Dear Adrian,
The pgqsl_install.sh script is in ${CMAKE_BINARY_DIR}/Code/PgSQL/rdkit,
not in the ${CMAKE_SOURCE_DIR}/Code/PgSQL/rdkit, so you will find it in
Code/PgSQL/rdkit/pgqsl_install.sh in the directory tree where you are
actually building the RDKit.
Please get in touch if you still have trouble building the cartridge.
Kind regards,
Paolo
On 07/28/16 10:46, Adrian Jasiński wrote:
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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