=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Building for libpll-0.3.2 CDPATH="${ZSH_VERSION+.}:" && cd . && /opt/pkg/bin/mksh /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2/missing aclocal-1.14 -I m4 --install WARNING: 'aclocal' is missing on your system. You should only need it if you modified 'acinclude.m4' or 'configure.ac'. You might want to install the Automake and Perl packages. Grab them from any GNU archive site. CDPATH="${ZSH_VERSION+.}:" && cd . && /opt/pkg/bin/mksh /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2/missing autoconf WARNING: 'autoconf' is missing on your system. You should only need it if you modified 'configure.ac'. You might want to install the Autoconf and GNU m4 packages. Grab them from any GNU archive site. (CDPATH="${ZSH_VERSION+.}:" && cd . && /opt/pkg/bin/mksh /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2/missing autoheader) WARNING: 'autoheader' is missing on your system. You should only need it if you modified 'acconfig.h' or 'configure.ac'. You might want to install the Autoconf and GNU m4 packages. Grab them from any GNU archive site. rm -f stamp-h1 touch ./config.h.in /opt/pkg/bin/mksh ./config.status --recheck cd . && /opt/pkg/bin/mksh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged /opt/pkg/bin/bmake all-recursive Making all in src cd . && /opt/pkg/bin/mksh /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2/missing automake-1.14 --foreign WARNING: 'automake' is missing on your system. You should only need it if you modified 'Makefile.am', 'acinclude.m4' or 'configure.ac'. You might want to install the Automake and Perl packages. Grab them from any GNU archive site. /opt/pkg/bin/mksh ./config.status --recheck cd . && /opt/pkg/bin/mksh ./config.status Makefile config.status: creating Makefile cd .. && /opt/pkg/bin/bmake am--refresh /opt/pkg/bin/mksh ./config.status --recheck /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fasta.lo -MD -MP -MF .deps/libpll_la-fasta.Tpo -c -o libpll_la-fasta.lo `test -f 'fasta.c' || echo './'`fasta.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fasta.lo -MD -MP -MF .deps/libpll_la-fasta.Tpo -c fasta.c -fno-common -DPIC -o .libs/libpll_la-fasta.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fasta.lo -MD -MP -MF .deps/libpll_la-fasta.Tpo -c fasta.c -o libpll_la-fasta.o >/dev/null 2>&1 mv -f .deps/libpll_la-fasta.Tpo .deps/libpll_la-fasta.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-gamma.lo -MD -MP -MF .deps/libpll_la-gamma.Tpo -c -o libpll_la-gamma.lo `test -f 'gamma.c' || echo './'`gamma.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-gamma.lo -MD -MP -MF .deps/libpll_la-gamma.Tpo -c gamma.c -fno-common -DPIC -o .libs/libpll_la-gamma.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-gamma.lo -MD -MP -MF .deps/libpll_la-gamma.Tpo -c gamma.c -o libpll_la-gamma.o >/dev/null 2>&1 mv -f .deps/libpll_la-gamma.Tpo .deps/libpll_la-gamma.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-likelihood.lo -MD -MP -MF .deps/libpll_la-likelihood.Tpo -c -o libpll_la-likelihood.lo `test -f 'likelihood.c' || echo './'`likelihood.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-likelihood.lo -MD -MP -MF .deps/libpll_la-likelihood.Tpo -c likelihood.c -fno-common -DPIC -o .libs/libpll_la-likelihood.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-likelihood.lo -MD -MP -MF .deps/libpll_la-likelihood.Tpo -c likelihood.c -o libpll_la-likelihood.o >/dev/null 2>&1 mv -f .deps/libpll_la-likelihood.Tpo .deps/libpll_la-likelihood.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-list.lo -MD -MP -MF .deps/libpll_la-list.Tpo -c -o libpll_la-list.lo `test -f 'list.c' || echo './'`list.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT 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-Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-pll.lo -MD -MP -MF .deps/libpll_la-pll.Tpo -c -o libpll_la-pll.lo `test -f 'pll.c' || echo './'`pll.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-pll.lo -MD -MP -MF .deps/libpll_la-pll.Tpo -c pll.c -fno-common -DPIC -o .libs/libpll_la-pll.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-pll.lo -MD -MP -MF .deps/libpll_la-pll.Tpo -c pll.c -o libpll_la-pll.o >/dev/null 2>&1 mv -f .deps/libpll_la-pll.Tpo .deps/libpll_la-pll.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-output.lo -MD -MP -MF .deps/libpll_la-output.Tpo -c -o libpll_la-output.lo `test -f 'output.c' || echo './'`output.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-output.lo -MD -MP -MF .deps/libpll_la-output.Tpo -c output.c -fno-common -DPIC -o .libs/libpll_la-output.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-output.lo -MD -MP -MF .deps/libpll_la-output.Tpo -c output.c -o libpll_la-output.o >/dev/null 2>&1 mv -f .deps/libpll_la-output.Tpo .deps/libpll_la-output.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree.lo -MD -MP -MF .deps/libpll_la-utree.Tpo -c -o libpll_la-utree.lo `test -f 'utree.c' || echo './'`utree.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree.lo -MD -MP -MF .deps/libpll_la-utree.Tpo -c utree.c -fno-common -DPIC -o .libs/libpll_la-utree.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE 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--mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-derivatives.lo -MD -MP -MF .deps/libpll_la-derivatives.Tpo -c -o libpll_la-derivatives.lo `test -f 'derivatives.c' || echo './'`derivatives.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-derivatives.lo -MD -MP -MF .deps/libpll_la-derivatives.Tpo -c derivatives.c -fno-common -DPIC -o .libs/libpll_la-derivatives.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-derivatives.lo -MD -MP -MF .deps/libpll_la-derivatives.Tpo -c derivatives.c -o libpll_la-derivatives.o >/dev/null 2>&1 mv -f .deps/libpll_la-derivatives.Tpo .deps/libpll_la-derivatives.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-partials.lo -MD -MP -MF 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-std=c99 -O3 -fPIC -g -MT libpll_la-core_partials.lo -MD -MP -MF .deps/libpll_la-core_partials.Tpo -c -o libpll_la-core_partials.lo `test -f 'core_partials.c' || echo './'`core_partials.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_partials.lo -MD -MP -MF .deps/libpll_la-core_partials.Tpo -c core_partials.c -fno-common -DPIC -o .libs/libpll_la-core_partials.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_partials.lo -MD -MP -MF .deps/libpll_la-core_partials.Tpo -c core_partials.c -o libpll_la-core_partials.o >/dev/null 2>&1 mv -f .deps/libpll_la-core_partials.Tpo .deps/libpll_la-core_partials.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_pmatrix.lo -MD -MP -MF .deps/libpll_la-core_pmatrix.Tpo -c -o libpll_la-core_pmatrix.lo `test -f 'core_pmatrix.c' || echo './'`core_pmatrix.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_pmatrix.lo -MD -MP -MF .deps/libpll_la-core_pmatrix.Tpo -c core_pmatrix.c -fno-common -DPIC -o .libs/libpll_la-core_pmatrix.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_pmatrix.lo -MD -MP -MF .deps/libpll_la-core_pmatrix.Tpo -c core_pmatrix.c -o libpll_la-core_pmatrix.o >/dev/null 2>&1 mv -f .deps/libpll_la-core_pmatrix.Tpo .deps/libpll_la-core_pmatrix.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_likelihood.lo -MD -MP -MF .deps/libpll_la-core_likelihood.Tpo -c -o libpll_la-core_likelihood.lo `test -f 'core_likelihood.c' || echo './'`core_likelihood.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_likelihood.lo -MD -MP -MF .deps/libpll_la-core_likelihood.Tpo -c core_likelihood.c -fno-common -DPIC -o .libs/libpll_la-core_likelihood.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_likelihood.lo -MD -MP -MF .deps/libpll_la-core_likelihood.Tpo -c core_likelihood.c -o libpll_la-core_likelihood.o >/dev/null 2>&1 mv -f .deps/libpll_la-core_likelihood.Tpo .deps/libpll_la-core_likelihood.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fast_parsimony.lo -MD -MP -MF .deps/libpll_la-fast_parsimony.Tpo -c -o libpll_la-fast_parsimony.lo `test -f 'fast_parsimony.c' || echo './'`fast_parsimony.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fast_parsimony.lo -MD -MP -MF .deps/libpll_la-fast_parsimony.Tpo -c fast_parsimony.c -fno-common -DPIC -o .libs/libpll_la-fast_parsimony.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fast_parsimony.lo -MD -MP -MF .deps/libpll_la-fast_parsimony.Tpo -c fast_parsimony.c -o libpll_la-fast_parsimony.o >/dev/null 2>&1 mv -f .deps/libpll_la-fast_parsimony.Tpo .deps/libpll_la-fast_parsimony.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-stepwise.lo -MD -MP -MF .deps/libpll_la-stepwise.Tpo -c -o libpll_la-stepwise.lo `test -f 'stepwise.c' || echo './'`stepwise.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-stepwise.lo -MD -MP -MF .deps/libpll_la-stepwise.Tpo -c stepwise.c -fno-common -DPIC -o .libs/libpll_la-stepwise.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-stepwise.lo -MD -MP -MF .deps/libpll_la-stepwise.Tpo -c stepwise.c -o libpll_la-stepwise.o >/dev/null 2>&1 mv -f .deps/libpll_la-stepwise.Tpo .deps/libpll_la-stepwise.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-random.lo -MD -MP -MF .deps/libpll_la-random.Tpo -c -o libpll_la-random.lo `test -f 'random.c' || echo './'`random.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-random.lo -MD -MP -MF .deps/libpll_la-random.Tpo -c random.c -fno-common -DPIC -o .libs/libpll_la-random.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-random.lo -MD -MP -MF .deps/libpll_la-random.Tpo -c random.c -o libpll_la-random.o >/dev/null 2>&1 mv -f .deps/libpll_la-random.Tpo .deps/libpll_la-random.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-phylip.lo -MD -MP -MF .deps/libpll_la-phylip.Tpo -c -o libpll_la-phylip.lo `test -f 'phylip.c' || echo './'`phylip.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-phylip.lo -MD -MP -MF .deps/libpll_la-phylip.Tpo -c phylip.c -fno-common -DPIC -o .libs/libpll_la-phylip.o libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-phylip.lo -MD -MP -MF .deps/libpll_la-phylip.Tpo -c phylip.c -o libpll_la-phylip.o >/dev/null 2>&1 mv -f .deps/libpll_la-phylip.Tpo .deps/libpll_la-phylip.Plo /opt/pkg/bin/mksh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-hardware.lo -MD -MP -MF .deps/libpll_la-hardware.Tpo -c -o libpll_la-hardware.lo `test -f 'hardware.c' || echo './'`hardware.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-hardware.lo -MD -MP -MF .deps/libpll_la-hardware.Tpo -c hardware.c -fno-common -DPIC -o .libs/libpll_la-hardware.o hardware.c:80:3: error: invalid output constraint '=a' in asm cpuid(0,0,a,b,c,d); ^ hardware.c:64:14: note: expanded from macro 'cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ hardware.c:85:5: error: invalid output constraint '=a' in asm cpuid(1,0,a,b,c,d); ^ hardware.c:64:14: note: expanded from macro 'cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ hardware.c:98:7: error: invalid output constraint '=a' in asm cpuid(7,0,a,b,c,d); ^ hardware.c:64:14: note: expanded from macro 'cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ 3 errors generated. *** [libpll_la-hardware.lo] Error code 1 bmake[2]: stopped in /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2/src 1 error bmake[2]: stopped in /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2/src *** [all-recursive] Error code 1 bmake[1]: stopped in /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2 1 error bmake[1]: stopped in /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2 *** [all] Error code 2 bmake: stopped in /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2 1 error bmake: stopped in /Users/pbulk/build/biology/libpll/work/libpll-src-0.3.2 *** Error code 2 Stop. bmake[1]: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/libpll *** Error code 1 Stop. bmake: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/libpll