Re: [Fink-users] failed to install apbs
Really sorry, but it didn't work for me... even after a fresh install. # # make install DESTDIR=%d # install it ourselves: mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin cp bin/apbs bin/ApbsClient.py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/. echo '#!/sw/bin/python2.6' | /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo from ZSI.generate.commands import wsdl2py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo wsdl2py() /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py chmod a+x /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs cp -r examples /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r tools /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc ln -s /sw/share/apbs/doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc/apbs # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ZSI cp -r contrib/opal/ZSI/ZSI/* /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ZSI/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs cp **/*.h /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/. cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc.h' with `contrib/maloc/src/aaa_inc/maloc/maloc.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc_base.h' with `contrib/maloc/src/aaa_inc/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/aaa_inc/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/aaa_inc/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/aaa_inc/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/aaa_inc/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/aaa_inc/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/aaa_inc/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/aaa_inc/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/aaa_inc/maloc/vset.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/aaa_inc/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsys.h' with `contrib/maloc/src/aaa_inc/maloc/vsys.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc_base.h' with `contrib/maloc/src/base/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/psh/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/psh/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/psh/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/psh/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/vsh/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/vsys/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/vsys/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/vsys/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/vsys/maloc/vset.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsys.h' with `contrib/maloc/src/vsys/maloc/vsys.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./efence.h' with `contrib/maloc/tools/tests/zfence/efence.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcsm.h' with `src/fem/apbs/vcsm.h' cp: will not overwrite
Re: [Fink-users] failed to install apbs
And I know why: where just 'cp' replace with '/bin/cp'. I guess I had problem because I use package 'coreutils' Many thansk William! Cheers, Alan On Sun, Aug 2, 2009 at 12:13, Alan alanwil...@gmail.com wrote: Really sorry, but it didn't work for me... even after a fresh install. # # make install DESTDIR=%d # install it ourselves: mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin cp bin/apbs bin/ApbsClient.py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/. echo '#!/sw/bin/python2.6' | /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo from ZSI.generate.commands import wsdl2py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo wsdl2py() /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py chmod a+x /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs cp -r examples /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r tools /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc ln -s /sw/share/apbs/doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc/apbs # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ZSI cp -r contrib/opal/ZSI/ZSI/* /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ZSI/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs cp **/*.h /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/. cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc.h' with `contrib/maloc/src/aaa_inc/maloc/maloc.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc_base.h' with `contrib/maloc/src/aaa_inc/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/aaa_inc/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/aaa_inc/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/aaa_inc/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/aaa_inc/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/aaa_inc/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/aaa_inc/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/aaa_inc/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/aaa_inc/maloc/vset.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/aaa_inc/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsys.h' with `contrib/maloc/src/aaa_inc/maloc/vsys.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc_base.h' with `contrib/maloc/src/base/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/psh/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/psh/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/psh/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/psh/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/vsh/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/vsys/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/vsys/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/vsys/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/vsys/maloc/vset.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsys.h' with
Re: [Fink-users] failed to install apbs
OK, I will fix it. corutils is always full of surprises. On Aug 2, 2009, at 4:23 AM, Alan wrote: And I know why: where just 'cp' replace with '/bin/cp'. I guess I had problem because I use package 'coreutils' Many thansk William! Cheers, Alan On Sun, Aug 2, 2009 at 12:13, Alan alanwil...@gmail.com wrote: Really sorry, but it didn't work for me... even after a fresh install. # # make install DESTDIR=%d # install it ourselves: mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin cp bin/apbs bin/ApbsClient.py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/. echo '#!/sw/bin/python2.6' | /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo from ZSI.generate.commands import wsdl2py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo wsdl2py() /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py chmod a+x /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs cp -r examples /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r tools /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc ln -s /sw/share/apbs/doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc/apbs # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ ZSI cp -r contrib/opal/ZSI/ZSI/* /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ ZSI/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs cp **/*.h /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/ apbs/. cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc.h' with `contrib/maloc/src/aaa_inc/maloc/maloc.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./ maloc_base.h' with `contrib/maloc/src/aaa_inc/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/aaa_inc/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/aaa_inc/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/aaa_inc/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/aaa_inc/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/aaa_inc/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/aaa_inc/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/aaa_inc/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/aaa_inc/maloc/vset.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/aaa_inc/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsys.h' with `contrib/maloc/src/aaa_inc/maloc/vsys.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./ maloc_base.h' with `contrib/maloc/src/base/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/psh/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/psh/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/psh/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/psh/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/vsh/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/vsys/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/vsys/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/vsys/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/vsys/maloc/vset.h' cp: will not
Re: [Fink-users] failed to install apbs
Hi there,
Well, I found this:
find /sw/src/fink.build | grep site
/sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/@INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly being
replaced in apbs.info:
sed 's|@INSTALL_DIR@|%d|g' %{PatchFile} | patch -p1
In a test, I commented out in apbs.info any reference to python, including
the patch and I got apbs deb and working.
Dear William, would be possible to you to send me your apbs.info and
apbs.patch from sw64/ as well as your apbs deb package?
Many thanks in advance.
Alan
On Fri, Jul 31, 2009 at 19:35, Alexander Hansen alexanderk.han...@gmail.com
wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
William Scott wrote:
There's something funny going on in the install script. For one thing,
it's installing files in
/sw/src/fink.build/root-apbs-1.1.0-2/sw/src/fink.build/apbs-1.1.0-2/
I also found the ordering a bit suspect:
make install DESTDIR=%d
rm -Rf **/CVS # fink validate complains if this junk is left behind.
# rm -Rf **/.svn # fink validate complains if this junk is left behind.
mkdir -p %i/share/%n
mkdir -p %i/lib
I'd have assumed that we'd want to create those directories before 'make
install'.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkpzNMMACgkQB8UpO3rKjQ9ATgCeK9rkwdv7mt61pFn/rdc4RRwu
zPEAniLUCPlwooATD+lGYN9Fd+2w6cto
=V8ih
-END PGP SIGNATURE-
I'll be happy to change anything, but in my hands it works, and
validates:
% fink -v validate apbs_1.1.0-2_darwin-x86_64.deb
apbs-dev_1.1.0-2_darwin-x86_64.deb
Validating .deb file apbs_1.1.0-2_darwin-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/
It doesn't work here (10.5.7/i386)--I get an identical error to Alan.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkpzOVcACgkQB8UpO3rKjQ8DhACfbIuQE5rffn1Qn/6lAI0wc5hy
cngAoKMDRmgsyg53OZLJ9Kwf3zvGyAhM
=350/
-END PGP SIGNATURE-
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
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Re: [Fink-users] failed to install apbs
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Alan wrote:
Hi there,
Well, I found this:
find /sw/src/fink.build | grep site
/sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/@INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly being
replaced in apbs.info:
sed 's|@INSTALL_DIR@|%d|g' %{PatchFile} | patch -p1
In a test, I commented out in apbs.info any reference to python, including
the patch and I got apbs deb and working.
Dear William, would be possible to you to send me your apbs.info and
apbs.patch from sw64/ as well as your apbs deb package?
Many thanks in advance.
Alan
It uses the same .info and .patch files on 32bit and 64bit ; that's not
the issue.
I was able to get apbs to build correctly on a clean 32 bit tree, so the
issue is presumably interference with some other installed package.
Unfortunately when I checked, the build logs didn't show any substantive
differences until the point of failure, so it's not clear yet what the
offending package might be.
You can get a .deb yourself, as William has been good enough to provide
an unofficial binary repository:
http://finkers.wordpress.com/2009/06/01/fink-and-binary-distributions/
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkp0UkMACgkQB8UpO3rKjQ8T/ACggeFPd0peqyGbFYYaE4eHUTHu
bQ0An0HYuQ7tkRP/uxPFNky6UTijxQFG
=hf6+
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Re: [Fink-users] failed to install apbs
Dear Alexander,
When you did a fresh install, the first package you installed was fink
install apbs and the lots of dependences (including python 2.6) came
together, right?
Looking at the error and log I have the suspicion that if I install apbs and
then during the process python 2.6 is build I will not have such a problem
as you saw by yourself.
I will test something here...
Cheers,
Alan
On Sat, Aug 1, 2009 at 15:33, Alexander Hansen
alexanderk.han...@gmail.comwrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Alan wrote:
Hi there,
Well, I found this:
find /sw/src/fink.build | grep site
/sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/@INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly being
replaced in apbs.info:
sed 's|@INSTALL_DIR@|%d|g' %{PatchFile} | patch -p1
In a test, I commented out in apbs.info any reference to python,
including
the patch and I got apbs deb and working.
Dear William, would be possible to you to send me your apbs.info and
apbs.patch from sw64/ as well as your apbs deb package?
Many thanks in advance.
Alan
It uses the same .info and .patch files on 32bit and 64bit ; that's not
the issue.
I was able to get apbs to build correctly on a clean 32 bit tree, so the
issue is presumably interference with some other installed package.
Unfortunately when I checked, the build logs didn't show any substantive
differences until the point of failure, so it's not clear yet what the
offending package might be.
You can get a .deb yourself, as William has been good enough to provide
an unofficial binary repository:
http://finkers.wordpress.com/2009/06/01/fink-and-binary-distributions/
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkp0UkMACgkQB8UpO3rKjQ8T/ACggeFPd0peqyGbFYYaE4eHUTHu
bQ0An0HYuQ7tkRP/uxPFNky6UTijxQFG
=hf6+
-END PGP SIGNATURE-
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
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Re: [Fink-users] failed to install apbs
Hi Alan:
It looks like there are multiple problems with this package and I
think I am going to throw the vile thing into the fire and start over.
I can't give you my debians because they were built for /sw64 instead
of /sw.
If you need apbs in a hurry for a pymol plugin, you can grab David
Gohara's very fast (intel only) pre-compiled version from here:
http://sourceforge.net/projects/apbs/
and redirect pymol to it.
I will try to get the fink package fixed as soon as possible.
Sorry for this.
Bill
On Aug 1, 2009, at 6:11 AM, Alan wrote:
Hi there,
Well, I found this:
find /sw/src/fink.build | grep site
/sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/
@INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly
being
replaced in apbs.info:
sed 's|@INSTALL_DIR@|%d|g' %{PatchFile} | patch -p1
In a test, I commented out in apbs.info any reference to python,
including
the patch and I got apbs deb and working.
Dear William, would be possible to you to send me your apbs.info and
apbs.patch from sw64/ as well as your apbs deb package?
Many thanks in advance.
Alan
On Fri, Jul 31, 2009 at 19:35, Alexander Hansen alexanderk.han...@gmail.com
wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
William Scott wrote:
There's something funny going on in the install script. For one
thing,
it's installing files in
/sw/src/fink.build/root-apbs-1.1.0-2/sw/src/fink.build/
apbs-1.1.0-2/
I also found the ordering a bit suspect:
make install DESTDIR=%d
rm -Rf **/CVS # fink validate complains if this junk is left
behind.
# rm -Rf **/.svn # fink validate complains if this junk is left
behind.
mkdir -p %i/share/%n
mkdir -p %i/lib
I'd have assumed that we'd want to create those directories
before 'make
install'.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkpzNMMACgkQB8UpO3rKjQ9ATgCeK9rkwdv7mt61pFn/rdc4RRwu
zPEAniLUCPlwooATD+lGYN9Fd+2w6cto
=V8ih
-END PGP SIGNATURE-
I'll be happy to change anything, but in my hands it works, and
validates:
% fink -v validate apbs_1.1.0-2_darwin-x86_64.deb
apbs-dev_1.1.0-2_darwin-x86_64.deb
Validating .deb file apbs_1.1.0-2_darwin-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/
It doesn't work here (10.5.7/i386)--I get an identical error to Alan.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkpzOVcACgkQB8UpO3rKjQ8DhACfbIuQE5rffn1Qn/6lAI0wc5hy
cngAoKMDRmgsyg53OZLJ9Kwf3zvGyAhM
=350/
-END PGP SIGNATURE-
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
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Re: [Fink-users] failed to install apbs
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
This corrects the problem you found.
However there are some additional problems in that it tries to install
the examples, doc and tools directly into /sw/share, so I need to fix
that as well.
On Aug 1, 2009, at 6:11 AM, Alan wrote:
Hi there,
Well, I found this:
find /sw/src/fink.build | grep site
/sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/
@INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly
being
replaced in apbs.info:
sed 's|@INSTALL_DIR@|%d|g' %{PatchFile} | patch -p1
In a test, I commented out in apbs.info any reference to python,
including
the patch and I got apbs deb and working.
Dear William, would be possible to you to send me your apbs.info and
apbs.patch from sw64/ as well as your apbs deb package?
Many thanks in advance.
Alan
On Fri, Jul 31, 2009 at 19:35, Alexander Hansen alexanderk.han...@gmail.com
wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
William Scott wrote:
There's something funny going on in the install script. For one
thing,
it's installing files in
/sw/src/fink.build/root-apbs-1.1.0-2/sw/src/fink.build/
apbs-1.1.0-2/
I also found the ordering a bit suspect:
make install DESTDIR=%d
rm -Rf **/CVS # fink validate complains if this junk is left
behind.
# rm -Rf **/.svn # fink validate complains if this junk is left
behind.
mkdir -p %i/share/%n
mkdir -p %i/lib
I'd have assumed that we'd want to create those directories
before 'make
install'.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkpzNMMACgkQB8UpO3rKjQ9ATgCeK9rkwdv7mt61pFn/rdc4RRwu
zPEAniLUCPlwooATD+lGYN9Fd+2w6cto
=V8ih
-END PGP SIGNATURE-
I'll be happy to change anything, but in my hands it works, and
validates:
% fink -v validate apbs_1.1.0-2_darwin-x86_64.deb
apbs-dev_1.1.0-2_darwin-x86_64.deb
Validating .deb file apbs_1.1.0-2_darwin-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/
It doesn't work here (10.5.7/i386)--I get an identical error to Alan.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkpzOVcACgkQB8UpO3rKjQ8DhACfbIuQE5rffn1Qn/6lAI0wc5hy
cngAoKMDRmgsyg53OZLJ9Kwf3zvGyAhM
=350/
-END PGP SIGNATURE-
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
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Re: [Fink-users] failed to install apbs
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
This corrects the problem you found.
However there are some additional problems in that it tries to install
the examples, doc and tools directly into /sw/share, so I need to fix
that as well.
Also, there is a problem with the source tarball. I get a checksum
mismatch (same after repeated downloads):
The checksum of the file apbs-1.1.0-source.tar.gz of package apbs-1.1.0-3 is
incorrect. The most likely cause for this is a corrupted or incomplete
download
Expected: 8b844ba848cf853da712bbbf9f2e1553
Actual: MD5(ca31ba09714e4fc9acce91e7961569cd)
SHA1(7274a3a896da551f2bb689bb32ea5c852cbd32bb)
And the patch does not apply:
sed 's|@INSTALL_DIR@|/sw/src/fink.build/root-apbs-1.1.0-3|g'
/sw/fink/dists/unstable/main/finkinfo/sci/apbs.patch | patch -p1
patching file tools/python/Makefile.in
Hunk #1 FAILED at 52.
Hunk #2 FAILED at 234.
The reason is that in the source file there is
${top_builddir}/contrib/blas/.libs/libapbsblas.a, whereas the patch file
talks about ${top_builddir}/contrib/lib/libapbsblas.a.
--
Martin
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Re: [Fink-users] failed to install apbs
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$${prefix}/lib/python${PY_VERSION}/site-
packages
should be
+sitepk...@install_dir@${prefix}/lib/python${PY_VERSION}/site-
packages
This corrects the problem you found.
However there are some additional problems in that it tries to
install the examples, doc and tools directly into /sw/share, so I
need to fix that as well.
Also, there is a problem with the source tarball. I get a checksum
mismatch (same after repeated downloads):
The checksum of the file apbs-1.1.0-source.tar.gz of package
apbs-1.1.0-3 is
incorrect. The most likely cause for this is a corrupted or incomplete
download
Expected: 8b844ba848cf853da712bbbf9f2e1553
Actual: MD5(ca31ba09714e4fc9acce91e7961569cd)
SHA1(7274a3a896da551f2bb689bb32ea5c852cbd32bb)
And the patch does not apply:
sed 's|@INSTALL_DIR@|/sw/src/fink.build/root-apbs-1.1.0-3|g' /sw/
fink/dists/unstable/main/finkinfo/sci/apbs.patch | patch -p1
patching file tools/python/Makefile.in
Hunk #1 FAILED at 52.
Hunk #2 FAILED at 234.
The reason is that in the source file there is ${top_builddir}/
contrib/blas/.libs/libapbsblas.a, whereas the patch file talks about
${top_builddir}/contrib/lib/libapbsblas.a.
--
Martin
Thanks. Looks like what was on the apbs site is different than what
is on the fink server. Another day of my life wasted.
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Re: [Fink-users] failed to install apbs
Hopefully it will work now. (revision 4)
On Sat, August 1, 2009 3:48 pm, Martin Costabel wrote:
William G. Scott wrote:
It turns out there is a typo on line 38 of the patch file
+sitepk...@install_dir$${prefix}/lib/python${PY_VERSION}/site-packages
should be
+sitepk...@install_dir@${prefix}/lib/python${PY_VERSION}/site-packages
This corrects the problem you found.
However there are some additional problems in that it tries to install
the examples, doc and tools directly into /sw/share, so I need to fix
that as well.
Also, there is a problem with the source tarball. I get a checksum
mismatch (same after repeated downloads):
The checksum of the file apbs-1.1.0-source.tar.gz of package apbs-1.1.0-3
is
incorrect. The most likely cause for this is a corrupted or incomplete
download
Expected: 8b844ba848cf853da712bbbf9f2e1553
Actual: MD5(ca31ba09714e4fc9acce91e7961569cd)
SHA1(7274a3a896da551f2bb689bb32ea5c852cbd32bb)
And the patch does not apply:
sed 's|@INSTALL_DIR@|/sw/src/fink.build/root-apbs-1.1.0-3|g'
/sw/fink/dists/unstable/main/finkinfo/sci/apbs.patch | patch -p1
patching file tools/python/Makefile.in
Hunk #1 FAILED at 52.
Hunk #2 FAILED at 234.
The reason is that in the source file there is
${top_builddir}/contrib/blas/.libs/libapbsblas.a, whereas the patch file
talks about ${top_builddir}/contrib/lib/libapbsblas.a.
--
Martin
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
--
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Re: [Fink-users] failed to install apbs
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Alan wrote:
Dear William,
My system is Mac OSX 10.5.7 with Fink 64 bits updated and I use
zsh-templates from svn.
I am trying:
fink install apbs, and it fails with:
[snip]
/bin/rm -rf /sw/src/fink.build/root-apbs-1.1.0-2
/bin/mkdir -p /sw/src/fink.build/root-apbs-1.1.0-2/sw
/bin/mkdir -p /sw/src/fink.build/root-apbs-1.1.0-2/DEBIAN
/usr/sbin/chown -R root:admin /sw/src/fink.build/root-apbs-1.1.0-2
/var/tmp/tmp.2.h0L77s
#
#
# #
# /etc/zshenv #
# #
#
#
# File: /etc/zshenv
# Version: 2.0.0
###
# Created by William G. Scott on January 2, 2009.
# Copyright (c) . All rights reserved.
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2 of the License, or
#(at your option) any later version.
#
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with this program; if not, write to the Free Software
#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
02110-1301
#USA
#
#cf. URL: http://www.fsf.org/licensing/licenses/gpl.html
#
##
##
## Define the minimal $PATH
###
##
# This file is always read, even with zsh -f .
# Therefore this file should contain only directives that cannot be over-
# ridden with zsh -f
#
# Uncomment for debug
# print reading /etc/zshenv with $0
#
# Create the minimal $PATH and $MANPATH assignments:
if [[ -x /usr/libexec/path_helper ]]; then
eval $(/usr/libexec/path_helper -s)
fi
##
##
Define $ZDOT
##
# Uncomment to assign $ZDOT as appropriate
# ZDOT=/Library/init/zsh ; export ZDOT
# otherwise, use the following assignment:
if [[ -z $ZDOT -d /Library/init/zsh ]]; then
ZDOT=/Library/init/zsh ; export ZDOT
elif [[ -z $ZDOT -d $HOME/Library/init/zsh ]]; then
ZDOT=$HOME/Library/init/zsh ; export ZDOT
elif [[ -d /etc/zsh/init/zsh ]]; then
ZDOT=/etc/zsh/init/zsh ; export ZDOT
fi
##
##
#zshenv.d
##
##
# Put any additional directives for the systemwide zshenv in files within
# ${ZDOT}/zshenv.d
# See ${ZDOT}/zshenv.d/README for additional information. In general, you
# shouldn't need to add in anything.
if [[ -d ${ZDOT}/zshenv.d ]]; then
foreach file in $(command ls ${ZDOT}/zshenv.d/* | grep -v disabled |
grep -v README )
source $file
end
fi
##
# The user's own directives can be put into ~/.zshenv
#!/bin/zsh -efv
make install DESTDIR=/sw/src/fink.build/root-apbs-1.1.0-2
Making install in contrib
Making install in maloc
Making install in src
Making install in base
Making install in .
cp -p ../../src/base/maloc/*.h ../aaa_inc/maloc/.
make[6]: Nothing to be done for `install-exec-am'.
make[6]: Nothing to be done for `install-data-am'.
Making install in vsys
Making install in .
cp -p ../../src/vsys/maloc/*.h ../aaa_inc/maloc/.
make[6]: Nothing to be done for `install-exec-am'.
make[6]: Nothing to be done for
Re: [Fink-users] failed to install apbs
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 William Scott wrote: There's something funny going on in the install script. For one thing, it's installing files in /sw/src/fink.build/root-apbs-1.1.0-2/sw/src/fink.build/apbs-1.1.0-2/ I also found the ordering a bit suspect: make install DESTDIR=%d rm -Rf **/CVS # fink validate complains if this junk is left behind. # rm -Rf **/.svn # fink validate complains if this junk is left behind. mkdir -p %i/share/%n mkdir -p %i/lib I'd have assumed that we'd want to create those directories before 'make install'. - -- Alexander Hansen Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkpzNMMACgkQB8UpO3rKjQ9ATgCeK9rkwdv7mt61pFn/rdc4RRwu zPEAniLUCPlwooATD+lGYN9Fd+2w6cto =V8ih -END PGP SIGNATURE- I'll be happy to change anything, but in my hands it works, and validates: % fink -v validate apbs_1.1.0-2_darwin-x86_64.deb apbs-dev_1.1.0-2_darwin-x86_64.deb Validating .deb file apbs_1.1.0-2_darwin-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/ It doesn't work here (10.5.7/i386)--I get an identical error to Alan. - -- Alexander Hansen Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkpzOVcACgkQB8UpO3rKjQ8DhACfbIuQE5rffn1Qn/6lAI0wc5hy cngAoKMDRmgsyg53OZLJ9Kwf3zvGyAhM =350/ -END PGP SIGNATURE- -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] failed to install apbs
There's something funny going on in the install script. For one thing, it's installing files in /sw/src/fink.build/root-apbs-1.1.0-2/sw/src/fink.build/apbs-1.1.0-2/ I also found the ordering a bit suspect: make install DESTDIR=%d rm -Rf **/CVS # fink validate complains if this junk is left behind. # rm -Rf **/.svn # fink validate complains if this junk is left behind. mkdir -p %i/share/%n mkdir -p %i/lib I'd have assumed that we'd want to create those directories before 'make install'. - -- Alexander Hansen Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkpzNMMACgkQB8UpO3rKjQ9ATgCeK9rkwdv7mt61pFn/rdc4RRwu zPEAniLUCPlwooATD+lGYN9Fd+2w6cto =V8ih -END PGP SIGNATURE- I'll be happy to change anything, but in my hands it works, and validates: % fink -v validate apbs_1.1.0-2_darwin-x86_64.deb apbs-dev_1.1.0-2_darwin-x86_64.deb Validating .deb file apbs_1.1.0-2_darwin-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/ -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
