From nobody Mon Mar 07 22:45:16 2022 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 64A121A09BC2; Mon, 7 Mar 2022 22:45:16 +0000 (UTC) (envelope-from git@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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4KCD7J2M6Gz4cp2; Mon, 7 Mar 2022 22:45:16 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1646693116; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=XpSBtYZGfzIPwRSOlGkhnW5h9W2BuEpFT9evYSUKuqw=; b=E7hpn0+1ezu2ghDYicAAr5DteEhCL2DdNI+MtrBgesNuiytPtFsCkz/i4+AwFzdEP92WYz KaYZGJN7B0uUn88bDSdCctc171dmsbM7RxetjHxswduSoosar3bEJwjA1UMKV9Dq5TcnD8 yx9L+sm6yYGPCfQj2ffqyqK1+53LdQGbbFyDsUK8hA+7USHiYedeKuuOTu560IwIPsNzSv nm4S1BqkBppwAWTjjaVPHC80A7/rtjgQtbyV9cwpleNfM8fnZjjd4cHYifejF82uDCWycs 5G1ngsbndLn2IzJ0FEhqAZfTUHerfRf6G7rz/TfO6qCfSO9EAPM2XLiLRhBDrg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (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 307CF1122E; Mon, 7 Mar 2022 22:45:16 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 227MjGeg040494; Mon, 7 Mar 2022 22:45:16 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 227MjGHB040493; Mon, 7 Mar 2022 22:45:16 GMT (envelope-from git) Date: Mon, 7 Mar 2022 22:45:16 GMT Message-Id: <202203072245.227MjGHB040493@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Rene Ladan Subject: git: 4e051b961c7e - main - biology/gffread: remove local poudriere files List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: rene X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 4e051b961c7e0a940fd8e183113d85223b5b3f72 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1646693116; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=XpSBtYZGfzIPwRSOlGkhnW5h9W2BuEpFT9evYSUKuqw=; b=wOc+kwqq67a13lyu+d7Wr1yiR5pJJSlD6I6JnHpRQn40/uZUVVvbf3TaKQ0iDGw4l+kCew dpP/5wJ6FzTYyANLWv+A1trWY2b2HKRd2fkh2wEII0N62PyJHhRSd2bZ/V5KSaQrotrdLy Fk/AlnCeCg++Kw1QTdx9VTsWLzqVvBQaGXtOigSmP4FkDfZkY/YfQthFXZGbyvuj5g4ph6 d8sxi29a8OmOxOxEm3NHdb/44TfwyO+s4vW7q9AfaNguA0FWSI7XMLXG0XvcI9UiKRVDAU UqiB/Sr1YPhsgmaAEjEzaihLRTcONyamThwhdLTfKjoc6PIfQsmt14hBChpzZA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1646693116; a=rsa-sha256; cv=none; b=TIhx5hrC30HVKWkZXchzf826Ft7tJkzuwa4c5QnEAdADU7JYNGb3eIqdl0T/wVu9Xz1PrK UYZ4fOOMkUa5AF9dMgJkWI4Wugx6bj7D8gIkBrJXAS+xBcH7loRB40XL4wJWWY3UCrIiK/ vzOWY58s7tUKpbIzYImTlyrpo45o+dd//NiclKRFyhsIvVl194fDLkGzvUJqwWRKUGgUaR 22gxMMoHeTIUNiUJfx7yUHpEi2IGKwiQlinyBRraqdJppidyKCK1zfJBtD0gYAUkt8XdVU O3lPWY4woX/o0tBjgwTqDDDhBQQkBIeLVRue2cCSJP8BFh9PNKA9cmOgQXR6fA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by rene: URL: https://cgit.FreeBSD.org/ports/commit/?id=4e051b961c7e0a940fd8e183113d85223b5b3f72 commit 4e051b961c7e0a940fd8e183113d85223b5b3f72 Author: Rene Ladan AuthorDate: 2022-03-07 22:44:38 +0000 Commit: Rene Ladan CommitDate: 2022-03-07 22:44:38 +0000 biology/gffread: remove local poudriere files --- biology/gffread/gffread-0.12.7.log-12-2-amd64 | 262 ------------------------- biology/gffread/gffread-0.12.7.log-13-0-amd64 | 264 -------------------------- 2 files changed, 526 deletions(-) diff --git a/biology/gffread/gffread-0.12.7.log-12-2-amd64 b/biology/gffread/gffread-0.12.7.log-12-2-amd64 deleted file mode 100644 index 03ec053fefed..000000000000 --- a/biology/gffread/gffread-0.12.7.log-12-2-amd64 +++ /dev/null @@ -1,262 +0,0 @@ -build started at Wed Nov 10 14:44:00 CST 2021 -port directory: /usr/ports/wip/gffread -package name: gffread-0.12.7 -building for: FreeBSD 12-2-amd64-default 12.2-RELEASE-p10 FreeBSD 12.2-RELEASE-p10 amd64 -maintained by: jwb@FreeBSD.org -Makefile ident: -Poudriere version: 3.3.7_1 -Host OSVERSION: 1300139 -Jail OSVERSION: 1202000 -Job Id: - ----Begin Environment--- -SHELL=/bin/csh -OSVERSION=1202000 -UNAME_v=FreeBSD 12.2-RELEASE-p10 -UNAME_r=12.2-RELEASE-p10 -BLOCKSIZE=K -MAIL=/var/mail/root -WARNING_WAIT=0 -STATUS=1 -HOME=/root -PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin -LOCALBASE=/usr/local -USER=root -TRYBROKEN=yes -LIBEXECPREFIX=/usr/local/libexec/poudriere -POUDRIERE_VERSION=3.3.7_1 -MASTERMNT=/usr/local/poudriere/data/.m/12-2-amd64-default/ref -DEV_WARNING_WAIT=0 -POUDRIERE_BUILD_TYPE=bulk -PACKAGE_BUILDING=yes -SAVED_TERM=xterm-256color -GID=0 -UID=0 -PWD=/usr/local/poudriere/data/.m/12-2-amd64-default/ref/.p -NO_WARNING_PKG_INSTALL_EOL=yes -P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS -MASTERNAME=12-2-amd64-default -SCRIPTPREFIX=/usr/local/share/poudriere -OLDPWD=/usr/local/poudriere/data/.m/12-2-amd64-default/ref/.p -SCRIPTPATH=/usr/local/share/poudriere/testport.sh -POUDRIEREPATH=/usr/local/bin/poudriere ----End Environment--- - ----Begin Poudriere Port Flags/Env--- -PORT_FLAGS= -PKGENV=PACKAGES=/tmp/pkgs PKGREPOSITORY=/tmp/pkgs PKGLATESTREPOSITORY=/tmp/pkgs/Latest -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/wip/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/wip/gffread/work/.cache HOME=/wrkdirs/usr/ports/wip/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/wip/gffread/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/wip/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/wip/gffread/work/.cache HOME=/wrkdirs/usr/ports/wip/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/wip/gffread/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=12.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gffread" EXAMPLESDIR="share/examples/gffread" DATADIR="share/gffread" WWWDIR="www/gffread" ETCDIR="etc/gffread" ---End PLIST_SUB-- - ---SUB_LIST-- -PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gffread DOCSDIR=/usr/local/share/doc/gffread EXAMPLESDIR=/usr/local/share/examples/gffread WWWDIR=/usr/local/www/gffread ETCDIR=/usr/local/etc/gffread ---End SUB_LIST-- - ----Begin make.conf--- -USE_PACKAGE_DEPENDS=yes -BATCH=yes -WRKDIRPREFIX=/wrkdirs -PORTSDIR=/usr/ports -PACKAGES=/packages -DISTDIR=/distfiles -FORCE_PACKAGE=yes -PACKAGE_BUILDING=yes -PACKAGE_BUILDING_FLAVORS=yes -#### /usr/local/etc/poudriere.d/make.conf #### -# Added by auto-admin from /usr/local/sbin/port-poudriere-setup -USE_LOCAL_MK=yes -# End auto-admin addition -#### Misc Poudriere #### -.include "/etc/make.conf.ports_env" ----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) 12013 -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 -=========================================================================== -=================================================== -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - not found -===> Installing existing package /packages/All/pkg-1.17.3.pkg -[12-2-amd64-default] Installing pkg-1.17.3... -[12-2-amd64-default] Extracting pkg-1.17.3: .......... done -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Returning to build of gffread-0.12.7 -=========================================================================== -=================================================== -=========================================================================== -=================================================== -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -=========================================================================== -=================================================== -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. -=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. -=========================================================================== -=================================================== -=========================================================================== -=================================================== -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -===> Extracting for gffread-0.12.7 -=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. -=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. -=========================================================================== -=================================================== -=========================================================================== -=================================================== -===> Patching for gffread-0.12.7 -===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/wip/gffread/files -=========================================================================== -=================================================== -===> gffread-0.12.7 depends on package: gmake>=4.3 - not found -===> Installing existing package /packages/All/gmake-4.3_2.pkg -[12-2-amd64-default] Installing gmake-4.3_2... -[12-2-amd64-default] `-- Installing gettext-runtime-0.21... -[12-2-amd64-default] | `-- Installing indexinfo-0.3.1... -[12-2-amd64-default] | `-- Extracting indexinfo-0.3.1: .... done -[12-2-amd64-default] `-- Extracting gettext-runtime-0.21: .......... done -[12-2-amd64-default] Extracting gmake-4.3_2: .......... done -===> gffread-0.12.7 depends on package: gmake>=4.3 - found -===> Returning to build of gffread-0.12.7 -=========================================================================== -=================================================== -=========================================================================== -=>> Recording filesystem state for prebuild... done -=================================================== -===> gffread-0.12.7 depends on package: gmake>=4.3 - found -===> Configuring for gffread-0.12.7 -=========================================================================== -=================================================== -===> Building for gffread-0.12.7 -gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gff_utils.cpp -o gff_utils.o -gclib/gff.cpp:37:12: warning: unused variable 'CLASSCODE_J_RANK' [-Wunused-const-variable] -const byte CLASSCODE_J_RANK = 6; // all junctional based overlaps - ^ -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gffread.cpp -o gffread.o -1 warning generated. -c++ -fstack-protector-strong -o gffread gclib/GBase.o gclib/GArgs.o gclib/GFaSeqGet.o gclib/gdna.o gclib/codons.o gclib/gff.o gclib/GStr.o gclib/GFastaIndex.o gff_utils.o gffread.o -gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -=========================================================================== -=>> Checking for filesystem violations... done -=================================================== -=========================================================================== -=>> Recording filesystem state for prestage... done -=================================================== -===> Staging for gffread-0.12.7 -===> Generating temporary packing list -gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -install -c gffread /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin -strip /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin/gffread -gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -====> Compressing man pages (compress-man) -=========================================================================== -====> Running Q/A tests (stage-qa) -====> Checking for pkg-plist issues (check-plist) -===> Parsing plist -===> Checking for items in STAGEDIR missing from pkg-plist -===> Checking for items in pkg-plist which are not in STAGEDIR -===> No pkg-plist issues found (check-plist) -=>> Checking for staging violations... done -=================================================== -===> Building package for gffread-0.12.7 -install -l rs /tmp/pkgs/gffread-0.12.7.pkg /tmp/pkgs/gffread-0.12.7.txz -=========================================================================== -=>> Recording filesystem state for preinst... done -=================================================== -===> Installing for gffread-0.12.7 -===> Checking if gffread is already installed -===> Registering installation for gffread-0.12.7 -[12-2-amd64-default] Installing gffread-0.12.7... -=========================================================================== -=>> Checking shared library dependencies - 0x0000000000000001 NEEDED Shared library: [libc++.so.1] - 0x0000000000000001 NEEDED Shared library: [libc.so.7] - 0x0000000000000001 NEEDED Shared library: [libcxxrt.so.1] - 0x0000000000000001 NEEDED Shared library: [libm.so.5] -=================================================== -===> Deinstalling for gffread -===> Deinstalling gffread-0.12.7 -Updating database digests format: ..... done -Checking integrity... done (0 conflicting) -Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): - -Installed packages to be REMOVED: - gffread: 0.12.7 - -Number of packages to be removed: 1 -[12-2-amd64-default] [1/1] Deinstalling gffread-0.12.7... -[12-2-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done -=========================================================================== -=>> Checking for extra files and directories -[00:00:24] Installing from package -[12-2-amd64-default] Installing gffread-0.12.7... -[12-2-amd64-default] Extracting gffread-0.12.7: .... done -[00:00:24] Cleaning up -===> Cleaning for gffread-0.12.7 -[00:00:24] Deinstalling package -Updating database digests format: . done -Checking integrity... done (0 conflicting) -Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): - -Installed packages to be REMOVED: - gffread: 0.12.7 - -Number of packages to be removed: 1 -[12-2-amd64-default] [1/1] Deinstalling gffread-0.12.7... -[12-2-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done -build of wip/gffread | gffread-0.12.7 ended at Wed Nov 10 14:44:09 CST 2021 -build time: 00:00:09 diff --git a/biology/gffread/gffread-0.12.7.log-13-0-amd64 b/biology/gffread/gffread-0.12.7.log-13-0-amd64 deleted file mode 100644 index d28b274e37cf..000000000000 --- a/biology/gffread/gffread-0.12.7.log-13-0-amd64 +++ /dev/null @@ -1,264 +0,0 @@ -build started at Wed Nov 10 14:44:25 CST 2021 -port directory: /usr/ports/wip/gffread -package name: gffread-0.12.7 -building for: FreeBSD 13-0-amd64-default 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 amd64 -maintained by: jwb@FreeBSD.org -Makefile ident: -Poudriere version: 3.3.7_1 -Host OSVERSION: 1300139 -Jail OSVERSION: 1300139 -Job Id: - ----Begin Environment--- -SHELL=/bin/csh -OSVERSION=1300139 -UNAME_v=FreeBSD 13.0-RELEASE-p4 -UNAME_r=13.0-RELEASE-p4 -BLOCKSIZE=K -MAIL=/var/mail/root -MM_CHARSET=UTF-8 -LANG=C.UTF-8 -WARNING_WAIT=0 -STATUS=1 -HOME=/root -PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin -LOCALBASE=/usr/local -USER=root -TRYBROKEN=yes -LIBEXECPREFIX=/usr/local/libexec/poudriere -POUDRIERE_VERSION=3.3.7_1 -MASTERMNT=/usr/local/poudriere/data/.m/13-0-amd64-default/ref -DEV_WARNING_WAIT=0 -POUDRIERE_BUILD_TYPE=bulk -PACKAGE_BUILDING=yes -SAVED_TERM=xterm-256color -GID=0 -UID=0 -PWD=/usr/local/poudriere/data/.m/13-0-amd64-default/ref/.p -NO_WARNING_PKG_INSTALL_EOL=yes -P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS -MASTERNAME=13-0-amd64-default -SCRIPTPREFIX=/usr/local/share/poudriere -OLDPWD=/usr/local/poudriere/data/.m/13-0-amd64-default/ref/.p -SCRIPTPATH=/usr/local/share/poudriere/testport.sh -POUDRIEREPATH=/usr/local/bin/poudriere ----End Environment--- - ----Begin Poudriere Port Flags/Env--- -PORT_FLAGS= -PKGENV=PACKAGES=/tmp/pkgs PKGREPOSITORY=/tmp/pkgs PKGLATESTREPOSITORY=/tmp/pkgs/Latest -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/wip/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/wip/gffread/work/.cache HOME=/wrkdirs/usr/ports/wip/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/wip/gffread/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/wip/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/wip/gffread/work/.cache HOME=/wrkdirs/usr/ports/wip/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/wip/gffread/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/gffread" EXAMPLESDIR="share/examples/gffread" DATADIR="share/gffread" WWWDIR="www/gffread" ETCDIR="etc/gffread" ---End PLIST_SUB-- - ---SUB_LIST-- -PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gffread DOCSDIR=/usr/local/share/doc/gffread EXAMPLESDIR=/usr/local/share/examples/gffread WWWDIR=/usr/local/www/gffread ETCDIR=/usr/local/etc/gffread ---End SUB_LIST-- - ----Begin make.conf--- -USE_PACKAGE_DEPENDS=yes -BATCH=yes -WRKDIRPREFIX=/wrkdirs -PORTSDIR=/usr/ports -PACKAGES=/packages -DISTDIR=/distfiles -FORCE_PACKAGE=yes -PACKAGE_BUILDING=yes -PACKAGE_BUILDING_FLAVORS=yes -#### /usr/local/etc/poudriere.d/make.conf #### -# Added by auto-admin from /usr/local/sbin/port-poudriere-setup -USE_LOCAL_MK=yes -# End auto-admin addition -#### Misc Poudriere #### -.include "/etc/make.conf.ports_env" ----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) 12013 -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 -=========================================================================== -=================================================== -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - not found -===> Installing existing package /packages/All/pkg-1.17.3.pkg -[13-0-amd64-default] Installing pkg-1.17.3... -[13-0-amd64-default] Extracting pkg-1.17.3: .......... done -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Returning to build of gffread-0.12.7 -=========================================================================== -=================================================== -=========================================================================== -=================================================== -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -=========================================================================== -=================================================== -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. -=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. -=========================================================================== -=================================================== -=========================================================================== -=================================================== -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -===> Extracting for gffread-0.12.7 -=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. -=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. -=========================================================================== -=================================================== -=========================================================================== -=================================================== -===> Patching for gffread-0.12.7 -===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/wip/gffread/files -=========================================================================== -=================================================== -===> gffread-0.12.7 depends on package: gmake>=4.3 - not found -===> Installing existing package /packages/All/gmake-4.3_2.pkg -[13-0-amd64-default] Installing gmake-4.3_2... -[13-0-amd64-default] `-- Installing gettext-runtime-0.21... -[13-0-amd64-default] | `-- Installing indexinfo-0.3.1... -[13-0-amd64-default] | `-- Extracting indexinfo-0.3.1: .... done -[13-0-amd64-default] `-- Extracting gettext-runtime-0.21: .......... done -[13-0-amd64-default] Extracting gmake-4.3_2: .......... done -===> gffread-0.12.7 depends on package: gmake>=4.3 - found -===> Returning to build of gffread-0.12.7 -=========================================================================== -=================================================== -=========================================================================== -=>> Recording filesystem state for prebuild... done -=================================================== -===> gffread-0.12.7 depends on package: gmake>=4.3 - found -===> Configuring for gffread-0.12.7 -=========================================================================== -=================================================== -===> Building for gffread-0.12.7 -gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gff_utils.cpp -o gff_utils.o -gclib/gff.cpp:37:12: warning: unused variable 'CLASSCODE_J_RANK' [-Wunused-const-variable] -const byte CLASSCODE_J_RANK = 6; // all junctional based overlaps - ^ -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gffread.cpp -o gffread.o -1 warning generated. -c++ -fstack-protector-strong -o gffread gclib/GBase.o gclib/GArgs.o gclib/GFaSeqGet.o gclib/gdna.o gclib/codons.o gclib/gff.o gclib/GStr.o gclib/GFastaIndex.o gff_utils.o gffread.o -gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -=========================================================================== -=>> Checking for filesystem violations... done -=================================================== -=========================================================================== -=>> Recording filesystem state for prestage... done -=================================================== -===> Staging for gffread-0.12.7 -===> Generating temporary packing list -gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -install -c gffread /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin -strip /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin/gffread -gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -====> Compressing man pages (compress-man) -=========================================================================== -====> Running Q/A tests (stage-qa) -====> Checking for pkg-plist issues (check-plist) -===> Parsing plist -===> Checking for items in STAGEDIR missing from pkg-plist -===> Checking for items in pkg-plist which are not in STAGEDIR -===> No pkg-plist issues found (check-plist) -=>> Checking for staging violations... done -=================================================== -===> Building package for gffread-0.12.7 -install -l rs /tmp/pkgs/gffread-0.12.7.pkg /tmp/pkgs/gffread-0.12.7.txz -=========================================================================== -=>> Recording filesystem state for preinst... done -=================================================== -===> Installing for gffread-0.12.7 -===> Checking if gffread is already installed -===> Registering installation for gffread-0.12.7 -[13-0-amd64-default] Installing gffread-0.12.7... -=========================================================================== -=>> Checking shared library dependencies - 0x0000000000000001 NEEDED Shared library: [libc++.so.1] - 0x0000000000000001 NEEDED Shared library: [libc.so.7] - 0x0000000000000001 NEEDED Shared library: [libcxxrt.so.1] - 0x0000000000000001 NEEDED Shared library: [libm.so.5] -=================================================== -===> Deinstalling for gffread -===> Deinstalling gffread-0.12.7 -Updating database digests format: ..... done -Checking integrity... done (0 conflicting) -Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): - -Installed packages to be REMOVED: - gffread: 0.12.7 - -Number of packages to be removed: 1 -[13-0-amd64-default] [1/1] Deinstalling gffread-0.12.7... -[13-0-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done -=========================================================================== -=>> Checking for extra files and directories -[00:00:25] Installing from package -[13-0-amd64-default] Installing gffread-0.12.7... -[13-0-amd64-default] Extracting gffread-0.12.7: .... done -[00:00:25] Cleaning up -===> Cleaning for gffread-0.12.7 -[00:00:25] Deinstalling package -Updating database digests format: . done -Checking integrity... done (0 conflicting) -Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): - -Installed packages to be REMOVED: - gffread: 0.12.7 - -Number of packages to be removed: 1 -[13-0-amd64-default] [1/1] Deinstalling gffread-0.12.7... -[13-0-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done -build of wip/gffread | gffread-0.12.7 ended at Wed Nov 10 14:44:34 CST 2021 -build time: 00:00:09