From owner-freebsd-pkg-fallout@freebsd.org Sat Nov 7 01:55:39 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 24FBC2DC0CA for ; Sat, 7 Nov 2020 01:55:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 4CSgMH0VSLz3ND7 for ; Sat, 7 Nov 2020 01:55:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 110C62DC1EE; Sat, 7 Nov 2020 01:55:39 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 10C6C2DC0C9 for ; Sat, 7 Nov 2020 01:55:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4CSgMG73trz3NGZ; Sat, 7 Nov 2020 01:55:38 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy9.nyi.freebsd.org (beefy9.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:ec]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id E52092E57D; Sat, 7 Nov 2020 01:55:38 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy9.nyi.freebsd.org (localhost [127.0.0.1]) by beefy9.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 0A71tc0e092946; Sat, 7 Nov 2020 01:55:38 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy9.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 0A71tcDs092945; Sat, 7 Nov 2020 01:55:38 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 7 Nov 2020 01:55:38 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202011070155.0A71tcDs092945@beefy9.nyi.freebsd.org> To: jwb@FreeBSD.org Subject: [package - 114amd64-default][biology/vt] Failed for vt-0.57721_1 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 07 Nov 2020 01:55:39 -0000 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@FreeBSD.org Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/vt/Makefile 544091 2020-08-03 17:42:32Z jwb $ Log URL: http://beefy9.nyi.freebsd.org/data/114amd64-default/554339/logs/vt-0.57721_1.log Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=114amd64-default&build=554339 Log: =>> Building biology/vt build started at Sat Nov 7 01:51:41 UTC 2020 port directory: /usr/ports/biology/vt package name: vt-0.57721_1 building for: FreeBSD 114amd64-default-job-04 11.4-RELEASE-p4 FreeBSD 11.4-RELEASE-p4 amd64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/vt/Makefile 544091 2020-08-03 17:42:32Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300121 Jail OSVERSION: 1104001 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1104001 UNAME_v=FreeBSD 11.4-RELEASE-p4 UNAME_r=11.4-RELEASE-p4 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/114amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/114amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=114amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/114amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vt/work HOME=/wrkdirs/usr/ports/biology/vt/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vt/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- OPENSSLBASE=/usr OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vt/work HOME=/wrkdirs/usr/ports/biology/vt/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vt/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=11.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vt" EXAMPLESDIR="share/examples/vt" DATADIR="share/vt" WWWDIR="www/vt" ETCDIR="etc/vt" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vt DOCSDIR=/usr/local/share/doc/vt EXAMPLESDIR=/usr/local/share/examples/vt WWWDIR=/usr/local/www/vt ETCDIR=/usr/local/etc/vt --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=11.4-RELEASE-p4 OSREL=11.4 OSVERSION=1104001 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License MIT accepted by the user =========================================================================== =================================================== ===> vt-0.57721_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.15.10.txz [114amd64-default-job-04] Installing pkg-1.15.10... [114amd64-default-job-04] 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by vt-0.57721_1 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for vt-0.57721_1 ===> Applying FreeBSD patches for vt-0.57721_1 from /usr/ports/biology/vt/files =========================================================================== =================================================== ===> vt-0.57721_1 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [114amd64-default-job-04] Installing gmake-4.3_2... [114amd64-default-job-04] `-- Installing gettext-runtime-0.21... [114amd64-default-job-04] | `-- Installing indexinfo-0.3.1... [114amd64-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done [114amd64-default-job-04] `-- Extracting gettext-runtime-0.21: .......... done [114amd64-default-job-04] 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 =========================================================================== =================================================== ===> vt-0.57721_1 depends on shared library: libhts.so.3 - not found ===> Installing existing package /packages/All/htslib-1.11.0.txz [114amd64-default-job-04] Installing htslib-1.11.0... [114amd64-default-job-04] `-- Installing curl-7.73.0... [114amd64-default-job-04] | `-- Installing ca_root_nss-3.58... [114amd64-default-job-04] | `-- Extracting ca_root_nss-3.58: ........ done [114amd64-default-job-04] | `-- Installing libnghttp2-1.41.0... 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