From owner-freebsd-pkg-fallout@freebsd.org Wed Mar 25 16:49:33 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 D4E842A6028 for ; Wed, 25 Mar 2020 16:49:33 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (mailman.nyi.freebsd.org [IPv6:2610:1c1:1:606c::50:13]) by mx1.freebsd.org (Postfix) with ESMTP id 48nYxQ6zzwz4fKy for ; Wed, 25 Mar 2020 16:49:30 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 2FB172A6025; Wed, 25 Mar 2020 16:49:28 +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 1C8CF2A6024 for ; Wed, 25 Mar 2020 16:49:28 +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) server-signature RSA-PSS (4096 bits) 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 48nYxM39nNz4fHy for ; Wed, 25 Mar 2020 16:49:27 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:eb]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 610731E255 for ; Wed, 25 Mar 2020 16:49:23 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (localhost [127.0.0.1]) by beefy8.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 02PGnNQK084770 for ; Wed, 25 Mar 2020 16:49:23 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy8.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 02PGnNt5084769; Wed, 25 Mar 2020 16:49:23 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 25 Mar 2020 16:49:23 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202003251649.02PGnNt5084769@beefy8.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/cufflinks] Failed for cufflinks-2.2.1.83_2 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 25 Mar 2020 16:49:34 -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: yuri@FreeBSD.org Last committer: jbeich@FreeBSD.org Ident: $FreeBSD: head/biology/cufflinks/Makefile 519824 2019-12-11 17:53:48Z jbeich $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p529018_s359264/logs/cufflinks-2.2.1.83_2.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p529018_s359264 Log: =>> Building biology/cufflinks build started at Wed Mar 25 16:47:04 UTC 2020 port directory: /usr/ports/biology/cufflinks package name: cufflinks-2.2.1.83_2 building for: FreeBSD head-armv6-default-job-13 13.0-CURRENT FreeBSD 13.0-CURRENT 1300085 arm maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/cufflinks/Makefile 519824 2019-12-11 17:53:48Z jbeich $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300076 Jail OSVERSION: 1300085 Job Id: 13 !!! Jail is newer than host. (Jail: 1300085, Host: 1300076) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300085 UNAME_v=FreeBSD 13.0-CURRENT 1300085 UNAME_r=13.0-CURRENT BLOCKSIZE=K STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv6-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-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/eigen3 " 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-- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /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_9d218390=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-rc4-5-g52c365aa9ca) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-rc4-5-g52c365aa9ca) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-rc4-5-g52c365aa9ca) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300085 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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 BSL accepted by the user =========================================================================== =================================================== ===> cufflinks-2.2.1.83_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.13.2.txz [head-armv6-default-job-13] Installing pkg-1.13.2... [head-armv6-default-job-13] Extracting pkg-1.13.2: .......... done ===> cufflinks-2.2.1.83_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cufflinks-2.2.1.83_2 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building =========================================================================== =================================================== ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz. =========================================================================== -- cufflinks 2.2.2 Configuration Results -- C++ compiler: /nxb-bin/usr/bin/c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -fstack-protector-strong -L/usr/lib GCC version: FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-rc4-5-g52c365aa9ca) Host System type: armv6-portbld-freebsd13.0 Install prefix: /usr/local Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. =========================================================================== =================================================== ===> Building for cufflinks-2.2.1.83_2 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050' gmake all-recursive gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050' Making all in src gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/src' /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT cufflinks.o -MD -MP -MF .deps/cufflinks.Tpo -c -o cufflinks.o cufflinks.cpp In file included from cufflinks.cpp:15: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from cufflinks.cpp:19: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ In file included from cufflinks.cpp:20: In file included from ./clustering.h:38: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from cufflinks.cpp:28: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cufflinks.cpp:693:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] bool ref_guided = (ref_scaffs != NULL); ^ cufflinks.cpp:690:5: note: previous statement is here if (bundle.hits().size() >= max_frags_per_bundle) ^ cufflinks.cpp:1279:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] if (!final_est_run && bundle_mode==REF_DRIVEN) // Bias needs to be learned ^ cufflinks.cpp:1275:5: note: previous statement is here if (allow_junk_filtering) ^ cufflinks.cpp:1176:17: warning: unused variable 'map_mass' [-Wunused-variable] long double map_mass = rg_props->normalized_map_mass(); ^ cufflinks.cpp:1522:3: error: reference to 'thread' is ambiguous thread asmbl(assemble_bundle, ^ /usr/include/c++/v1/__threading_support:605:24: note: candidate found by name lookup is 'std::__1::thread' class _LIBCPP_TYPE_VIS thread; ^ /usr/local/include/boost/thread/detail/thread.hpp:163:29: note: candidate found by name lookup is 'boost::thread' class BOOST_THREAD_DECL thread ^ In file included from cufflinks.cpp:23: In file included from ./filters.h:18: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 47 warnings and 1 error generated. gmake[3]: *** [Makefile:1672: cufflinks.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/src' gmake[2]: *** [Makefile:400: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050' gmake[1]: *** [Makefile:341: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050' *** Error code 1 Stop. make: stopped in /usr/ports/biology/cufflinks