From owner-freebsd-pkg-fallout@freebsd.org Fri Dec 1 13:04:37 2017 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 52C78DFFE39 for ; Fri, 1 Dec 2017 13:04:37 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id 3F6201166 for ; Fri, 1 Dec 2017 13:04:37 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 3B03FDFFE38; Fri, 1 Dec 2017 13:04:37 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 3AAE5DFFE37 for ; Fri, 1 Dec 2017 13:04:37 +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 TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 153B51164; Fri, 1 Dec 2017 13:04:37 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy9.nyi.freebsd.org (localhost [127.0.0.1]) by beefy9.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id vB1D4aAa050576; Fri, 1 Dec 2017 13:04:36 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy9.nyi.freebsd.org (8.15.2/8.15.2/Submit) id vB1D4aM5050542; Fri, 1 Dec 2017 13:04:36 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Fri, 1 Dec 2017 13:04:36 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201712011304.vB1D4aM5050542@beefy9.nyi.freebsd.org> To: bacon4000@gmail.com Subject: [package - 110amd64-default][biology/bwa] Failed for bwa-0.7.17 in patch Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 01 Dec 2017 13:04:37 -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: bacon4000@gmail.com Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/bwa/Makefile 455045 2017-11-28 15:21:01Z jwb $ Log URL: http://beefy9.nyi.freebsd.org/data/110amd64-default/455158/logs/bwa-0.7.17.log Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=110amd64-default&build=455158 Log: ====>> Building biology/bwa build started at Fri Dec 1 13:04:34 UTC 2017 port directory: /usr/ports/biology/bwa building for: FreeBSD 110amd64-default-job-19 11.0-RELEASE-p16 FreeBSD 11.0-RELEASE-p16 amd64 maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: head/biology/bwa/Makefile 455045 2017-11-28 15:21:01Z jwb $ Poudriere version: 3.1.22 Host OSVERSION: 1200052 Jail OSVERSION: 1100122 Job Id: 19 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p16 UNAME_r=11.0-RELEASE-p16 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110amd64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=bwa-0.7.17 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110amd64-default/ref/.p/pool MASTERNAME=110amd64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.22 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bwa/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-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bwa/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 LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -msse2 -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -msse2 -fstack-protector -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=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.24.3 PERL_VER=5.24 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.24 DOCSDIR="share/doc/bwa" EXAMPLESDIR="share/examples/bwa" DATADIR="share/bwa" WWWDIR="www/bwa" ETCDIR="etc/bwa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bwa DOCSDIR=/usr/local/share/doc/bwa EXAMPLESDIR=/usr/local/share/examples/bwa WWWDIR=/usr/local/www/bwa ETCDIR=/usr/local/etc/bwa --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=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 #### ARCH=amd64 CONFIGURE_MAX_CMD_LEN=262144 HAVE_COMPAT_IA32_KERN=YES OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _OSRELEASE=11.0-RELEASE-p16 #### Misc Poudriere #### GID=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 GPLv3 accepted by the user =========================================================================== =================================================== ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.2.txz [110amd64-default-job-19] Installing pkg-1.10.2... [110amd64-default-job-19] Extracting pkg-1.10.2: .......... done ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bwa-0.7.17 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user => lh3-bwa-v0.7.17_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/lh3/bwa/tar.gz/v0.7.17?dummy=/lh3-bwa-v0.7.17_GH0.tar.gz fetch: https://codeload.github.com/lh3/bwa/tar.gz/v0.7.17?dummy=/lh3-bwa-v0.7.17_GH0.tar.gz: size unknown fetch: https://codeload.github.com/lh3/bwa/tar.gz/v0.7.17?dummy=/lh3-bwa-v0.7.17_GH0.tar.gz: size of remote file is not known lh3-bwa-v0.7.17_GH0.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by bwa-0.7.17 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building ===> Extracting for bwa-0.7.17 => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bwa-0.7.17 ===> Applying FreeBSD patches for bwa-0.7.17 Ignoring previously applied (or reversed) patch. 1 out of 1 hunks ignored--saving rejects to bwt_lite.c.rej => FreeBSD patch patch-bwt_lite.c failed to apply cleanly. => Patch(es) patch-Makefile applied cleanly. *** Error code 1 Stop. make: stopped in /usr/ports/biology/bwa