[Bug 472150] Review Request: coot - crystallographic macromolecular building toolkit

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https://bugzilla.redhat.com/show_bug.cgi?id=472150





--- Comment #3 from Adam Huffman <bloch at verdurin.com>  2008-11-20 06:05:56 EDT ---
Have just updated to new mmdb and latest version of refmac-dictionary.

There's still a problem building coot:

(cd .libs && rm -f libcoot-shelx.so.0 && ln -s libcoot-shelx.so.0.0.0
libcoot-shelx.so.0)
(cd .libs && rm -f libcoot-shelx.so && ln -s libcoot-shelx.so.0.0.0
libcoot-shelx.so)
creating libcoot-shelx.la
(cd .libs && rm -f libcoot-shelx.la && ln -s ../libcoot-shelx.la
libcoot-shelx.la)
/bin/sh ../libtool --tag=CXX   --mode=link g++ -DHAVE_GSL 
-DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-fno-strict-aliasing   -o testshelxreader test-shelx-reader.o
./libcoot-shelx.la ./libcoot-coord-utils.la ./libcoot-utils.la -lclipper
-lsrfftw -lsfftw -lm -lmmdb -lgpp4   -lmmdb   
/bin/sh ../libtool --tag=CXX   --mode=link g++ -DHAVE_GSL 
-DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-fno-strict-aliasing   -o testcootutils test-utils.o ./libcoot-shelx.la
./libcoot-coord-utils.la ./libcoot-utils.la -lclipper -lsrfftw -lsfftw -lm
-lmmdb -lgpp4   -lmmdb   
g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -fno-strict-aliasing -o
.libs/testshelxreader test-shelx-reader.o  ./.libs/libcoot-shelx.so
./.libs/libcoot-coord-utils.so ./.libs/libcoot-utils.so -lclipper -lsrfftw
-lsfftw -lm -lgpp4 -lmmdb
g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -fno-strict-aliasing -o
.libs/testcootutils test-utils.o  ./.libs/libcoot-shelx.so
./.libs/libcoot-coord-utils.so ./.libs/libcoot-utils.so -lclipper -lsrfftw
-lsfftw -lm -lgpp4 -lmmdb
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::SetSpaceGroup(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::ReadCoorFile(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetAtom(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFStruct::GetReal(double&, char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFFile::ReadMMCIFFile(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetModel(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::WriteMMDBF(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFLoop::GetReal(double&, char*, int, unsigned
char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetResidue(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFData::GetLoop(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFData::GetStructure(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetChain(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `FirstOccurence(char*, char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFLoop::GetInteger(int&, char*, int, unsigned
char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFLoop::GetString(char*, int, int&)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::WriteCIFASCII(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFStruct::GetString(char*, int&)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::WritePDBASCII(char*, unsigned char)'
collect2: ld returned 1 exit status
make[1]: *** [testshelxreader] Error 1
make[1]: *** Waiting for unfinished jobs....
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::SetSpaceGroup(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::ReadCoorFile(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetAtom(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFStruct::GetReal(double&, char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFFile::ReadMMCIFFile(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetModel(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::WriteMMDBF(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFLoop::GetReal(double&, char*, int, unsigned
char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetResidue(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFData::GetLoop(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFData::GetStructure(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBCoorManager::GetChain(char*)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `FirstOccurence(char*, char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFLoop::GetInteger(int&, char*, int, unsigned
char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFLoop::GetString(char*, int, int&)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::WriteCIFASCII(char*, unsigned char)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMCIFStruct::GetString(char*, int&)'
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../lib64/libclipper.so:
undefined reference to `CMMDBFile::WritePDBASCII(char*, unsigned char)'
collect2: ld returned 1 exit status
make[1]: *** [testcootutils] Error 1
make[1]: Leaving directory `/home/adam/rpmbuild/BUILD/coot-0.5/coot-utils'
make: *** [all-recursive] Error 1
error: Bad exit status from /var/tmp/rpm-tmp.53148 (%build)


RPM build errors:
    Bad exit status from /var/tmp/rpm-tmp.53148 (%build)

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