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biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc

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GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.
This commit is contained in:
Jason W. Bacon 2021-11-10 14:49:10 -06:00
parent 4b239d9549
commit 8d2198bb6d
7 changed files with 626 additions and 0 deletions
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1
biology/Makefile
View File

@ -57,6 +57,7 @@
SUBDIR += gemma
SUBDIR += generand
SUBDIR += gff2ps
SUBDIR += gffread
SUBDIR += gmap
SUBDIR += gperiodic
SUBDIR += graphlan

22
biology/gffread/Makefile Normal file
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@ -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>

5
biology/gffread/distinfo Normal file
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@ -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

68
biology/gffread/files/patch-Makefile Normal file
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@ -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

262
biology/gffread/gffread-0.12.7.log-12-2-amd64 Normal file
View File

@ -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

264
biology/gffread/gffread-0.12.7.log-13-0-amd64 Normal file
View File

@ -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
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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

4
biology/gffread/pkg-descr Normal file
View File

@ -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