Date: Fri, 1 Dec 2017 11:01:00 GMT From: pkg-fallout@FreeBSD.org To: bacon4000@gmail.com Cc: pkg-fallout@FreeBSD.org Subject: [package - 110i386-default][biology/bwa] Failed for bwa-0.7.17 in patch Message-ID: <201712011101.vB1B10RN040960@beefy10.nyi.freebsd.org>
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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://beefy10.nyi.freebsd.org/data/110i386-default/455158/logs/bwa-0.7.17.log Build URL: http://beefy10.nyi.freebsd.org/build.html?mastername=110i386-default&build=455158 Log: ====>> Building biology/bwa build started at Fri Dec 1 11:00:58 UTC 2017 port directory: /usr/ports/biology/bwa building for: FreeBSD 110i386-default-job-15 11.0-RELEASE-p16 FreeBSD 11.0-RELEASE-p16 i386 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: 15 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 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/110i386-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/110i386-default/ref/.p/pool MASTERNAME=110i386-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 MACHINE=i386 MACHINE_ARCH=i386 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 #### ARCH=i386 CONFIGURE_MAX_CMD_LEN=262144 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) 524288 stack size (kbytes, -s) 65536 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-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.2.txz [110i386-default-job-15] Installing pkg-1.10.2... [110i386-default-job-15] 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 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> 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 =========================================================================== =======================<phase: checksum >============================ ===> 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. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> 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. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> 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
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