[exp - 121amd64-default-build-as-user][biology/vt] Failed for vt-0.57721_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Mon Nov 9 11:41:19 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: head/biology/vt/Makefile 544091 2020-08-03 17:42:32Z jwb $
Log URL: http://package19.nyi.freebsd.org/data/121amd64-default-build-as-user/554426/logs/vt-0.57721_1.log
Build URL: http://package19.nyi.freebsd.org/build.html?mastername=121amd64-default-build-as-user&build=554426
Log:
=>> Building biology/vt
build started at Mon Nov 9 11:38:14 UTC 2020
port directory: /usr/ports/biology/vt
package name: vt-0.57721_1
building for: FreeBSD 121amd64-default-build-as-user-job-01 12.1-RELEASE-p10 FreeBSD 12.1-RELEASE-p10 amd64
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/vt/Makefile 544091 2020-08-03 17:42:32Z jwb $
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> vt-0.57721_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.10.txz
[121amd64-default-build-as-user-job-01] Installing pkg-1.15.10...
[121amd64-default-build-as-user-job-01] Extracting pkg-1.15.10: .......... done
===> vt-0.57721_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vt-0.57721_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vt-0.57721_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vt-0.57721_1 for building
=> SHA256 Checksum OK for atks-vt-0.57721_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vt-0.57721_1 for building
===> Extracting for vt-0.57721_1
=> SHA256 Checksum OK for atks-vt-0.57721_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for vt-0.57721_1
===> Applying FreeBSD patches for vt-0.57721_1 from /usr/ports/biology/vt/files
===========================================================================
=======================<phase: build-depends >============================
===> vt-0.57721_1 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[121amd64-default-build-as-user-job-01] Installing gmake-4.3_2...
[121amd64-default-build-as-user-job-01] `-- Installing gettext-runtime-0.21...
[121amd64-default-build-as-user-job-01] | `-- Installing indexinfo-0.3.1...
[121amd64-default-build-as-user-job-01] | `-- Extracting indexinfo-0.3.1: .... done
[121amd64-default-build-as-user-job-01] `-- Extracting gettext-runtime-0.21: .......... done
[121amd64-default-build-as-user-job-01] Extracting gmake-4.3_2: .......... done
===> vt-0.57721_1 depends on package: gmake>=4.3 - found
===> Returning to build of vt-0.57721_1
===========================================================================
=======================<phase: lib-depends >============================
===> vt-0.57721_1 depends on shared library: libhts.so.3 - not found
===> Installing existing package /packages/All/htslib-1.11.0.txz
[121amd64-default-build-as-user-job-01] Installing htslib-1.11.0...
[121amd64-default-build-as-user-job-01] `-- Installing curl-7.73.0...
[121amd64-default-build-as-user-job-01] | `-- Installing ca_root_nss-3.58...
[121amd64-default-build-as-user-job-01] | `-- Extracting ca_root_nss-3.58: ........ done
[121amd64-default-build-as-user-job-01] | `-- Installing libnghttp2-1.41.0...
[121amd64-default-build-as-user-job-01] | `-- Extracting libnghttp2-1.41.0: .......... done
[121amd64-default-build-as-user-job-01] `-- Extracting curl-7.73.0: .......... done
[121amd64-default-build-as-user-job-01] `-- Installing libdeflate-1.6...
[121amd64-default-build-as-user-job-01] `-- Extracting libdeflate-1.6: .......... done
<snip>
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qweibull.c -o qweibull.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dexp.c -o dexp.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fprec.c -o fprec.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pf.c -o pf.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qcauchy.c -o qcauchy.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rbeta.c -o rbeta.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sign.c -o sign.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c df.c -o df.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fround.c -o fround.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pgamma.c -o pgamma.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qchisq.c -o qchisq.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rbinom.c -o rbinom.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c signrank.c -o signrank.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dgamma.c -o dgamma.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fsign.c -o fsign.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pgeom.c -o pgeom.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qexp.c -o qexp.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rcauchy.c -o rcauchy.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dgeom.c -o dgeom.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c ftrunc.c -o ftrunc.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c phyper.c -o phyper.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qf.c -o qf.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rchisq.c -o rchisq.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c stirlerr.c -o stirlerr.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dhyper.c -o dhyper.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gamma.c -o gamma.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c plnorm.c -o plnorm.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qgamma.c -o qgamma.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rexp.c -o rexp.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c toms708.c -o toms708.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dlnorm.c -o dlnorm.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gamma_cody.c -o gamma_cody.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c plogis.c -o plogis.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qgeom.c -o qgeom.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rf.c -o rf.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c wilcox.c -o wilcox.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dlogis.c -o dlogis.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gammalims.c -o gammalims.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnbeta.c -o pnbeta.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qhyper.c -o qhyper.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rgamma.c -o rgamma.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sunif.c -o sunif.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sexp.c -o sexp.o
cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c snorm.c -o snorm.o
rm -rf libRmath.a
ar -rc libRmath.a bd0.o dnbeta.o i1mach.o pnbinom.o qlnorm.o rgeom.o bessel_i.o dnbinom.o imax2.o pnchisq.o qlogis.o rhyper.o bessel_j.o dnchisq.o imin2.o pnf.o qnbeta.o rlnorm.o bessel_k.o dnf.o lbeta.o pnorm.o qnbinom.o rlogis.o bessel_y.o dnorm.o lgamma.o pnt.o qnchisq.o rmultinom.o beta.o dnt.o lgammacor.o polygamma.o qnf.o rnbinom.o chebyshev.o dpois.o log1p.o ppois.o qnorm.o rnchisq.o choose.o dt.o mlutils.o pt.o qnt.o rnorm.o d1mach.o dunif.o pbeta.o ptukey.o qpois.o rpois.o dbeta.o dweibull.o pbinom.o punif.o qt.o rt.o dbinom.o expm1.o pcauchy.o pweibull.o qtukey.o runif.o dcauchy.o fmax2.o pchisq.o qbeta.o qunif.o rweibull.o dchisq.o fmin2.o pexp.o qbinom.o qweibull.o dexp.o fprec.o pf.o qcauchy.o rbeta.o sign.o df.o fround.o pgamma.o qchisq.o rbinom.o signrank.o dgamma.o fsign.o pgeom.o qexp.o rcauchy.o dgeom.o ftrunc.o phyper.o qf.o rchisq.o stirlerr.o dhyper.o gamma.o plnorm.o qgamma.o rexp.o toms708.o dlnorm.o gamma_cody.o plogis.o qgeom.o rf.o wilcox.o dlogis.o gammalim
s.o pnbeta.o qhyper.o rgamma.o sunif.o sexp.o snorm.o
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/Rmath'
cd lib/pcre2; gmake libpcre2.a || exit 1;
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/pcre2'
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_auto_possess.o -c pcre2_auto_possess.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_chartables.o -c pcre2_chartables.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_compile.o -c pcre2_compile.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_config.o -c pcre2_config.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_context.o -c pcre2_context.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_dfa_match.o -c pcre2_dfa_match.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_error.o -c pcre2_error.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_jit_compile.o -c pcre2_jit_compile.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_maketables.o -c pcre2_maketables.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match.o -c pcre2_match.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match_data.o -c pcre2_match_data.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_newline.o -c pcre2_newline.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ord2utf.o -c pcre2_ord2utf.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_pattern_info.o -c pcre2_pattern_info.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_string_utils.o -c pcre2_string_utils.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_study.o -c pcre2_study.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substitute.o -c pcre2_substitute.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substring.o -c pcre2_substring.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_tables.o -c pcre2_tables.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ucd.o -c pcre2_ucd.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_valid_utf.o -c pcre2_valid_utf.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_xclass.o -c pcre2_xclass.c
ar -rc libpcre2.a pcre2_auto_possess.o pcre2_chartables.o pcre2_compile.o pcre2_config.o pcre2_context.o pcre2_dfa_match.o pcre2_error.o pcre2_jit_compile.o pcre2_maketables.o pcre2_match.o pcre2_match_data.o pcre2_newline.o pcre2_ord2utf.o pcre2_pattern_info.o pcre2_string_utils.o pcre2_study.o pcre2_substitute.o pcre2_substring.o pcre2_tables.o pcre2_ucd.o pcre2_valid_utf.o pcre2_xclass.o
ranlib libpcre2.a
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/pcre2'
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ahmm.o -c ahmm.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o align.o -c align.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o allele.o -c allele.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_1000g.o -c annotate_1000g.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_dbsnp_rsid.o -c annotate_dbsnp_rsid.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_indels.o -c annotate_indels.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_indels2.o -c annotate_indels2.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_regions.o -c annotate_regions.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_variants.o -c annotate_variants.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_vntrs.o -c annotate_vntrs.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o augmented_bam_record.o -c augmented_bam_record.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_genotyping_buffered_reader.o -c bcf_genotyping_buffered_reader.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_single_genotyping_buffered_reader.o -c bcf_single_genotyping_buffered_reader.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bam_ordered_reader.o -c bam_ordered_reader.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp
bcf_ordered_writer.cpp:128:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
bcf_hdr_write(file, hdr);
^~~~~~~~~~~~~ ~~~~~~~~~
bcf_ordered_writer.cpp:167:43: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
bcf_get_pos1(v),
^~~~~~~~~~~~~~~
./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1'
#define bcf_get_pos1(v) ((v)->pos+1)
^~~~~~~~~~~~
bcf_ordered_writer.cpp:169:43: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
bcf_get_pos1(buffer.front()),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1'
#define bcf_get_pos1(v) ((v)->pos+1)
^~~~~~~~~~~~
bcf_ordered_writer.cpp:171:43: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
bcf_get_pos1(buffer.front())-bcf_get_pos1(v)+1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1'
#define bcf_get_pos1(v) ((v)->pos+1)
^
bcf_ordered_writer.cpp:194:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
bcf_write(file, hdr, v);
^~~~~~~~~ ~~~~~~~~~~~~
bcf_ordered_writer.cpp:244:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
bcf_write(file, hdr, buffer.back());
^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~
bcf_ordered_writer.cpp:260:21: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
bcf_write(file, hdr, buffer.back());
^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~
7 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_synced_reader.o -c bcf_synced_reader.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bed.o -c bed.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o candidate_motif_picker.o -c candidate_motif_picker.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o candidate_region_extractor.o -c candidate_region_extractor.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o cat.o -c cat.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o chmm.o -c chmm.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o complex_genotyping_record.o -c complex_genotyping_record.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_concordance.o -c compute_concordance.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_features.o -c compute_features.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_features2.o -c compute_features2.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_rl_dist.o -c compute_rl_dist.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o config.o -c config.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate_multiallelics.o -c consolidate_multiallelics.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate_vntrs.o -c consolidate_vntrs.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate.o -c consolidate.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o construct_probes.o -c construct_probes.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose.o -c decompose.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose2.o -c decompose2.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose_blocksub.o -c decompose_blocksub.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o discover.o -c discover.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o duplicate.o -c duplicate.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o estimate.o -c estimate.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o estimator.o -c estimator.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o extract_vntrs.o -c extract_vntrs.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o filter.o -c filter.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o filter_overlap.o -c filter_overlap.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o flank_detector.o -c flank_detector.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o fuzzy_aligner.o -c fuzzy_aligner.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o fuzzy_partition.o -c fuzzy_partition.cpp
fuzzy_partition.cpp:153:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
bcf_hdr_sync(odr->hdr);
^~~~~~~~~~~~ ~~~~~~~~
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o gencode.o -c gencode.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genome_interval.o -c genome_interval.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genotype.o -c genotype.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genotyping_record.o -c genotyping_record.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ghmm.o -c ghmm.cpp
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o hts_utils.o -c hts_utils.cpp
hts_utils.cpp:50:25: error: member access into incomplete type 'const faidx_t'
iter = kh_get(s, fai->hash, c_name);
^
/usr/local/include/htslib/faidx.h:69:8: note: forward declaration of 'faidx_t'
struct faidx_t;
^
hts_utils.cpp:51:26: error: member access into incomplete type 'const faidx_t'
if(iter == kh_end(fai->hash)) return 0;
^
/usr/local/include/htslib/faidx.h:69:8: note: forward declaration of 'faidx_t'
struct faidx_t;
^
hts_utils.cpp:52:23: error: member access into incomplete type 'const faidx_t'
val = kh_value(fai->hash, iter);
^
/usr/local/include/htslib/faidx.h:69:8: note: forward declaration of 'faidx_t'
struct faidx_t;
^
hts_utils.cpp:60:29: error: member access into incomplete type 'const faidx_t'
int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
^
/usr/local/include/htslib/faidx.h:69:8: note: forward declaration of 'faidx_t'
struct faidx_t;
^
hts_utils.cpp:69:29: error: member access into incomplete type 'const faidx_t'
while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
^
/usr/local/include/htslib/faidx.h:69:8: note: forward declaration of 'faidx_t'
struct faidx_t;
^
hts_utils.cpp:428:21: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
if ( h->dirty ) bcf_hdr_sync(h);
^~~~~~~~~~~~ ~
1 warning and 5 errors generated.
gmake[1]: *** [Makefile:175: hts_utils.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/vt
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