+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/lucy-1.20/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/lucy-1.20/work.log WARNING: [license.mk] Every package should define a LICENSE. ===> Building for lucy-1.20 --- beep --- --- lucy.o --- --- qual_trim.o --- --- abi.o --- --- lucy.o --- gcc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/usr/include -I/usr/include -c lucy.c --- beep --- done! --- qual_trim.o --- gcc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/usr/include -I/usr/include -c qual_trim.c --- abi.o --- gcc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/usr/include -I/usr/include -c abi.c --- vector.o --- gcc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/usr/include -I/usr/include -c vector.c --- abi.o --- abi.c:24:8: error: type defaults to 'int' in declaration of 'condition' [-Wimplicit-int] 24 | static condition[]={ | ^~~~~~~~~ abi.c: In function 'abi_code': abi.c:70:15: error: implicit declaration of function 'random' [-Wimplicit-function-declaration] 70 | case 5: tmp=random()%2 ? 2 : 0; break; | ^~~~~~ abi.c:82:5: error: implicit declaration of function 'giveup' [-Wimplicit-function-declaration] 82 | giveup("how can other cases happen in tag_code?"); | ^~~~~~ *** [abi.o] Error code 1 bmake: stopped making "all" in /home/pbulk/build/biology/lucy/work/lucy-1.20p --- lucy.o --- lucy.c: In function 'worker': lucy.c:172:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 172 | int id=(int)arg; | ^ lucy.c: In function 'work_splice': lucy.c:206:5: error: implicit declaration of function 'splice_align_left' [-Wimplicit-function-declaration] 206 | splice_align_left(id, target_seq[id], | ^~~~~~~~~~~~~~~~~ lucy.c:247:7: error: implicit declaration of function 'splice_align_right' [-Wimplicit-function-declaration] 247 | splice_align_right(id, target_seq[id]+seqs[i].left, | ^~~~~~~~~~~~~~~~~~ lucy.c: At top level: lucy.c:284:1: error: return type defaults to 'int' [-Wimplicit-int] 284 | main (argc, argv) | ^~~~ lucy.c: In function 'main': lucy.c:361:9: error: implicit declaration of function 'set_bracket' [-Wimplicit-function-declaration] 361 | set_bracket(bracket_size, bracket_err); | ^~~~~~~~~~~ lucy.c:469:5: error: implicit declaration of function 'default_windows' [-Wimplicit-function-declaration] 469 | default_windows(); | ^~~~~~~~~~~~~~~ lucy.c:531:51: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 531 | if (pthread_create(&threads[i], NULL, worker, (void*)i)) | ^ lucy.c:639:7: error: implicit declaration of function 'quality_trim' [-Wimplicit-function-declaration] 639 | quality_trim(conf_val_raw, j, minimum, &(ptr->left), &(ptr->right)); | ^~~~~~~~~~~~ lucy.c:669:5: error: implicit declaration of function 'prepare_abi_mask' [-Wimplicit-function-declaration] 669 | prepare_abi_mask(); | ^~~~~~~~~~~~~~~~ lucy.c:713:9: error: implicit declaration of function 'abi_align' [-Wimplicit-function-declaration] 713 | abi_align(phred_seq, ptr->len, abi_seq, bases, &left, &right); | ^~~~~~~~~ lucy.c:792:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 792 | (i=(int)fgets(buf, BUFFER_LENGTH, spl_file)) && buf[0]!='>'; ) { | ^ lucy.c:891:14: error: implicit declaration of function 'poly_at_left' [-Wimplicit-function-declaration] 891 | left=poly_at_left(&phred_seq[seqs[i].left], | ^~~~~~~~~~~~ lucy.c:894:15: error: implicit declaration of function 'poly_at_right' [-Wimplicit-function-declaration] 894 | right=poly_at_right(&phred_seq[seqs[i].right], | ^~~~~~~~~~~~~ lucy.c:934:5: error: implicit declaration of function 'construct_vector_tags' [-Wimplicit-function-declaration] 934 | construct_vector_tags(vec_seq, bases); | ^~~~~~~~~~~~~~~~~~~~~ lucy.c:947:11: error: implicit declaration of function 'match_vector_tags' [-Wimplicit-function-declaration] 947 | j=match_vector_tags(phred_seq+seqs[i].left, bases); | ^~~~~~~~~~~~~~~~~ lucy.c:959:5: error: implicit declaration of function 'destroy_vector_tags' [-Wimplicit-function-declaration] 959 | destroy_vector_tags(); | ^~~~~~~~~~~~~~~~~~~ *** [lucy.o] Error code 1 bmake: stopped making "all" in /home/pbulk/build/biology/lucy/work/lucy-1.20p bmake: 2 errors bmake: stopped making "all" in /home/pbulk/build/biology/lucy/work/lucy-1.20p *** Error code 2 Stop. bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/lucy *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/lucy