I'm using Ubuntu 16.04 LTS,
I successfully installed latest rdkit version 2016_03_03 from source,
but when I tried to install Cartridge I found difficulties.
Theres no good instruction in RDKit documentation how to install it.
Only info is in README file but it is not valid.
Possibly there should be some notes added to
http://www.rdkit.org/docs/Install.html or in Cartridge tab:
http://www.rdkit.org/docs/Cartridge.html
First theres no file:
pgsql_install.sh in:
\Code\PgSQL\rdkit\pgsql_install.sh (It should be accroding README file in
\Code\PgSQL\rdkit\README)
Second when I tried run "make" command I got an error:
gcc -Wall -Wmissing-prototypes -Wpointer-arith
-Wdeclaration-after-statement -Wendif-labels
-Wmissing-format-attribute -Wformat-security -fno-strict-aliasing
-fwrapv -fexcess-precision=standard -g -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -I/usr/include/mit-krb5 -fPIC -pie
-fno-omit-frame-pointer -fpic -I/usr/local/include
-I/home/adrian/mm/apps/rdkit/current/Code -DRDKITVER='"007300"'
-mpopcnt -I. -I./ -I/usr/include/postgresql/9.5/server
-I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
-D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/tcl8.6 -fPIC -c
-o mol_op.o mol_op.c
mol_op.c: In function ‘mol_substruct_count’:
mol_op.c:137:3: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
bool uniquify = PG_GETARG_BOOL(2);
^
mol_op.c: In function ‘mol_formula’:
mol_op.c:203:3: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
bool separateIsotopes = PG_GETARG_BOOL(1);
^
mol_op.c: In function ‘mol_inchi’:
mol_op.c:222:3: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
char *res = pnstrdup(str, strlen(str));
^
mol_op.c: In function ‘mol_inchikey’:
mol_op.c:238:3: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
char *res = pnstrdup(str, strlen(str));
^
mol_op.c: In function ‘mol_murckoscaffold’:
mol_op.c:249:3: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
CROMol scaffold = MolMurckoScaffold(mol);
^
mol_op.c:251:3: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
Mol *res = deconstructROMol(scaffold);
^
In file included from mol_op.c:34:0:
mol_op.c: In function ‘fmcs_mol2s_transition’:
/usr/include/postgresql/9.5/server/fmgr.h:224:29: warning:
initialization makes pointer from integer without a cast
[-Wint-conversion]
#define PG_GETARG_DATUM(n) (fcinfo->arg[n])
^
mol_op.c:334:18: note: in expansion of macro ‘PG_GETARG_DATUM’
CROMol mol = PG_GETARG_DATUM(1);
^
In file included from /usr/include/postgresql/9.5/server/postgres.h:48:0,
from rdkit.h:40,
from mol_op.c:33:
mol_op.c:339:19: error: format not a string literal and no format
arguments [-Werror=format-security]
elog(WARNING, t);
^
/usr/include/postgresql/9.5/server/utils/elog.h:212:23: note: in
definition of macro ‘elog’
elog_finish(elevel, __VA_ARGS__); \
^
mol_op.c:344:5: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
char *smiles = makeMolText(mol, &len, false);
^
In file included from mol_op.c:34:0:
/usr/include/postgresql/9.5/server/fmgr.h:224:29: warning:
initialization makes pointer from integer without a cast
[-Wint-conversion]
#define PG_GETARG_DATUM(n) (fcinfo->arg[n])
^
mol_op.c:363:18: note: in expansion of macro ‘PG_GETARG_DATUM’
CROMol mol = PG_GETARG_DATUM(1);
^
In file included from /usr/include/postgresql/9.5/server/postgres.h:48:0,
from rdkit.h:40,
from mol_op.c:33:
mol_op.c:368:19: error: format not a string literal and no format
arguments [-Werror=format-security]
elog(WARNING, t);
^
/usr/include/postgresql/9.5/server/utils/elog.h:212:23: note: in
definition of macro ‘elog’
elog_finish(elevel, __VA_ARGS__); \
^
mol_op.c:373:5: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
char *smiles = makeMolText(mol, &len, false);
^
mol_op.c: In function ‘fmcs_mols’:
mol_op.c:411:3: warning: ISO C90 forbids mixed declarations and code
[-Wdeclaration-after-statement]
int32 ts_size = VARHDRSZ + strlen(str);
^
In file included from mol_op.c:34:0:
mol_op.c: In function ‘fmcs_mol_transition’:
/usr/include/postgresql/9.5/server/fmgr.h:224:29: warning:
initialization makes pointer from integer without a cast
[-Wint-conversion]
#define PG_GETARG_DATUM(n) (fcinfo->arg[n])
^
mol_op.c:432:18: note: in expansion of macro ‘PG_GETARG_DATUM’
CROMol mol = PG_GETARG_DATUM(1);
^
In file included from rdkit.h:40:0,
from mol_op.c:33:
mol_op.c:439:21: warning: cast from pointer to integer of different
size [-Wpointer-to-int-cast]
PG_RETURN_INT32((int32)lst);
^
/usr/include/postgresql/9.5/server/postgres.h:388:39: note: in
definition of macro ‘SET_4_BYTES’
#define SET_4_BYTES(value) (((Datum) (value)) & 0xffffffff)
^
/usr/include/postgresql/9.5/server/fmgr.h:298:36: note: in expansion
of macro ‘Int32GetDatum’
#define PG_RETURN_INT32(x) return Int32GetDatum(x)
^
mol_op.c:439:5: note: in expansion of macro ‘PG_RETURN_INT32’
PG_RETURN_INT32((int32)lst);
^
In file included from mol_op.c:34:0:
/usr/include/postgresql/9.5/server/fmgr.h:224:29: warning:
initialization makes pointer from integer without a cast
[-Wint-conversion]
#define PG_GETARG_DATUM(n) (fcinfo->arg[n])
^
mol_op.c:443:18: note: in expansion of macro ‘PG_GETARG_DATUM’
CROMol mol = PG_GETARG_DATUM(1);
^
mol_op.c: At top level:
mol_op.c:478:2: warning: "/*" within comment [-Wcomment]
//*--/
^
mol_op.c: In function ‘fmcs_smiles_transition’:
mol_op.c:314:1: warning: control reaches end of non-void function
[-Wreturn-type]
}
^
mol_op.c: In function ‘fmcs_mol_transition’:
mol_op.c:451:1: warning: control reaches end of non-void function
[-Wreturn-type]
}
^
cc1: some warnings being treated as errors
Makefile:88: 'mol_op.o' faild
make: *** [mol_op.o] Error 1
regards
Adrian Jasinski
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