+ local run_cmd + run_cmd=run_su + shift + run_su /usr/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/biolibc-tools-0.1.4.9/work.log + su pbulk -c '"$@"' make /usr/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/biolibc-tools-0.1.4.9/work.log => Bootstrap dependency digest>=20211023: found digest-20220214 ===> Building for biolibc-tools-0.1.4.9 cd /home/pbulk/build/biology/biolibc-tools/work/biolibc-tools-6d9604303fa43418a423840c916407af2b069184 && /usr/pkg/bin/bmake PREFIX=/usr/pkg depend rm -f Makefile.depend for file in *.c; do cc -isystem /usr/pkg/include -isystem /usr/pkg/include -MM ${file} >> Makefile.depend; printf "\t\${CC} -c \${CFLAGS} ${file}\n\n" >> Makefile.depend; done --- depend --- --- fastx2tsv.o --- --- depend --- rm -f Makefile.depend --- fastx2tsv.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include fastx2tsv.c --- depend --- for file in *.c; do cc -isystem /usr/pkg/include -isystem /usr/pkg/include -MM ${file} >> Makefile.depend; printf "\t\${CC} -c \${CFLAGS} ${file}\n\n" >> Makefile.depend; done --- fastx2tsv.o --- fastx2tsv.c: In function 'main': fastx2tsv.c:42:2: warning: implicit declaration of function 'strtr'; did you mean 'strstr'? [-Wimplicit-function-declaration] 42 | strtr(bl_fastx_desc(&rec), "\t", " ", 0); | ^~~~~ | strstr --- fastx-derep.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include fastx-derep.c --- vcf-search.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include vcf-search.c --- fasta2seq.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include fasta2seq.c --- find-orfs.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include find-orfs.c --- gff3-to-bed.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include gff3-to-bed.c --- extract-seq.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include extract-seq.c --- chrom-lens.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include chrom-lens.c --- fastx-stats.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include fastx-stats.c --- ensemblid2gene.o --- cc -c -pipe -O2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/pkg/include -isystem /usr/pkg/include ensemblid2gene.c ensemblid2gene.c: In function 'main': ensemblid2gene.c:51:82: error: 'strptrcmp' undeclared (first use in this function); did you mean 'xt_strptrcmp'? 51 | qsort(id_list, id_count, sizeof(*id_list), (int(*)(const void *,const void*))strptrcmp); | ^~~~~~~~~ | xt_strptrcmp ensemblid2gene.c:51:82: note: each undeclared identifier is reported only once for each function it appears in ensemblid2gene.c:77:44: error: 'strptrcasecmp' undeclared (first use in this function); did you mean 'xt_strptrcasecmp'? 77 | (int (*)(const void *, const void *))strptrcasecmp); | ^~~~~~~~~~~~~ | xt_strptrcasecmp *** [ensemblid2gene.o] Error code 1 bmake: stopped in /home/pbulk/build/biology/biolibc-tools/work/biolibc-tools-6d9604303fa43418a423840c916407af2b069184 1 error bmake: stopped in /home/pbulk/build/biology/biolibc-tools/work/biolibc-tools-6d9604303fa43418a423840c916407af2b069184 *** Error code 2 Stop. bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-netbsd-trunk-x86_64/biology/biolibc-tools *** Error code 1 Stop. bmake: stopped in /data/jenkins/workspace/pkgsrc-netbsd-trunk-x86_64/biology/biolibc-tools