Sorry for this. I will have to fix this over the weekend. They keep messing
with their tar ball
upstream, too, without changing the revision number, which is a stage 4B
metastatic
brain tumor of a headache.
Also, it isn't the mmdb-dev dependency.
Bill
On Sep 30, 2011, at 5:43 AM, Tim Schulte wrote:
> First of all, thanks for your help.
> Secondly, the error messages I have found are pasted below.
> If you need I can send as well the whole log file.
>
>
>
> Am 9/30/11 1:52 PM, schrieb Alexander Hansen:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> On 9/30/11 4:55 AM, Tim Schulte wrote:
>>> Dear fink users and developers, I have tried to update the CCP4
>>> software package to the latest version, but got following error
>>> messages. Any help is appreciated.
>>>
>>> *Error after downloading*
>>>
>>> The checksum of the file ccp4-6.2.0-core-src.tar.gz of package
>>> ccp4-6.2.0-102 is incorrect. The most likely cause for this is a
>>> corrupted or incomplete download Expected:
>>> bfb843b62401816942cafeb94cdeb051 Actual:
>>> MD5(1a087d3310d70501ac370804a11f341d)
>>> SHA1(8d4f00b9d8d3f595157f78ab2214bf7ac8d6b974) It is recommended
>>> that you download it again. How do you want to proceed?
>>>
>>> (1) Give up (2) Delete it and download again (3) Assume it
>>> is a partial download and try to continue (4) Don't download,
>>> use existing file
>>>
>>>
>>>
>>> *Error message when installing the package using option (4):*
>>>
>>> ranlib ../liblapack.a ### execution of /var/tmp/tmp.2.0TUY2S
>>> failed, exit code 2 Removing runtime build-lock... Removing
>>> build-lock package... /sw/bin/dpkg-lockwait -r
>>> fink-buildlock-ccp4-6.2.0-102 (Reading database ... 112338 files
>>> and directories currently installed.) Removing
>>> fink-buildlock-ccp4-6.2.0-102 ... Reading buildlock packages...
>> <snip>
>>
>>> Failed: phase compiling: ccp4-6.2.0-102 failed
>>>
>>> *System information* Package manager version: 0.31.2 Distribution
>>> version: selfupdate-rsync Thu Sep 29 21:15:50 2011, 10.6, i386
>>> Trees: local/main stable/main stable/crypto Xcode: 3.2.6
>>>
>>>
>>>
>> The incorrect source MD5 and your build failure are separate issues.
>>
>> We need to see a few lines more output before what you have posted.
>> fink now builds packages using multiple threads, but one penalty for
>> that is that a failure in one thread won't necessarily end the others.
>> Look for an earlier error message.
> Here are some errors:
> ...
>
> g++ -dynamiclib -single_module ${wl}-undefined ${wl}dynamic_lookup -o
> .libs/libssm.0.0.0.dylib .libs/ssm_superpose.o .libs/ss_csia.o
> .libs/ss_vxedge.o .libs/ssm_align.o .libs/ss_graph.o
> -L/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/src -lmmdb -lccp4c -lm
> -install_name /sw/lib/ccp4-6.2.0/libssm.0.dylib -compatibility_version 1
> -current_version 1.0
> ld: library not found for -lmmdb
> collect2: ld returned 1 exit status
> make[1]: [libssm.la] Error 1 (ignored)
> /bin/sh ./libtool --tag=CXX --mode=link g++ -O2
> -L/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/src -lmmdb -lccp4c
> -L/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/src -lccp4c -o superpose
> superpose.o libssm.la -lm
> gcc -DHAVE_CONFIG_H -I. -I. -I. -I. -I./../fftw -I. -O2 -DGFORTRAN
> -DPROTOTYPE -MT fni_15.lo -MD -MP -MF .deps/fni_15.Tpo -c fni_15.c
> -fno-common -DPIC -o .libs/fni_15.o
> libtool: link: cannot find the library `libssm.la' or unhandled argument
> `libssm.la'
> make[1]: [superpose] Error 1 (ignored)
> gcc -DHAVE_CONFIG_H -I. -I. -I. -I. -I./../fftw -I. -O2 -DGFORTRAN
> -DPROTOTYPE -MT fni_15.lo -MD -MP -MF .deps/fni_15.Tpo -c fni_15.c -o
> fni_15.o >/dev/null 2>&1
> /bin/sh ./libtool --tag=CXX --mode=link g++ -O2
> -L/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/src -lmmdb -lccp4c
> -L/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/src -lccp4c -o libssm.la
> -rpath /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib ssm_superpose.lo
> ss_csia.lo ss_vxedge.lo ssm_align.lo ss_graph.lo -lm
> gfortran -O2 -fno-second-underscore -c ztpmv.f
> if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.
> -I. -I./../fftw -I. -O2 -DGFORTRAN -DPROTOTYPE -MT fni_16.lo -MD -MP -MF
> ".deps/fni_16.Tpo" -c -o fni_16.lo fni_16.c; \
> then mv -f ".deps/fni_16.Tpo" ".deps/fni_16.Plo"; else rm -f
> ".deps/fni_16.Tpo"; exit 1; fi
> g++ -dynamiclib -single_module ${wl}-undefined ${wl}dynamic_lookup -o
> .libs/libssm.0.0.0.dylib .libs/ssm_superpose.o .libs/ss_csia.o
> .libs/ss_vxedge.o .libs/ssm_align.o .libs/ss_graph.o
> -L/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/lib/src -lmmdb -lccp4c -lm
> -install_name /sw/lib/ccp4-6.2.0/libssm.0.dylib -compatibility_version 1
> -current_version 1.0
> ld: library not found for -lmmdb
> collect2: ld returned 1 exit status
> make[1]: *** [libssm.la] Error 1
> make: *** [ssm] Error 2
> make: *** Waiting for unfinished jobs....
> ( cd src; make lapackccp4)
> gfortran -O2 -fno-second-underscore -c ztrsv.f
> gcc -DHAVE_CONFIG_H -I. -I. -I. -I. -I./../fftw -I. -O2 -DGFORTRAN
> -DPROTOTYPE -MT fni_16.lo -MD -MP -MF .deps/fni_16.Tpo -c fni_16.c
> -fno-common -DPIC -o .libs/fni_16.o
>
> ...
>
>> - -- Alexander Hansen
>> Fink User Liaison
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.10 (Darwin)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>
>> iEYEARECAAYFAk6FrWgACgkQB8UpO3rKjQ8kFACfcfd/JDdQbf+2qKXNbEKTyHyY
>> IzoAoKG6hNNrnYhBD87Exm/Dc5ayESKy
>> =RP1M
>> -----END PGP SIGNATURE-----
>
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
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