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 <[email protected]> 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 <[email protected] >> >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<< ------------------------------------------------------------------------------ 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. 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