2009, at 11:25 AM, fink-users-requ...@lists.sourceforge.net wrote:
Right. And Bill's binary distribution is unofficial, so an upgrade path
isn't guaranteed.
The official binary distribution was set up only to use the latest
version of X11 officially put out by Apple, and
Dear Felix:
As far as I understand it, if you upgraded 32-bit fink to 10.6, you are going
to have to periodically delete *.la files in /sw/lib (they get reinstalled when
dev packages are reinstalled).
Since you are already using my unofficial debian repository,
fink -b install coot
or
sudo
fixed it. Sorry.
On Dec 4, 2009, at 5:05 PM, Alexander Hansen wrote:
Thanks. Now it's clear which checksum is causing the issue. It looks
like the stable patch file didn't get updated to be in sync with that in
unstable.
$ md5 /sw/fink/dists/unstable/main/finkinfo/sci/coot.patch
MD5
On Dec 4, 2009, at 4:32 PM, Martin Costabel wrote:
Fink on 10.6 really wants to keep /sw/var/lib/fink/path-prefix-10.6 at the
beginning of PATH.
Fixed it just now. Oddly, for some reason I did run into this problem on my
10.6 32-bit testing.
On Sep 16, 2009, at 7:11 AM, Benda, Christian wrote:
echo $PWD should be the same as $CCP4
/sw/src/fink.build/ccp4-6.1.2-4/ccp4-6.1.2 should be the same as
[[ $CCP4 == $PWD ]] || exit 1
This is a failsafe I put in that caused it to stop. (The temporary
value of $CCP4 should match the
This is a bit odd:
I turned off PAM authentication in /etc/sshd_config to use only
PubkeyAuthentication ( this is working fine on a ppc 10.5).
I then reboot, login, and get
Bug: launchctl.c:2325 (23930):13: (dbfd = open
(g_job_overrides_db_path, O_RDONLY | O_EXLOCK | O_CREAT, S_IRUSR |
and 10.5)?
On Sep 10, 2009, at 11:10 AM, Robert Wyatt wrote:
William G. Scott wrote:
This is a bit odd:
I turned off PAM authentication in /etc/sshd_config to use only
PubkeyAuthentication ( this is working fine on a ppc 10.5).
I then reboot, login, and get
Bug: launchctl.c:2325 (23930):13
Hi Koen:
Try revision 3 (now in cvs)
Bill
On Sep 7, 2009, at 3:11 PM, Koen van der Drift wrote:
Hi Bill,
The latest rnaview fails as follows:
..
/bin/rm -rf /sw/src/fink.build/root-rnaview-1.0-2
/bin/mkdir -p /sw/src/fink.build/root-rnaview-1.0-2/sw
/bin/mkdir -p
Hi Steffen:
On Sep 4, 2009, at 7:43 AM, Steffen Schmidt wrote:
Hi ccp4 build fails (see below) - I recompiled fink on snow leopard
(core duo) using fink in 64bit only configuration. Besides there is
also the problem that e.g. gd2 compilations fails and that it
complains the the .la
to do a superposition of two molecules. (The superposition itself
seems to work ok if you issue the scheme or python command).
On Aug 29, 2009, at 7:09 AM, William G. Scott wrote:
Hi Nayden:
I only got ahold of 10.6 late yesterday afternoon, after I found out
from Apple my pre-ordered copy
Hi Nayden:
I only got ahold of 10.6 late yesterday afternoon, after I found out
from Apple my pre-ordered copy would not be shipped until September
8th. So I will have to get back to you after I try to compile it.
Bill
On Aug 29, 2009, at 5:43 AM, Alexander Hansen wrote:
nayden wrote:
On Aug 26, 2009, at 3:45 AM, Alan wrote:
It's because apbs-mpi.info is replacing /sw/bin/apbs instead of
putting
another binary called, e.g., /sw/bin/apbs_mpi
Is renaming the binary sufficient, or is it a different binary? (I
have to stop reading email in the middle of the night.)
Hi Alan:
Sorry, I was away in the most inaccessible part of Utah I could find.
I think Jack Howarth fixed it in my absence, but if not, please let me
know. Sorry for this continuing nightmare.
Bill
On Aug 14, 2009, at 12:35 AM, Alan wrote:
Starting to answer myself, I did this test
it will work now. (revision 4)
On Sat, August 1, 2009 3:48 pm, Martin Costabel wrote:
William G. Scott wrote:
It turns out there is a typo on line 38 of the patch file
+sitepk...@install_dir$${prefix}/lib/python${PY_VERSION}/site-
packages
should be
+sitepk...@install_dir@${prefix}/lib
-x86_64.deb...
Package looks good!
Validating .deb file
I'm trying to find if there is a missing dependency. We have the
identical setup, apart from my /sw64 vs. his /sw.
(I've emailed him back off-list).
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott
dependency. We have the
identical setup, apart from my /sw64 vs. his /sw.
(I've emailed him back off-list).
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
It doesn't work here (10.5.7/i386)--I get an identical error to Alan.
- --
Alexander Hansen
Fink User
On Aug 1, 2009, at 3:48 PM, Martin Costabel wrote:
William G. Scott wrote:
It turns out there is a typo on line 38 of the patch file
+sitepk...@install_dir$${prefix}/lib/python${PY_VERSION}/site-
packages
should be
+sitepk...@install_dir@${prefix}/lib/python${PY_VERSION}/site-
packages
On a fresh clean install of fink on 10.4, libxml2-2.6.32-1 hangs
indefinitely during the build at this point:
gcc -g -O2 -pedantic -W -Wformat -Wunused -Wimplicit -Wreturn-type -
Wswitch -Wcomment -Wtrigraphs -Wformat -Wchar-subscripts -
Wuninitialized -Wparentheses -Wshadow -Wpointer-arith
Using the slightly older version in stable, I get it to hang at a
different point:
creating xpath2
Rebuilt web page
On Sep 24, 2008, at 5:38 PM, William G. Scott wrote:
On a fresh clean install of fink on 10.4, libxml2-2.6.32-1 hangs
indefinitely during the build at this point:
gcc -g
Do you have ccp4 installed with fink?
On my machine this is messing it up.
The simplest fix at the moment is to first uninstall ccp4, then
install libxslt, then reinstall ccp4.
I will fix the ccp4 package as soon as possible (or figure out how to
keep libxslt out of it).
fink remove
I updated it some more for gtk+2 and pangocairo.
I'd be delighted if someone could test it
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Aug 16, 2008, at 4:47 AM, Alexander Hansen wrote:
On Aug 15, 2008, at 11:28 PM, William Scott wrote:
Hi folks:
I have
Hi Michael:
I had the compilation of gtk+2-2.12.10-1 fail on a couple of machines
as well.
In my case, it was because an older version of gtk+2-dev was present.
When I removed that, it worked.
In your case, it might require the very latest X11, which you can get
here:
Hi Martin:
Thanks for figuring this out. I'll put in some sort of build
conflicts field in coot as soon as I have worked out if it is indeed
guile (or one of the guile-type packages).
All the best,
Bill
On Apr 4, 2008, at 12:34 PM, Martin Costabel wrote:
Robert T Wyatt wrote:
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