Date: Wed, 10 Nov 2021 20:50:48 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 8d2198bb6d6b - main - biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc Message-ID: <202111102050.1AAKomHf045035@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=8d2198bb6d6b84739448087c8284079281149086 commit 8d2198bb6d6b84739448087c8284079281149086 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-11-10 20:49:10 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-11-10 20:49:10 +0000 biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more. --- biology/Makefile | 1 + biology/gffread/Makefile | 22 +++ biology/gffread/distinfo | 5 + biology/gffread/files/patch-Makefile | 68 +++++++ biology/gffread/gffread-0.12.7.log-12-2-amd64 | 262 +++++++++++++++++++++++++ biology/gffread/gffread-0.12.7.log-13-0-amd64 | 264 ++++++++++++++++++++++++++ biology/gffread/pkg-descr | 4 + 7 files changed, 626 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 708965107df8..1c79cff38867 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -57,6 +57,7 @@ SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps + SUBDIR += gffread SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan diff --git a/biology/gffread/Makefile b/biology/gffread/Makefile new file mode 100644 index 000000000000..01b7bee64778 --- /dev/null +++ b/biology/gffread/Makefile @@ -0,0 +1,22 @@ +PORTNAME= gffread +DISTVERSIONPREFIX= v +DISTVERSION= 0.12.7 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= GFF/GTF format conversions, filtering, FASTA extraction, etc + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= gmake +USE_GITHUB= yes + +GH_ACCOUNT= gpertea +GH_TUPLE= gpertea:gclib:v${DISTVERSION}:gpertea/gclib + +INSTALL_TARGET= install-strip + +PLIST_FILES= bin/gffread + +.include <bsd.port.mk> diff --git a/biology/gffread/distinfo b/biology/gffread/distinfo new file mode 100644 index 000000000000..14af8eee92bf --- /dev/null +++ b/biology/gffread/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1636511584 +SHA256 (gpertea-gffread-v0.12.7_GH0.tar.gz) = 6f3417090b3beb74f435bf5d462c87475b3c704a8a0d71821f6c1321c47dbbbe +SIZE (gpertea-gffread-v0.12.7_GH0.tar.gz) = 403734 +SHA256 (gpertea-gclib-v0.12.7_GH0.tar.gz) = 9c74db64c4ee1fb93a6c02fa227258baafc337303f26ce3ba0cf37dfc1ba687f +SIZE (gpertea-gclib-v0.12.7_GH0.tar.gz) = 259314 diff --git a/biology/gffread/files/patch-Makefile b/biology/gffread/files/patch-Makefile new file mode 100644 index 000000000000..f78ea90049d9 --- /dev/null +++ b/biology/gffread/files/patch-Makefile @@ -0,0 +1,68 @@ +--- Makefile.orig 2021-07-23 14:21:36 UTC ++++ Makefile +@@ -1,11 +1,11 @@ +-GCLDIR := $(if $(GCLDIR),$(GCLDIR),../gclib) ++GCLDIR := $(if $(GCLDIR),$(GCLDIR),gclib) + + SEARCHDIRS := -I. -I${GCLDIR} + + SYSTYPE := $(shell uname) + + CXX := $(if $(CXX),$(CXX),g++) +-LINKER := $(if $(LINKER),$(LINKER),g++) ++LINKER := $(if $(LINKER),$(LINKER),${CXX}) + + LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g) + +@@ -15,7 +15,7 @@ BASEFLAGS := -Wall -Wextra -std=c++11 ${SEARCHDIRS} - + + GCCV8 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 8) + ifeq "$(GCCV8)" "1" +- BASEFLAGS += -Wno-class-memaccess ++ # BASEFLAGS += -Wno-class-memaccess + endif + + CXXFLAGS := $(if $(CXXFLAGS),$(BASEFLAGS) $(CXXFLAGS),$(BASEFLAGS)) +@@ -33,7 +33,7 @@ else #debug builds + LDFLAGS += -pg + else + #CXXFLAGS += -g -O0 -DNDEBUG +- CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG ++ #CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG + endif + ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS))) + #use sanitizer in gcc 4.9+ +@@ -79,11 +79,8 @@ OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArgs.o ${GCLDIR}/ + + .PHONY : all + +-all static release debug memcheck memdebug profile gprof prof: ../gclib gffread ++all static release debug memcheck memdebug profile gprof prof: ${GCLDIR} gffread + +-../gclib: +- git clone https://github.com/gpertea/gclib.git ../gclib +- + $(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/gff.h + gffread.o : gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h + gff_utils.o : gff_utils.h $(GCLDIR)/gff.h +@@ -97,9 +94,19 @@ gffread: $(OBJS) gffread.o + + # target for removing all object files + +-.PHONY : clean ++.PHONY : clean install install-strip ++ + clean: + @${RM} gffread gffread.o* gffread.exe $(OBJS) + @${RM} core.* + ++INSTALL ?= install ++STRIP ?= strip ++PREFIX ?= /usr/local ++DESTDIR ?= . + ++install: ++ ${INSTALL} -c gffread ${DESTDIR}${PREFIX}/bin ++ ++install-strip: install ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/gffread diff --git a/biology/gffread/gffread-0.12.7.log-12-2-amd64 b/biology/gffread/gffread-0.12.7.log-12-2-amd64 new file mode 100644 index 000000000000..03ec053fefed --- /dev/null +++ b/biology/gffread/gffread-0.12.7.log-12-2-amd64 @@ -0,0 +1,262 @@ +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-- +=======================<phase: check-sanity >============================ +===> License MIT accepted by the user +=========================================================================== +=======================<phase: pkg-depends >============================ +===> 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 +=========================================================================== +=======================<phase: fetch-depends >============================ +=========================================================================== +=======================<phase: fetch >============================ +===> 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 +=========================================================================== +=======================<phase: checksum >============================ +===> 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. +=========================================================================== +=======================<phase: extract-depends>============================ +=========================================================================== +=======================<phase: extract >============================ +===> 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. +=========================================================================== +=======================<phase: patch-depends >============================ +=========================================================================== +=======================<phase: patch >============================ +===> Patching for gffread-0.12.7 +===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/wip/gffread/files +=========================================================================== +=======================<phase: build-depends >============================ +===> 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 +=========================================================================== +=======================<phase: lib-depends >============================ +=========================================================================== +=>> Recording filesystem state for prebuild... done +=======================<phase: configure >============================ +===> gffread-0.12.7 depends on package: gmake>=4.3 - found +===> Configuring for gffread-0.12.7 +=========================================================================== +=======================<phase: build >============================ +===> 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 +=======================<phase: run-depends >============================ +=========================================================================== +=>> Recording filesystem state for prestage... done +=======================<phase: stage >============================ +===> 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 +=======================<phase: package >============================ +===> 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 +=======================<phase: install >============================ +===> 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] +=======================<phase: deinstall >============================ +===> 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 new file mode 100644 index 000000000000..d28b274e37cf --- /dev/null +++ b/biology/gffread/gffread-0.12.7.log-13-0-amd64 @@ -0,0 +1,264 @@ +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-- +=======================<phase: check-sanity >============================ +===> License MIT accepted by the user +=========================================================================== +=======================<phase: pkg-depends >============================ +===> 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 +=========================================================================== +=======================<phase: fetch-depends >============================ +=========================================================================== +=======================<phase: fetch >============================ +===> 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 +=========================================================================== +=======================<phase: checksum >============================ +===> 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. +=========================================================================== +=======================<phase: extract-depends>============================ +=========================================================================== +=======================<phase: extract >============================ +===> 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. +=========================================================================== +=======================<phase: patch-depends >============================ +=========================================================================== +=======================<phase: patch >============================ +===> Patching for gffread-0.12.7 +===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/wip/gffread/files +=========================================================================== +=======================<phase: build-depends >============================ +===> 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 +=========================================================================== +=======================<phase: lib-depends >============================ +=========================================================================== +=>> Recording filesystem state for prebuild... done +=======================<phase: configure >============================ +===> gffread-0.12.7 depends on package: gmake>=4.3 - found +===> Configuring for gffread-0.12.7 +=========================================================================== +=======================<phase: build >============================ +===> 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 +=======================<phase: run-depends >============================ +=========================================================================== +=>> Recording filesystem state for prestage... done +=======================<phase: stage >============================ +===> 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 +=======================<phase: package >============================ +===> 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 +=======================<phase: install >============================ +===> 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] +=======================<phase: deinstall >============================ +===> 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 diff --git a/biology/gffread/pkg-descr b/biology/gffread/pkg-descr new file mode 100644 index 000000000000..4e33e0a24e3f --- /dev/null +++ b/biology/gffread/pkg-descr @@ -0,0 +1,4 @@ +GFF/GTF utility providing format conversions, filtering, FASTA sequence +extraction and more. + +WWW: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
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