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On 9/30/11 8:43 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: 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
>
libmmdb.dylib seems to be the culprit. You should be able to work
around the issue by installing mmdb-dev.
It looks like ccp4 is missing a build dependency on mmdb-dev, and
possibly a dependency on mmdb.
- --
Alexander Hansen
Fink User Liaison
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