+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/pdbalign-20030812/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/pdbalign-20030812/work.log WARNING: [license.mk] Every package should define a LICENSE. ===> Building for pdbalign-20030812 --- pdbalign.o --- --- distalign.o --- --- pdbdist.o --- --- pdbalign.o --- gcc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -c -o pdbalign.o pdbalign.c --- distalign.o --- gcc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -c -o distalign.o distalign.c --- pdbdist.o --- gcc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -c -o pdbdist.o pdbdist.c --- distalign.o --- distalign.c: In function 'ParseMSFFile': distalign.c:110:9: error: implicit declaration of function 'exit' [-Wimplicit-function-declaration] 110 | exit(1); | ^~~~ distalign.c:12:1: note: include '' or provide a declaration of 'exit' 11 | #include +++ |+#include 12 | distalign.c:110:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 110 | exit(1); | ^~~~ distalign.c:110:9: note: include '' or provide a declaration of 'exit' distalign.c:129:31: error: implicit declaration of function 'malloc' [-Wimplicit-function-declaration] 129 | { if( !(ptr=(SeqRecord*)malloc(sizeof(SeqRecord))) ) | ^~~~~~ distalign.c:129:31: note: include '' or provide a declaration of 'malloc' distalign.c:129:31: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] distalign.c:129:31: note: include '' or provide a declaration of 'malloc' distalign.c:131:13: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 131 | exit(1); | ^~~~ distalign.c:131:13: note: include '' or provide a declaration of 'exit' distalign.c:19:19: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 19 | #define _fmalloc malloc | ^~~~~~ distalign.c:164:39: note: in expansion of macro '_fmalloc' 164 | if( !(ptr->seq = (char __far*)_fmalloc(alignlen)) ) | ^~~~~~~~ distalign.c:19:19: note: include '' or provide a declaration of 'malloc' 19 | #define _fmalloc malloc | ^~~~~~ distalign.c:164:39: note: in expansion of macro '_fmalloc' 164 | if( !(ptr->seq = (char __far*)_fmalloc(alignlen)) ) | ^~~~~~~~ distalign.c:166:13: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 166 | exit(1); | ^~~~ distalign.c:166:13: note: include '' or provide a declaration of 'exit' distalign.c:178:65: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 178 | { fputs("Error: No alignment sequences found!\n",stderr); exit(1); | ^~~~ distalign.c:178:65: note: include '' or provide a declaration of 'exit' --- pdbdist.o --- pdbdist.c: In function 'ReadPDBFloat': pdbdist.c:93:14: error: type of 'begin' defaults to 'int' [-Wimplicit-int] 93 | static float ReadPDBFloat( begin, len ) | ^~~~~~~~~~~~ pdbdist.c:93:14: error: type of 'len' defaults to 'int' [-Wimplicit-int] pdbdist.c: In function 'ReadPDBInteger': pdbdist.c:108:12: error: type of 'begin' defaults to 'int' [-Wimplicit-int] 108 | static int ReadPDBInteger( begin, len ) | ^~~~~~~~~~~~~~ pdbdist.c:108:12: error: type of 'len' defaults to 'int' [-Wimplicit-int] --- distalign.o --- distalign.c: In function 'ParsePDBFile': distalign.c:360:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 360 | exit(1); | ^~~~ distalign.c:360:9: note: include '' or provide a declaration of 'exit' distalign.c:19:19: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 19 | #define _fmalloc malloc | ^~~~~~ distalign.c:363:26: note: in expansion of macro '_fmalloc' 363 | Offset = (int __far*)_fmalloc(alignlen*sizeof(int)); | ^~~~~~~~ distalign.c:19:19: note: include '' or provide a declaration of 'malloc' 19 | #define _fmalloc malloc | ^~~~~~ distalign.c:363:26: note: in expansion of macro '_fmalloc' 363 | Offset = (int __far*)_fmalloc(alignlen*sizeof(int)); | ^~~~~~~~ distalign.c:368:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 368 | exit(1); | ^~~~ distalign.c:368:9: note: include '' or provide a declaration of 'exit' distalign.c:407:21: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 407 | exit(1); | ^~~~ distalign.c:407:21: note: include '' or provide a declaration of 'exit' distalign.c: In function 'CreateDistanceSequence': distalign.c:514:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 514 | if( !(ptr=(SeqRecord*)malloc(sizeof(SeqRecord))) ) | ^~~~~~ distalign.c:514:27: note: include '' or provide a declaration of 'malloc' distalign.c:516:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 516 | exit(1); | ^~~~ distalign.c:516:9: note: include '' or provide a declaration of 'exit' distalign.c:524:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 524 | if( !(ptr->seq=(char*)malloc(alignlen)) ) | ^~~~~~ distalign.c:524:27: note: include '' or provide a declaration of 'malloc' distalign.c:526:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 526 | exit(1); | ^~~~ distalign.c:526:9: note: include '' or provide a declaration of 'exit' distalign.c: In function 'CreateEntropySequence': distalign.c:766:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 766 | if( !(ptr=(SeqRecord*)malloc(sizeof(SeqRecord))) ) | ^~~~~~ distalign.c:766:27: note: include '' or provide a declaration of 'malloc' distalign.c:768:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 768 | exit(1); | ^~~~ distalign.c:768:9: note: include '' or provide a declaration of 'exit' distalign.c:776:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 776 | if( !(ptr->seq=(char*)malloc(alignlen)) ) | ^~~~~~ distalign.c:776:27: note: include '' or provide a declaration of 'malloc' distalign.c:778:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 778 | exit(1); | ^~~~ distalign.c:778:9: note: include '' or provide a declaration of 'exit' distalign.c: In function 'CreatePairwiseSequence': distalign.c:798:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 798 | if( !(ptr=(SeqRecord*)malloc(sizeof(SeqRecord))) ) | ^~~~~~ distalign.c:798:27: note: include '' or provide a declaration of 'malloc' distalign.c:800:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 800 | exit(1); | ^~~~ distalign.c:800:9: note: include '' or provide a declaration of 'exit' distalign.c:808:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 808 | if( !(ptr->seq=(char*)malloc(alignlen)) ) | ^~~~~~ distalign.c:808:27: note: include '' or provide a declaration of 'malloc' distalign.c:810:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 810 | exit(1); | ^~~~ distalign.c:810:9: note: include '' or provide a declaration of 'exit' distalign.c: In function 'CreateZvelebilSequence': distalign.c:831:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 831 | if( !(ptr=(SeqRecord*)malloc(sizeof(SeqRecord))) ) | ^~~~~~ distalign.c:831:27: note: include '' or provide a declaration of 'malloc' distalign.c:833:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 833 | exit(1); | ^~~~ distalign.c:833:9: note: include '' or provide a declaration of 'exit' distalign.c:841:27: warning: incompatible implicit declaration of built-in function 'malloc' [-Wbuiltin-declaration-mismatch] 841 | if( !(ptr->seq=(char*)malloc(alignlen)) ) | ^~~~~~ distalign.c:841:27: note: include '' or provide a declaration of 'malloc' distalign.c:843:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 843 | exit(1); | ^~~~ distalign.c:843:9: note: include '' or provide a declaration of 'exit' distalign.c: In function 'WriteMSFFile': distalign.c:870:13: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 870 | exit(1); | ^~~~ distalign.c:870:13: note: include '' or provide a declaration of 'exit' distalign.c: In function 'DisplayUsage': distalign.c:937:5: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 937 | exit(1); | ^~~~ distalign.c:937:5: note: include '' or provide a declaration of 'exit' distalign.c: In function 'main': distalign.c:998:9: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 998 | exit(1); | ^~~~ distalign.c:998:9: note: include '' or provide a declaration of 'exit' distalign.c:1019:5: warning: incompatible implicit declaration of built-in function 'exit' [-Wbuiltin-declaration-mismatch] 1019 | exit(0); | ^~~~ distalign.c:1019:5: note: include '' or provide a declaration of 'exit' --- pdbdist.o --- *** [pdbdist.o] Error code 1 bmake: stopped making "all" in /home/pbulk/build/biology/pdbalign/work --- distalign.o --- *** [distalign.o] Error code 1 bmake: stopped making "all" in /home/pbulk/build/biology/pdbalign/work bmake: 2 errors bmake: stopped making "all" in /home/pbulk/build/biology/pdbalign/work *** Error code 2 Stop. bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/pdbalign *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/pdbalign