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
> `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 just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vfetk.h' with
> `src/fem/apbs/vfetk.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpee.h' with
> `src/fem/apbs/vpee.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./apolparm.h' with
> `src/generic/apbs/apolparm.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./femparm.h' with
> `src/generic/apbs/femparm.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./mgparm.h' with
> `src/generic/apbs/mgparm.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./nosh.h' with
> `src/generic/apbs/nosh.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./pbeparm.h' with
> `src/generic/apbs/pbeparm.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vacc.h' with
> `src/generic/apbs/vacc.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./valist.h' with
> `src/generic/apbs/valist.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vatom.h' with
> `src/generic/apbs/vatom.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcap.h' with
> `src/generic/apbs/vcap.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vclist.h' with
> `src/generic/apbs/vclist.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vgreen.h' with
> `src/generic/apbs/vgreen.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vhal.h' with
> `src/generic/apbs/vhal.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vparam.h' with
> `src/generic/apbs/vparam.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpbe.h' with
> `src/generic/apbs/vpbe.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vstring.h' with
> `src/generic/apbs/vstring.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vunit.h' with
> `src/generic/apbs/vunit.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vgrid.h' with
> `src/mg/apbs/vgrid.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmgrid.h' with
> `src/mg/apbs/vmgrid.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vopot.h' with
> `src/mg/apbs/vopot.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpmg.h' with
> `src/mg/apbs/vpmg.h'
> cp: will not overwrite just-created
> `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpmgp.h' with
> `src/mg/apbs/vpmgp.h'
> ### execution of /var/tmp/tmp.2.awaCJH failed, exit code 1
> Removing runtime build-lock...
> Removing build-lock package...
> /sw/bin/dpkg-lockwait -r fink-buildlock-apbs-1.1.0-4
> (Reading database ... 83144 files and directories currently installed.)
> Removing fink-buildlock-apbs-1.1.0-4 ...
> Failed: phase installing: apbs-1.1.0-4 failed
>
>
> On Sun, Aug 2, 2009 at 02:45, William Scott <wgsc...@chemistry.ucsc.edu>wrote:
>
>>
>> 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/
>>
>>
>>
>
>
> --
> 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<<
>
--
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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