=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for biolibc-tools-0.1.4.3 cd /tmp/biology/biolibc-tools/work/biolibc-tools-dfa8f2ff93779a5b54bdccf29f60c8072c73a069 && /usr/bin/make 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 --- --- fastx-derep.o --- --- vcf-search.o --- --- fastx2tsv.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include fastx2tsv.c --- depend --- rm -f Makefile.depend --- fastx-derep.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include fastx-derep.c --- vcf-search.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include vcf-search.c --- depend --- for file in *.c; do gcc -isystem /usr/pkg/include -isystem /usr/pkg/include -MM ${file} >> Makefile.depend; printf "\t\${CC} -c \${CFLAGS} ${file}\n\n" >> Makefile.depend; done --- fasta2seq.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include fasta2seq.c --- find-orfs.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include find-orfs.c --- gff2bed.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include gff2bed.c --- extract-seq.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include extract-seq.c --- chrom-lens.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include chrom-lens.c --- fastx-stats.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include fastx-stats.c --- ensemblid2gene.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include ensemblid2gene.c --- vcf-downsample.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include vcf-downsample.c --- deromanize.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include deromanize.c --- blt.o --- gcc -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -DLIBEXECDIR=\"/usr/pkg/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -isystem /usr/pkg/include -isystem /usr/pkg/include blt.c --- fastx2tsv --- gcc -o fastx2tsv fastx2tsv.o -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -lbiolibc -lxtend -lm --- vcf-search --- gcc -o vcf-search vcf-search.o -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -lbiolibc -lxtend -lm --- fasta2seq --- gcc -o fasta2seq fasta2seq.o -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -lbiolibc -lxtend -lm --- find-orfs --- --- deromanize.o --- deromanize.c:17:10: fatal error: xtend/stdlib.h: No such file or directory #include // romantoi() ^~~~~~~~~~~~~~~~ compilation terminated. --- find-orfs --- gcc -o find-orfs find-orfs.o -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -L/usr/pkg/lib -Wl,-rpath,/usr/pkg/lib -lbiolibc -lxtend -lm --- deromanize.o --- *** [deromanize.o] Error code 1 make: stopped in /tmp/biology/biolibc-tools/work/biolibc-tools-dfa8f2ff93779a5b54bdccf29f60c8072c73a069 1 error make: stopped in /tmp/biology/biolibc-tools/work/biolibc-tools-dfa8f2ff93779a5b54bdccf29f60c8072c73a069 *** Error code 2 Stop. make[1]: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/biolibc-tools *** Error code 1 Stop. make: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/biolibc-tools