Source: rdkit
Version: 201909.1-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200402 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/build-12'
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o rdkit_io.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_io.c
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o mol_op.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_murckoscaffold’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:263:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 263 | CROMol scaffold = MolMurckoScaffold(mol);
> | ^~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_hash’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:283:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 283 | char *res = pnstrdup(str, len);
> | ^~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_nm_hash’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:298:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 298 | char *str = computeNMMolHash(mol, opts);
> | ^~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:300:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 300 | char *res = pnstrdup(str, strlen(str));
> | ^~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:293:7: warning: unused variable
> ‘len’ [-Wunused-variable]
> 293 | int len;
> | ^~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function
> ‘mol_adjust_query_properties’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:313:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 313 | char *data = PG_GETARG_CSTRING(1);
> | ^~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:317:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 317 | Mol *res = deconstructROMol(adj);
> | ^~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_to_svg’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:332:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 332 | char *legend = PG_GETARG_CSTRING(1);
> | ^~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_smiles’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:356:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 356 | char *res = pnstrdup(str, strlen(str));
> | ^~~~
> In file included from /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:34:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function
> ‘fmcs_mol2s_transition’:
> /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of
> ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer
> from integer without a cast [-Wint-conversion]
> 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value)
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:408:18: note: in expansion of
> macro ‘PG_GETARG_DATUM’
> 408 | CROMol mol = PG_GETARG_DATUM(1);
> | ^~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:424:5: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 424 | text *ts = (text *)palloc(ts_size); // new return value
> | ^~~~
> In file included from /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:34:
> /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of
> ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer
> from integer without a cast [-Wint-conversion]
> 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value)
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:436:18: note: in expansion of
> macro ‘PG_GETARG_DATUM’
> 436 | CROMol mol = PG_GETARG_DATUM(1);
> | ^~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:444:5: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 444 | char *smiles = makeMolText(mol, &len, false, false);
> | ^~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mols’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:482:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 482 | int32 ts_size = VARHDRSZ + strlen(str);
> | ^~~~~
> In file included from /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:34:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol_transition’:
> /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of
> ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer
> from integer without a cast [-Wint-conversion]
> 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value)
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:504:18: note: in expansion of
> macro ‘PG_GETARG_DATUM’
> 504 | CROMol mol = PG_GETARG_DATUM(1);
> | ^~~~~~~~~~~~~~~
> In file included from /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:33:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:511:21: warning: cast from pointer
> to integer of different size [-Wpointer-to-int-cast]
> 511 | PG_RETURN_INT32((int32)lst);
> | ^
> /usr/include/postgresql/12/server/postgres.h:479:36: note: in definition of
> macro ‘Int32GetDatum’
> 479 | #define Int32GetDatum(X) ((Datum) (X))
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:511:5: note: in expansion of macro
> ‘PG_RETURN_INT32’
> 511 | PG_RETURN_INT32((int32)lst);
> | ^~~~~~~~~~~~~~~
> In file included from /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:34:
> /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of
> ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer
> from integer without a cast [-Wint-conversion]
> 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value)
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:515:18: note: in expansion of
> macro ‘PG_GETARG_DATUM’
> 515 | CROMol mol = PG_GETARG_DATUM(1);
> | ^~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function
> ‘fmcs_smiles_transition’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:388:1: warning: control reaches
> end of non-void function [-Wreturn-type]
> 388 | }
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol_transition’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:523:1: warning: control reaches
> end of non-void function [-Wreturn-type]
> 523 | }
> | ^
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o bfp_op.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_op.c
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o sfp_op.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/sfp_op.c
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o rxn_op.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rxn_op.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rxn_op.c:164:1: warning: multi-line comment
> [-Wcomment]
> 164 | // /* keep compiler quiet - no extra ; */
> \
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rxn_op.c: In function ‘reaction_to_svg’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rxn_op.c:179:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 179 | bool highlightByReactants = PG_GETARG_BOOL(1);
> | ^~~~
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o rdkit_gist.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘soergeldistsign’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:240:3: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 240 | uint8 *as = (uint8 *)VARDATA(a);
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘soergeldist’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:275:16: warning: implicit
> declaration of function ‘floor’ [-Wimplicit-function-declaration]
> 275 | return (int) floor(10000*soergeldistsign(a, b));
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:275:16: warning: incompatible
> implicit declaration of built-in function ‘floor’
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:42:1: note: include ‘<math.h>’
> or provide a declaration of ‘floor’
> 41 | #include "bitstring.h"
> +++ |+#include <math.h>
> 42 |
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:262:10: warning: unused
> variable ‘d’ [-Wunused-variable]
> 262 | double d;
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘gmol_consistent’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:526:7: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 526 | uint8 *k = (uint8 *)VARDATA(key);
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:538:7: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 538 | uint8 *k = (uint8 *)VARDATA(key);
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:570:7: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 570 | uint8 *k = (uint8 *)VARDATA(key);
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c: In function
> ‘rdkit_consistent’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:658:3: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 658 | int siglen = SIGLEN(query);
> | ^~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:673:5: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 673 | uint8 *k = (uint8 *)VARDATA(key);
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘gsfp_consistent’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:708:3: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 708 | int sum, overlapSum, overlapN;
> | ^~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:714:3: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 714 | int nKey = (ISALLTRUE(key)) ?
> | ^~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c: In function
> ‘greaction_consistent’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:787:7: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 787 | uint8 *k = (uint8 *)VARDATA(key);
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:804:7: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 804 | uint8 *k = (uint8 *)VARDATA(key);
> | ^~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:832:7: warning: ISO C90
> forbids mixed declarations and code [-Wdeclaration-after-statement]
> 832 | uint8 *k = (uint8 *)VARDATA(key);
> | ^~~~~
> At top level:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:646:1: warning:
> ‘rdkit_consistent’ defined but not used [-Wunused-function]
> 646 | rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, bytea
> *key, bytea *query)
> | ^~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:261:1: warning: ‘soergeldist’
> defined but not used [-Wunused-function]
> 261 | soergeldist(bytea *a, bytea *b) {
> | ^~~~~~~~~~~
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o bfp_gist.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_gist.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_gist.c: In function ‘merge_key’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_gist.c:699:3: warning: ISO C90 forbids
> mixed declarations and code [-Wdeclaration-after-statement]
> 699 | int siglen = GBFP_INNER_SIGLEN(result);
> | ^~~
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o bfp_gin.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_gin.c
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o low_gist.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/low_gist.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/low_gist.c: In function ‘gslfp_consistent’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/low_gist.c:410:30: warning: implicit
> declaration of function ‘searchSfpCache’ [-Wimplicit-function-declaration]
> 410 | fcinfo->flinfo->fn_extra = searchSfpCache(
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/low_gist.c:410:28: warning: assignment to
> ‘void *’ from ‘int’ makes pointer from integer without a cast
> [-Wint-conversion]
> 410 | fcinfo->flinfo->fn_extra = searchSfpCache(
> | ^
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o guc.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/guc.c
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o cache.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/cache.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/cache.c: In function ‘createCache’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/cache.c:312:17: warning: assignment
> discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
> 312 | methodsOrig = ctx->methods;
> | ^
> g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
> -Wno-unused-function -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o adapter.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/adapter.cpp
> gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code
> -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit
> -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal
> -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2
> -I/usr/include/mit-krb5 -fPIC -c -o bitstring.o
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bitstring.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bitstring.c: In function ‘bitstringUnion’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bitstring.c:72:7: warning: unused variable
> ‘i’ [-Wunused-variable]
> 72 | int i;
> | ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bitstring.c: In function
> ‘bitstringIntersection’:
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bitstring.c:106:7: warning: unused variable
> ‘i’ [-Wunused-variable]
> 106 | int i;
> | ^
> g++ -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security
> -fno-strict-aliasing -fwrapv -fexcess-precision=standard
> -Wno-format-truncation -Wno-stringop-truncation -g -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security
> -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -fPIC -shared -o rdkit.so rdkit_io.o mol_op.o bfp_op.o
> sfp_op.o rxn_op.o rdkit_gist.o bfp_gist.o bfp_gin.o low_gist.o guc.o cache.o
> adapter.o bitstring.o -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now
> -L/usr/lib/llvm-10/lib -L/usr/lib/x86_64-linux-gnu/mit-krb5 -Wl,--as-needed
> -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
> -L/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//lib -lRDKitMolDraw2D
> -lRDKitMolTransforms -lRDKitMolHash -lRDKitFMCS -lRDKitChemReactions
> -lRDKitChemTransforms -lRDKitFileParsers -lRDKitSmilesParse
> -lRDKitFingerprints -lRDKitSubgraphs -lRDKitDescriptors -lRDKitPartialCharges
> -lRDKitSubstructMatch -lRDKitGraphMol -lRDKitEigenSolvers -lRDKitDataStructs
> -lRDKitDepictor -lRDKitRDGeometryLib -lRDKitRDGeneral -pthread
> sed -e's/@RDKIT_PG_BFP_GIST_FETCH@/FUNCTION 9 gbfp_fetch (internal),/;' \
> -e's/@RDKIT_GIN_BFP_TRICONSISTENT@/FUNCTION 6
> gin_bfp_triconsistent(internal, int2, bfp, int4, internal, internal,
> internal),/' \
> -e's/@RDKIT_PARALLEL_SAFE@/PARALLEL SAFE/' \
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--3.8.sql
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o rdkit_io.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_io.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o mol_op.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:388:1: warning: non-void function
> does not return a value in all control paths [-Wreturn-type]
> }
> ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:408:12: warning: incompatible
> integer to pointer conversion initializing 'CROMol' (aka 'void *') with an
> expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion]
> CROMol mol = PG_GETARG_DATUM(1);
> ^ ~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:436:12: warning: incompatible
> integer to pointer conversion initializing 'CROMol' (aka 'void *') with an
> expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion]
> CROMol mol = PG_GETARG_DATUM(1);
> ^ ~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:504:12: warning: incompatible
> integer to pointer conversion initializing 'CROMol' (aka 'void *') with an
> expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion]
> CROMol mol = PG_GETARG_DATUM(1);
> ^ ~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:515:12: warning: incompatible
> integer to pointer conversion initializing 'CROMol' (aka 'void *') with an
> expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion]
> CROMol mol = PG_GETARG_DATUM(1);
> ^ ~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/mol_op.c:523:1: warning: non-void function
> does not return a value in all control paths [-Wreturn-type]
> }
> ^
> 6 warnings generated.
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o bfp_op.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_op.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o sfp_op.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/sfp_op.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o rxn_op.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rxn_op.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o rdkit_gist.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o bfp_gist.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_gist.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o bfp_gin.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/bfp_gin.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o low_gist.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/low_gist.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/low_gist.c:410:30: warning: implicit
> declaration of function 'searchSfpCache' is invalid in C99
> [-Wimplicit-function-declaration]
> fcinfo->flinfo->fn_extra = searchSfpCache(
> ^
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/low_gist.c:410:28: warning: incompatible
> integer to pointer conversion assigning to 'void *' from 'int'
> [-Wint-conversion]
> fcinfo->flinfo->fn_extra = searchSfpCache(
> ^ ~~~~~~~~~~~~~~~
> 2 warnings generated.
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o guc.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/guc.c
> /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2
> -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin
> -emit-llvm -c -o cache.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/cache.c
> /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/cache.c:312:17: warning: assigning to
> 'MemoryContextMethods *' (aka 'struct MemoryContextMethods *') from 'const
> MemoryContextMethods *' (aka 'const struct MemoryContextMethods *') discards
> qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
> methodsOrig = ctx->methods;
> ^ ~~~~~~~~~~~~
> 1 warning generated.
> /usr/bin/clang-10 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv
> -O2 -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I.
> -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server
> -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2
> -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -emit-llvm -c
> -o adapter.bc /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/adapter.cpp
> In file included from /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/adapter.cpp:54:
> /<<PKGBUILDDIR>>/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h:74:8: warning:
> 'tagAtoms' overrides a member function but is not marked 'override'
> [-Winconsistent-missing-override]
> void tagAtoms(const ROMol &mol) { tagAtoms(mol, 0.2); }
> ^
> /<<PKGBUILDDIR>>/Code/GraphMol/MolDraw2D/MolDraw2D.h:429:16: note: overridden
> virtual function is here
> virtual void tagAtoms(const ROMol &mol) { RDUNUSED_PARAM(mol); };
> ^
> 1 warning generated.
> opt-9 -module-summary -f adapter.bc -o adapter.bc
> make[2]: opt-9: Command not found
> make[2]: *** [/<<PKGBUILDDIR>>/Code/PgSQL/rdkit/Makefile:120: adapter.bc]
> Error 127
The full build log is available from:
http://qa-logs.debian.net/2020/04/02/rdkit_201909.1-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
