From owner-freebsd-pkg-fallout@freebsd.org Thu Nov 21 13:57:08 2019 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 E76B41BF88F for ; Thu, 21 Nov 2019 13:57:08 +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 47Jh2D6PLSz4QbB for ; Thu, 21 Nov 2019 13:57:08 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id DB7CE1BF88C; Thu, 21 Nov 2019 13:57:08 +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 DB3921BF88B for ; Thu, 21 Nov 2019 13:57:08 +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 47Jh2D6H2Hz4Qb9; Thu, 21 Nov 2019 13:57:08 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:f3]) (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 BC171C43F; Thu, 21 Nov 2019 13:57:08 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (localhost [127.0.0.1]) by beefy18.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id xALDv8Xi043194; Thu, 21 Nov 2019 13:57:08 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy18.nyi.freebsd.org (8.15.2/8.15.2/Submit) id xALDv8XF043012; Thu, 21 Nov 2019 13:57:08 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 21 Nov 2019 13:57:08 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201911211357.xALDv8XF043012@beefy18.nyi.freebsd.org> To: mzaki@m.u-tokyo.ac.jp Subject: [package - head-amd64-default][biology/muscle] Failed for muscle-3.8.31 in build Cc: pkg-fallout@FreeBSD.org 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: Thu, 21 Nov 2019 13:57:09 -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: mzaki@m.u-tokyo.ac.jp Last committer: linimon@FreeBSD.org Ident: $FreeBSD: head/biology/muscle/Makefile 425879 2016-11-11 09:31:02Z linimon $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p518072_s354837/logs/muscle-3.8.31.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p518072_s354837 Log: =>> Building biology/muscle build started at Thu Nov 21 13:56:21 UTC 2019 port directory: /usr/ports/biology/muscle package name: muscle-3.8.31 building for: FreeBSD head-amd64-default-job-06 13.0-CURRENT FreeBSD 13.0-CURRENT 1300059 amd64 maintained by: mzaki@m.u-tokyo.ac.jp Makefile ident: $FreeBSD: head/biology/muscle/Makefile 425879 2016-11-11 09:31:02Z linimon $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300047 Jail OSVERSION: 1300059 Job Id: 06 !!! Jail is newer than host. (Jail: 1300059, Host: 1300047) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300059 UNAME_v=FreeBSD 13.0-CURRENT 1300059 UNAME_r=13.0-CURRENT 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/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-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-- mzaki@m.u-tokyo.ac.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/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=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/muscle" EXAMPLESDIR="share/examples/muscle" DATADIR="share/muscle" WWWDIR="www/muscle" ETCDIR="etc/muscle" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/muscle DOCSDIR=/usr/local/share/doc/muscle EXAMPLESDIR=/usr/local/share/examples/muscle WWWDIR=/usr/local/www/muscle ETCDIR=/usr/local/etc/muscle --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 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0) Target: x86_64-unknown-freebsd13.0 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 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300059 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---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-- =================================================== =========================================================================== =================================================== ===> muscle-3.8.31 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz [head-amd64-default-job-06] Installing pkg-1.12.0... [head-amd64-default-job-06] Extracting pkg-1.12.0: .......... done ===> muscle-3.8.31 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of muscle-3.8.31 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by muscle-3.8.31 for building =========================================================================== =================================================== ===> Fetching all distfiles required by muscle-3.8.31 for building => SHA256 Checksum OK for muscle3.8.31_src.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by muscle-3.8.31 for building ===> Extracting for muscle-3.8.31 => SHA256 Checksum OK for muscle3.8.31_src.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for muscle-3.8.31 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for muscle-3.8.31 =========================================================================== =================================================== =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for muscle-3.8.31 =========================================================================== =================================================== ===> Building for muscle-3.8.31 --- muscle --- chmod +x ./mk ./mk ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported ./mk: cannot create /dev/tty: Operation not supported #define INFINITY __builtin_inff() ^ 1 error generated. In file included from treefrommsa.cpp:5: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ 1 warning generated. clang-cpp: error: no such file or directory: 'subfams.o' ls: muscle: No such file or directory sum: muscle: No such file or directory *** [muscle] Error code 1 make[1]: stopped in /wrkdirs/usr/ports/biology/muscle/work/muscle3.8.31/src 1 error make[1]: stopped in /wrkdirs/usr/ports/biology/muscle/work/muscle3.8.31/src ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/muscle