=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Skipping vulnerability checks.
WARNING: No /var/db/pkg/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /var/db/pkg fetch-pkg-vulnerabilities'.
===> Building for plinkseq-0.08nb5
cd /usr/pkgsrc/biology/plinkseq/work/plinkseq-0.08/lib && protoc --cpp_out=. pp.proto && mv pp.pb.cc pp.pb.cpp
[libprotobuf WARNING google/protobuf/compiler/parser.cc:649] No syntax specified for the proto file: pp.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
cd /usr/pkgsrc/biology/plinkseq/work/plinkseq-0.08/lib && protoc --cpp_out=. variant.proto && mv variant.pb.cc variant.pb.cpp
[libprotobuf WARNING google/protobuf/compiler/parser.cc:649] No syntax specified for the proto file: variant.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
/usr/bin/make  all-recursive
Making all in lib
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-varmeta.lo -MD -MP -MF .deps/libplinkseq_la-varmeta.Tpo -c varmeta.cpp -o libplinkseq_la-varmeta.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-pp.lo -MD -MP -MF .deps/libplinkseq_la-pp.Tpo -c pp.cpp -o libplinkseq_la-pp.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-pp.pb.lo -MD -MP -MF .deps/libplinkseq_la-pp.pb.Tpo -c pp.pb.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-pp.pb.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-pp.pb.lo -MD -MP -MF .deps/libplinkseq_la-pp.pb.Tpo -c pp.pb.cpp -o libplinkseq_la-pp.pb.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-statistics.lo -MD -MP -MF .deps/libplinkseq_la-statistics.Tpo -c statistics.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-statistics.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-statistics.lo -MD -MP -MF .deps/libplinkseq_la-statistics.Tpo -c statistics.cpp -o libplinkseq_la-statistics.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-dcdflib.lo -MD -MP -MF .deps/libplinkseq_la-dcdflib.Tpo -c dcdflib.cpp -o libplinkseq_la-dcdflib.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-bgzf.lo -MD -MP -MF .deps/libplinkseq_la-bgzf.Tpo -c bgzf.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-bgzf.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-bgzf.lo -MD -MP -MF .deps/libplinkseq_la-bgzf.Tpo -c bgzf.cpp -o libplinkseq_la-bgzf.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-fisher.lo -MD -MP -MF .deps/libplinkseq_la-fisher.Tpo -c fisher.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-fisher.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-fisher.lo -MD -MP -MF .deps/libplinkseq_la-fisher.Tpo -c fisher.cpp -o libplinkseq_la-fisher.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-glm.lo -MD -MP -MF .deps/libplinkseq_la-glm.Tpo -c glm.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-glm.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-glm.lo -MD -MP -MF .deps/libplinkseq_la-glm.Tpo -c glm.cpp -o libplinkseq_la-glm.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-matrix.lo -MD -MP -MF .deps/libplinkseq_la-matrix.Tpo -c matrix.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-matrix.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-matrix.lo -MD -MP -MF .deps/libplinkseq_la-matrix.Tpo -c matrix.cpp -o libplinkseq_la-matrix.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-iterate.lo -MD -MP -MF .deps/libplinkseq_la-iterate.Tpo -c iterate.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-iterate.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-iterate.lo -MD -MP -MF .deps/libplinkseq_la-iterate.Tpo -c iterate.cpp -o libplinkseq_la-iterate.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-vcfiterate.lo -MD -MP -MF .deps/libplinkseq_la-vcfiterate.Tpo -c vcfiterate.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-vcfiterate.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-vcfiterate.lo -MD -MP -MF .deps/libplinkseq_la-vcfiterate.Tpo -c vcfiterate.cpp -o libplinkseq_la-vcfiterate.o >/dev/null 2>&1
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libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-netdb.lo -MD -MP -MF .deps/libplinkseq_la-netdb.Tpo -c netdb.cpp  -fPIC -DPIC -o .libs/libplinkseq_la-netdb.o
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-netdb.lo -MD -MP -MF .deps/libplinkseq_la-netdb.Tpo -c netdb.cpp -o libplinkseq_la-netdb.o >/dev/null 2>&1
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libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-sqlite3.lo -MD -MP -MF .deps/libplinkseq_la-sqlite3.Tpo -c sqlite3.c  -fPIC -DPIC -o .libs/libplinkseq_la-sqlite3.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -O2 -D_FORTIFY_SOURCE=2 -MT libplinkseq_la-sqlite3.lo -MD -MP -MF .deps/libplinkseq_la-sqlite3.Tpo -c sqlite3.c -o libplinkseq_la-sqlite3.o >/dev/null 2>&1
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/bin/sh ../libtool --tag=CXX    --mode=link c++  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include   -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -o libplinkseq.la -rpath /usr/pkg/lib libplinkseq_la-eval.lo  libplinkseq_la-token.lo libplinkseq_la-vcfz.lo  libplinkseq_la-gstore.lo libplinkseq_la-globals.lo  libplinkseq_la-variant.lo libplinkseq_la-svar.lo  libplinkseq_la-genotype.lo libplinkseq_la-meta.lo  libplinkseq_la-regions.lo libplinkseq_la-filemap.lo  libplinkseq_la-vcf.lo libplinkseq_la-bcf.lo  libplinkseq_la-zfstream.lo libplinkseq_la-sqlwrap.lo  libplinkseq_la-helper.lo libplinkseq_la-locdb.lo  libplinkseq_la-vardb.lo libplinkseq_la-segments.lo  libplinkseq_la-varfunc.lo libplinkseq_la-variant.pb.lo  libplinkseq_la-refdb.lo libplinkseq_la-seqdb.lo  libplinkseq_la-annot.lo libplinkseq_la-inddb.lo  libplinkseq_la-mask.lo libplinkseq_la-reffuncs.lo  libplinkseq_la-vgroup.lo libplinkseq_la-allele.lo  libplinkseq_la-individual.lo libplinkseq_la-indmap.lo  libplinkseq_la-phmap.lo libplinkseq_la-permute.lo  libplinkseq_la-crandom.lo libplinkseq_la-defs.lo  libplinkseq_la-em.lo libplinkseq_la-bed.lo  libplinkseq_la-varmeta.lo libplinkseq_la-pp.lo  libplinkseq_la-pp.pb.lo libplinkseq_la-statistics.lo  libplinkseq_la-dcdflib.lo libplinkseq_la-bgzf.lo  libplinkseq_la-fisher.lo libplinkseq_la-glm.lo  libplinkseq_la-matrix.lo libplinkseq_la-iterate.lo  libplinkseq_la-vcfiterate.lo libplinkseq_la-netdb.lo  libplinkseq_la-sqlite3.lo -lz  -lprotobuf 

*** Warning: linker path does not have real file for library -latomic.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libatomic and none of the candidates passed a file format test
*** using a regex pattern. Last file checked: /usr/pkgsrc/biology/plinkseq/work/.buildlink/lib/libprotobuf-lite.so
*** The inter-library dependencies that have been dropped here will be
*** automatically added whenever a program is linked with this library
*** or is declared to -dlopen it.
libtool: link: c++ -shared  -fPIC -DPIC  .libs/libplinkseq_la-eval.o .libs/libplinkseq_la-token.o .libs/libplinkseq_la-vcfz.o .libs/libplinkseq_la-gstore.o .libs/libplinkseq_la-globals.o .libs/libplinkseq_la-variant.o .libs/libplinkseq_la-svar.o .libs/libplinkseq_la-genotype.o .libs/libplinkseq_la-meta.o .libs/libplinkseq_la-regions.o .libs/libplinkseq_la-filemap.o .libs/libplinkseq_la-vcf.o .libs/libplinkseq_la-bcf.o .libs/libplinkseq_la-zfstream.o .libs/libplinkseq_la-sqlwrap.o .libs/libplinkseq_la-helper.o .libs/libplinkseq_la-locdb.o .libs/libplinkseq_la-vardb.o .libs/libplinkseq_la-segments.o .libs/libplinkseq_la-varfunc.o .libs/libplinkseq_la-variant.pb.o .libs/libplinkseq_la-refdb.o .libs/libplinkseq_la-seqdb.o .libs/libplinkseq_la-annot.o .libs/libplinkseq_la-inddb.o .libs/libplinkseq_la-mask.o .libs/libplinkseq_la-reffuncs.o .libs/libplinkseq_la-vgroup.o .libs/libplinkseq_la-allele.o .libs/libplinkseq_la-individual.o .libs/libplinkseq_la-indmap.o .libs/libplinkseq_la-phmap.o .libs/libplinkseq_la-permute.o .libs/libplinkseq_la-crandom.o .libs/libplinkseq_la-defs.o .libs/libplinkseq_la-em.o .libs/libplinkseq_la-bed.o .libs/libplinkseq_la-varmeta.o .libs/libplinkseq_la-pp.o .libs/libplinkseq_la-pp.pb.o .libs/libplinkseq_la-statistics.o .libs/libplinkseq_la-dcdflib.o .libs/libplinkseq_la-bgzf.o .libs/libplinkseq_la-fisher.o .libs/libplinkseq_la-glm.o .libs/libplinkseq_la-matrix.o .libs/libplinkseq_la-iterate.o .libs/libplinkseq_la-vcfiterate.o .libs/libplinkseq_la-netdb.o .libs/libplinkseq_la-sqlite3.o   -Wl,-rpath,/usr/pkgsrc/biology/plinkseq/work/.buildlink/lib -Wl,-rpath,/usr/pkgsrc/biology/plinkseq/work/.buildlink/lib -L/usr/pkgsrc/biology/plinkseq/work/.buildlink/lib -lprotobuf -lz  -O2 -Wl,-zrelro -Wl,-rpath -Wl,/usr/pkg/lib   -pthread -Wl,-soname -Wl,libplinkseq.so.0 -o .libs/libplinkseq.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libplinkseq.so.0" && ln -s "libplinkseq.so.0.0.0" "libplinkseq.so.0")
libtool: link: (cd ".libs" && rm -f "libplinkseq.so" && ln -s "libplinkseq.so.0.0.0" "libplinkseq.so")
libtool: link: ar cru .libs/libplinkseq.a  libplinkseq_la-eval.o libplinkseq_la-token.o libplinkseq_la-vcfz.o libplinkseq_la-gstore.o libplinkseq_la-globals.o libplinkseq_la-variant.o libplinkseq_la-svar.o libplinkseq_la-genotype.o libplinkseq_la-meta.o libplinkseq_la-regions.o libplinkseq_la-filemap.o libplinkseq_la-vcf.o libplinkseq_la-bcf.o libplinkseq_la-zfstream.o libplinkseq_la-sqlwrap.o libplinkseq_la-helper.o libplinkseq_la-locdb.o libplinkseq_la-vardb.o libplinkseq_la-segments.o libplinkseq_la-varfunc.o libplinkseq_la-variant.pb.o libplinkseq_la-refdb.o libplinkseq_la-seqdb.o libplinkseq_la-annot.o libplinkseq_la-inddb.o libplinkseq_la-mask.o libplinkseq_la-reffuncs.o libplinkseq_la-vgroup.o libplinkseq_la-allele.o libplinkseq_la-individual.o libplinkseq_la-indmap.o libplinkseq_la-phmap.o libplinkseq_la-permute.o libplinkseq_la-crandom.o libplinkseq_la-defs.o libplinkseq_la-em.o libplinkseq_la-bed.o libplinkseq_la-varmeta.o libplinkseq_la-pp.o libplinkseq_la-pp.pb.o libplinkseq_la-statistics.o libplinkseq_la-dcdflib.o libplinkseq_la-bgzf.o libplinkseq_la-fisher.o libplinkseq_la-glm.o libplinkseq_la-matrix.o libplinkseq_la-iterate.o libplinkseq_la-vcfiterate.o libplinkseq_la-netdb.o libplinkseq_la-sqlite3.o
libtool: link: ranlib .libs/libplinkseq.a
libtool: link: ( cd ".libs" && rm -f "libplinkseq.la" && ln -s "../libplinkseq.la" "libplinkseq.la" )
Making all in client
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-util.o -MD -MP -MF .deps/pseq-util.Tpo -c -o pseq-util.o `test -f 'util.cpp' || echo './'`util.cpp
mv -f .deps/pseq-util.Tpo .deps/pseq-util.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-ibs.o -MD -MP -MF .deps/pseq-ibs.Tpo -c -o pseq-ibs.o `test -f 'ibs.cpp' || echo './'`ibs.cpp
mv -f .deps/pseq-ibs.Tpo .deps/pseq-ibs.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-main.o -MD -MP -MF .deps/pseq-main.Tpo -c -o pseq-main.o `test -f 'main.cpp' || echo './'`main.cpp
mv -f .deps/pseq-main.Tpo .deps/pseq-main.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-func.o -MD -MP -MF .deps/pseq-func.Tpo -c -o pseq-func.o `test -f 'func.cpp' || echo './'`func.cpp
mv -f .deps/pseq-func.Tpo .deps/pseq-func.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-summaries.o -MD -MP -MF .deps/pseq-summaries.Tpo -c -o pseq-summaries.o `test -f 'summaries.cpp' || echo './'`summaries.cpp
mv -f .deps/pseq-summaries.Tpo .deps/pseq-summaries.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-views.o -MD -MP -MF .deps/pseq-views.Tpo -c -o pseq-views.o `test -f 'views.cpp' || echo './'`views.cpp
mv -f .deps/pseq-views.Tpo .deps/pseq-views.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-assoc.o -MD -MP -MF .deps/pseq-assoc.Tpo -c -o pseq-assoc.o `test -f 'assoc.cpp' || echo './'`assoc.cpp
mv -f .deps/pseq-assoc.Tpo .deps/pseq-assoc.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-genic.o -MD -MP -MF .deps/pseq-genic.Tpo -c -o pseq-genic.o `test -f 'genic.cpp' || echo './'`genic.cpp
mv -f .deps/pseq-genic.Tpo .deps/pseq-genic.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-compare.o -MD -MP -MF .deps/pseq-compare.Tpo -c -o pseq-compare.o `test -f 'compare.cpp' || echo './'`compare.cpp
mv -f .deps/pseq-compare.Tpo .deps/pseq-compare.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-ibd.o -MD -MP -MF .deps/pseq-ibd.Tpo -c -o pseq-ibd.o `test -f 'ibd.cpp' || echo './'`ibd.cpp
mv -f .deps/pseq-ibd.Tpo .deps/pseq-ibd.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-loaders.o -MD -MP -MF .deps/pseq-loaders.Tpo -c -o pseq-loaders.o `test -f 'loaders.cpp' || echo './'`loaders.cpp
mv -f .deps/pseq-loaders.Tpo .deps/pseq-loaders.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-clusters.o -MD -MP -MF .deps/pseq-clusters.Tpo -c -o pseq-clusters.o `test -f 'clusters.cpp' || echo './'`clusters.cpp
mv -f .deps/pseq-clusters.Tpo .deps/pseq-clusters.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-varfunc.o -MD -MP -MF .deps/pseq-varfunc.Tpo -c -o pseq-varfunc.o `test -f 'varfunc.cpp' || echo './'`varfunc.cpp
mv -f .deps/pseq-varfunc.Tpo .deps/pseq-varfunc.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-glm-tests.o -MD -MP -MF .deps/pseq-glm-tests.Tpo -c -o pseq-glm-tests.o `test -f 'glm-tests.cpp' || echo './'`glm-tests.cpp
mv -f .deps/pseq-glm-tests.Tpo .deps/pseq-glm-tests.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-stepup.o -MD -MP -MF .deps/pseq-stepup.Tpo -c -o pseq-stepup.o `test -f 'stepup.cpp' || echo './'`stepup.cpp
mv -f .deps/pseq-stepup.Tpo .deps/pseq-stepup.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-kbac.o -MD -MP -MF .deps/pseq-kbac.Tpo -c -o pseq-kbac.o `test -f 'kbac.cpp' || echo './'`kbac.cpp
mv -f .deps/pseq-kbac.Tpo .deps/pseq-kbac.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-netassoc.o -MD -MP -MF .deps/pseq-netassoc.Tpo -c -o pseq-netassoc.o `test -f 'netassoc.cpp' || echo './'`netassoc.cpp
mv -f .deps/pseq-netassoc.Tpo .deps/pseq-netassoc.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-gseq.o -MD -MP -MF .deps/pseq-gseq.Tpo -c -o pseq-gseq.o `test -f 'gseq.cpp' || echo './'`gseq.cpp
mv -f .deps/pseq-gseq.Tpo .deps/pseq-gseq.Po
c++ -DHAVE_CONFIG_H -I. -I..  -I../lib  -I/usr/pkg/include -I/usr/include  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -MT pseq-extra.o -MD -MP -MF .deps/pseq-extra.Tpo -c -o pseq-extra.o `test -f 'extra.cpp' || echo './'`extra.cpp
mv -f .deps/pseq-extra.Tpo .deps/pseq-extra.Po
/bin/sh ../libtool --tag=CXX    --mode=link c++  -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include  -lz -ldl  -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -o pseq pseq-util.o pseq-ibs.o  pseq-main.o pseq-func.o  pseq-summaries.o pseq-views.o  pseq-assoc.o pseq-genic.o  pseq-compare.o pseq-ibd.o  pseq-loaders.o pseq-clusters.o  pseq-varfunc.o pseq-glm-tests.o  pseq-stepup.o pseq-kbac.o  pseq-netassoc.o pseq-gseq.o  pseq-extra.o ../lib/libplinkseq.la 
libtool: link: c++ -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkgsrc/biology/plinkseq/work/.buildlink/include -Wl,-zrelro -Wl,-rpath -Wl,/usr/pkg/lib -o .libs/pseq pseq-util.o pseq-ibs.o pseq-main.o pseq-func.o pseq-summaries.o pseq-views.o pseq-assoc.o pseq-genic.o pseq-compare.o pseq-ibd.o pseq-loaders.o pseq-clusters.o pseq-varfunc.o pseq-glm-tests.o pseq-stepup.o pseq-kbac.o pseq-netassoc.o pseq-gseq.o pseq-extra.o  -L/usr/pkgsrc/biology/plinkseq/work/.buildlink/lib -L../lib/.libs -lplinkseq -lprotobuf -latomic -lz -pthread -Wl,-rpath,/usr/pkg/lib -Wl,-rpath,/usr/pkgsrc/biology/plinkseq/work/.buildlink/lib
ld: cannot find -latomic
*** Error code 1

Stop.
make[2]: stopped in /usr/pkgsrc/biology/plinkseq/work/plinkseq-0.08/client
*** Error code 1

Stop.
make[1]: stopped in /usr/pkgsrc/biology/plinkseq/work/plinkseq-0.08
*** Error code 1

Stop.
make: stopped in /usr/pkgsrc/biology/plinkseq/work/plinkseq-0.08
*** Error code 1

Stop.
make[1]: stopped in /usr/pkgsrc/biology/plinkseq
*** Error code 1

Stop.
make: stopped in /usr/pkgsrc/biology/plinkseq