Hey, I have been trying to install Coot 0.9 from source or autobuild for Ubuntu 18.04.
1) Tried autobuild script but it gives me error: https://raw.githubusercontent.com/pemsley/coot/master/build-it USE LISTS 1 Fatal Error: Can't open module file ‘lists.mod’ for reading at (1): No such file or directory compilation terminated. make: *** [qinp.o] Error 1 make: *** Waiting for unfinished jobs.... local.c: In function ‘addlabel_’: local.c:689:9: warning: variable ‘out_size’ set but not used [-Wunused-but-set-variable] size_t out_size; /* out_size is just a dummy variable */ ^~~~~~~~ local.c:688:40: warning: variable ‘justify’ set but not used [-Wunused-but-set-variable] char *err, font[128], instring[128], *justify; ^~~~~~~ local.c:683:44: warning: variable ‘last_z’ set but not used [-Wunused-but-set-variable] static double last_x = 0.0, last_y = 0.0, last_z = 0.0; 2) or using autobuild script from here: https://raw.githubusercontent.com/pemsley/coot/refinement/build-it Then it just stops at certain point but Coot is not installed. Attached is the autobuild report file. 3) Tried manually, installed all the other software according to https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=Custom_building_Coot_from_source_code Up to Clipper part, all the programs are compiled and installed in /usr/local/xtal I’m not to able to install Clipper using these command as it has problem finding mmdb2 library The final lines are: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether to enable maintainer-specific portions of Makefiles... no checking for library containing cos... -lm checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for the pthreads library -lpthreads... no checking for the pthreads library -lpthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for MMDB_CCIF_Init in -lmmdb2... no configure: error: mmdb2 library not found 4) If I try to build Coot by using guidelines from INSTALL file from downloaded Coot-0.9: First build and install mmdb and clipper. Used commands: ./configure --prefix=$HOME/crystal --with-fftw=$HOME/crystal --with-mmdb=$HOME/crystal --with-ccp4=$HOME/crystal --enable-mmdb --enable-mtz --enable-cif --enable-minimol --enable-phs To build coot, you will almost certainly need to specify the prefix for clipper and mmdb. Here is how I do it: Again getting error with mmdb2 library: checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for MMDB_CCIF_Init in -lmmdb2... no configure: error: mmdb2 library not found I do not know why Clipper can not find the mmdb2 library The library is in $HOME/crystal/lib and mmdb2 in $HOME/crystal/mmdb2 5) If I install mmdb2 and clipper through Synaptic Package then 'mmdb' has not been declared. Coot will report the error: protein_db.cpp: In member function 'bool ProteinDB::Chain::add_pdb(clipper::String)': protein_db.cpp:199:26: error: 'mmdb' has not been declared const int mmdbflags = mmdb::MMDBF_IgnoreBlankLines | mmdb::MMDBF_IgnoreDuplSeqNum | mmdb::MMDBF_IgnoreNonCoorPDBErrors | mmdb::MMDBF_IgnoreRemarks; ^~~~ In file included from /usr/include/mmdb/mmdb_coormngr.h:45:0, from /usr/include/mmdb/mmdb_selmngr.h:45, from /usr/include/mmdb/mmdb_bondmngr.h:45, from /usr/include/mmdb/mmdb_manager.h:45, from /usr/include/clipper/mmdb/clipper_mmdb.h:51, from /usr/include/clipper/minimol/minimol_io.h:49, from /usr/local/include/clipper/clipper-minimol.h:8, from protein_db.h:10, from protein_db.cpp:4: protein_db.cpp:199:32: error: expected unqualified-id before numeric constant const int mmdbflags = mmdb::MMDBF_IgnoreBlankLines | mmdb::MMDBF_IgnoreDuplSeqNum | mmdb::MMDBF_IgnoreNonCoorPDBErrors | mmdb::MMDBF_IgnoreRemarks; ^ Makefile:575: recipe for target 'protein_db.lo' failed make[1]: *** [protein_db.lo] Error 1 make[1]: Leaving directory '/home/arto/programs/coot-0.9/protein_db' Makefile:700: recipe for target 'check-recursive' failed make: *** [check-recursive] Error 1 So, it is seemingly mmdb and clipper installation problem when trying install manually but how to resolve it? But with autobuild scripts there are some other reasons. Best, Arto ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
autobuild_result
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make_report__coot
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