[Gsrc-commit] trunk r7200: some bio additions and subtractions

[Carl Hansen]

------------------------------------------------------------
revno: 7200
revision-id: carlhansen1234@gmail.com-20201004205831-393ganov71ckmikp
parent: carlhansen1234@gmail.com-20201004203954-7djx3rhm3feyw2bm
committer: carlhansen1234@gmail.com
branch nick: trunk
timestamp: Sun 2020-10-04 13:58:31 -0700
message:
  some bio additions and subtractions
removed:
  pkg/bio/e-pcr/                 epcr-20160617195624-kwz1a09vkg4le6fu-17
  pkg/bio/e-pcr/Makefile         makefile-20160617195624-kwz1a09vkg4le6fu-99
  pkg/bio/e-pcr/config.mk        config.mk-20160617203024-1y1rgo7ffx9flvew-17
  pkg/bio/e-pcr/files/           files-20160617195624-kwz1a09vkg4le6fu-100
  pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff 
epcr2.3.12includestr-20160617195624-kwz1a09vkg4le6fu-207
  pkg/bio/e-pcr/sha256sums       sha256sums-20160617195624-kwz1a09vkg4le6fu-101
modified:
  pkg/bio/python-biopython/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-70
  pkg/bio/python-biopython/sha256sums 
sha256sums-20160617200040-lqf8h520dfq0rtk7-71
  pkg/freedesktop/farstream/Makefile 
makefile-20160617013746-7ygosxqw3lxxvo7f-444
  pkg/freedesktop/farstream/gpg-keyring 
gpgkeyring-20161015000741-8tjboemmin6id6i8-1
  pkg/freedesktop/farstream/sha256sums 
sha256sums-20160719044328-il4mkyh8p4egui5d-2
  pkg/freedesktop/harfbuzz/Makefile makefile-20160617013746-7ygosxqw3lxxvo7f-977
  pkg/freedesktop/harfbuzz/sha256sums 
sha256sums-20160617013746-7ygosxqw3lxxvo7f-981

=== removed directory 'pkg/bio/e-pcr'
=== removed file 'pkg/bio/e-pcr/Makefile'
--- a/pkg/bio/e-pcr/Makefile    2016-06-17 19:57:40 +0000
+++ b/pkg/bio/e-pcr/Makefile    1970-01-01 00:00:00 +0000
@@ -1,58 +0,0 @@
-# Copyright © 2013, 2014 Brandon Invergo <brandon@invergo.net>
-#
-# This file is part of GSRC.
-#
-# GSRC is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# GSRC is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
-# License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with GSRC.  If not, see <http://www.gnu.org/licenses/>.
-
-NAME = e-PCR
-GARNAME = e-pcr
-UPSTREAMNAME = e-PCR
-GARVERSION = 2.3.12-1
-HOME_URL = https://www.ncbi.nlm.nih.gov/tools/epcr/
-DESCRIPTION = Electronic PCR
-define BLURB
-e-PCR identifies sequence tagged sites (STS) within DNA sequences,
-allowing you to search for sub-sequences that closely match PCR
-primers.
-endef
-LICENSE = Public Domain
-CITE = PMID:9149949
-
-######################################################################
-
-MASTER_SITES = ftp://ftp.ncbi.nlm.nih.gov/
-MASTER_SUBDIR = pub/schuler/$(UPSTREAMNAME)/
-DISTFILES = $(DISTNAME)-src.tar.gz
-WORKSRC = $(WORKDIR)/$(subst -1,,$(DISTNAME))
-BUILD_SCRIPTS = $(WORKSRC)/Makefile
-INSTALL_SCRIPTS = $(WORKSRC)/Makefile
-
-BUILDDEPS =
-LIBDEPS =
-
-######################################################################
-
-include ../../../gar/gar.mk
-include config.mk
-
-BUILD_ARGS += links depend all OPTIMIZE=6 prefix=$(prefix)
-INSTALL_ARGS += dirs install
-
-pre-build:
-       sed -i 's/^LDFLAGS =/MYLDFLAGS = $$(LDFLAGS)/' 
$(WORKSRC)/stand/config.mk
-       for mf in $(WORKSRC)/stand/Makefile*; do \
-               sed -i 's/$$(LDFLAGS)/$$(MYLDFLAGS)/g' $$mf; \
-       done
-       $(MAKECOOKIE)
-

=== removed file 'pkg/bio/e-pcr/config.mk'
--- a/pkg/bio/e-pcr/config.mk   2016-06-17 20:32:01 +0000
+++ b/pkg/bio/e-pcr/config.mk   1970-01-01 00:00:00 +0000
@@ -1,4 +0,0 @@
-## Configuration options for e-pcr ##
-
-CONFIGURE_OPTS ?= 
-BUILD_OPTS ?=

=== removed directory 'pkg/bio/e-pcr/files'
=== removed file 'pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff'
--- a/pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff    2016-06-17 
19:57:40 +0000
+++ b/pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff    1970-01-01 
00:00:00 +0000
@@ -1,11 +0,0 @@
-diff -x config.log -x config.status -ru tmp/e-PCR-2.3.12/minilcs.hpp 
work/e-PCR-2.3.12/minilcs.hpp
---- tmp/e-PCR-2.3.12/minilcs.hpp       2009-07-01 15:46:08.000000000 +0100
-+++ work/e-PCR-2.3.12/minilcs.hpp      2014-04-08 14:32:07.095577869 +0100
-@@ -34,6 +34,7 @@
- #include <stdexcept>
- #include <algorithm>
- #include <vector>
-+#include <string.h>
- 
- #include <ctype.h>
- 

=== removed file 'pkg/bio/e-pcr/sha256sums'
--- a/pkg/bio/e-pcr/sha256sums  2016-06-17 19:57:40 +0000
+++ b/pkg/bio/e-pcr/sha256sums  1970-01-01 00:00:00 +0000
@@ -1,1 +0,0 @@
-92613a09cbba3eab66916488063b56e2a3b50a82e5308b1731b6b90d232b8275  
download/e-PCR-2.3.12-1-src.tar.gz

=== modified file 'pkg/bio/python-biopython/Makefile'
--- a/pkg/bio/python-biopython/Makefile 2016-06-17 20:01:53 +0000
+++ b/pkg/bio/python-biopython/Makefile 2020-10-04 20:58:31 +0000
@@ -18,7 +18,7 @@
 NAME = Biopython
 GARNAME = python-biopython
 UPSTREAMNAME = biopython
-GARVERSION = 1.67
+GARVERSION = 1.78
 HOME_URL = http://www.biopython.org
 DESCRIPTION = A set of Python modules for biological computation
 define BLURB
@@ -39,9 +39,10 @@
 INSTALL_SCRIPTS = $(WORKSRC)/setup.py
 
 BUILDDEPS =
-LIBDEPS = python-numpy
+LIBDEPS =
+#python-numpy
 
-PYTHON ?= $(prefix)/bin/python
+#PYTHON ?= $(prefix)/bin/python
 
 ######################################################################
 

=== modified file 'pkg/bio/python-biopython/sha256sums'
--- a/pkg/bio/python-biopython/sha256sums       2016-06-17 20:01:53 +0000
+++ b/pkg/bio/python-biopython/sha256sums       2020-10-04 20:58:31 +0000
@@ -1,1 +1,1 @@
-1ab322fe4d2f79d2d999c9d8faf8b4e0b4c41c4e8b5f0a97912dfa0e3aa249e6  
download/biopython-1.67.tar.gz
+1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564  
download/biopython-1.78.tar.gz

=== modified file 'pkg/freedesktop/farstream/Makefile'
--- a/pkg/freedesktop/farstream/Makefile        2016-10-15 00:15:54 +0000
+++ b/pkg/freedesktop/farstream/Makefile        2020-10-04 20:58:31 +0000
@@ -1,8 +1,7 @@
-# Copyright © 2016 Carl Hansen
-#
-# This file is part of GSRC.
-#
-# GSRC is free software: you can redistribute it and/or modify it
+# Copyright © 2016, 2020 Carl Hansen <carlhansen@gnu.org>
+#
+# This file is part of GSRC, the GNU Source Release Collection.
+# http://www.gnu.org/software/gsrc
 # under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
@@ -22,11 +21,15 @@
 
 NAME =    farstream
 GARNAME = farstream
-GARVERSION = 0.2.8
+GARVERSION = 0.2.9
 HOME_URL = http://www.freedesktop.org/
-DESCRIPTION = farstream
+DESCRIPTION =  audio/video protocols
 define BLURB
-
+The Farstream  project is an effort to create a framework to deal with
+all known audio/video conferencing protocols. On one side it offers
+a generic API that makes it possible to write plugins for different
+streaming protocols, on the other side it offers an API for clients to
+use those plugins.
 endef
 
 ######################################################################
@@ -36,8 +39,9 @@
 DISTFILES = $(GARNAME)-$(GARVERSION).tar.gz
 SIGFILES  = $(GARNAME)-$(GARVERSION).tar.gz.asc
 
-BUILDDEPS = libnice
-LIBDEPS = #  glib gobject-introspection 
+BUILDDEPS = libnice  
+#glib gobject-introspection 
+LIBDEPS =
 
 ######################################################################
 

=== modified file 'pkg/freedesktop/farstream/gpg-keyring'
Binary files a/pkg/freedesktop/farstream/gpg-keyring    2016-10-15 00:07:50 
+0000 and b/pkg/freedesktop/farstream/gpg-keyring   2020-10-04 20:58:31 +0000 
differ
=== modified file 'pkg/freedesktop/farstream/sha256sums'
--- a/pkg/freedesktop/farstream/sha256sums      2016-10-15 00:07:27 +0000
+++ b/pkg/freedesktop/farstream/sha256sums      2020-10-04 20:58:31 +0000
@@ -1,2 +1,2 @@
-2b3b9c6b4f64ace8c83e03d1da5c5a2884c1cae10b35471072b574201ab38908  
download/farstream-0.2.8.tar.gz
-eb60178a349aec154770077d7a0895595f171f3937354b0d56364aae48f7d497  
download/farstream-0.2.8.tar.gz.asc
+cb7d112433cf7c2e37a8ec918fb24f0ea5cb293cfa1002488e431de26482f47b  
download/farstream-0.2.9.tar.gz
+a4e2628c48313cd737ff68ff59319785a2d4e716b560cee30f68c8382826ef5e  
download/farstream-0.2.9.tar.gz.asc

=== modified file 'pkg/freedesktop/harfbuzz/Makefile'
--- a/pkg/freedesktop/harfbuzz/Makefile 2019-07-10 21:19:11 +0000
+++ b/pkg/freedesktop/harfbuzz/Makefile 2020-10-04 20:58:31 +0000
@@ -1,4 +1,4 @@
-# Copyright © 2016, 2017, 2018, 2019 Carl Hansen <carlhansen@gnu.org>
+# Copyright © 2016, 2017, 2018, 2019, 2020 Carl Hansen <carlhansen@gnu.org>
 #
 # This file is part of GSRC, the GNU Source Release Collection.
 # http://www.gnu.org/software/gsrc
@@ -23,19 +23,25 @@
 
 NAME =    harfbuzz
 GARNAME = harfbuzz
-GARVERSION = 2.5.3
+GARVERSION = 2.7.0
 HOME_URL = http://www.freedesktop.org/wiki/Software/HarfBuzz
 DESCRIPTION = An OpenType text-shaping engine, Middle Eastern scripts
 define BLURB
-
 endef
 
 ######################################################################
 
-MASTER_SITES = http://www.freedesktop.org/
-MASTER_SUBDIR =  software/$(GARNAME)/release/
-DISTFILES = $(GARNAME)-$(GARVERSION).tar.xz
-SIGFILES  = $(GARNAME)-$(GARVERSION).tar.xz.sha256
+MASTER_SITES = $(MASTER_GITHUB_GIT)
+MASTER_SUBDIR = $(GARNAME)/
+GIT_PATH = $(MASTER_SITES)$(MASTER_SUBDIR)$(GARNAME).git
+DISTFILES = $(DISTNAME).tar.gz
+NOCHECKSUM = $(DISTFILES)
+SIGFILES =  
+
+GIT_REVISION = master  
+
+NOCHECKSUM = $(DISTFILES)
+
 
 BUILDDEPS = 
 LIBDEPS = #  c++ glib libicu ragel
@@ -44,6 +50,6 @@
 
 ######################################################################
 
-include ../../../gar/gar.lib/auto.mk
+include ../../../gar/gar.lib/mesonninja.mk
 include config.mk
 

=== modified file 'pkg/freedesktop/harfbuzz/sha256sums'
--- a/pkg/freedesktop/harfbuzz/sha256sums       2019-07-10 21:19:11 +0000
+++ b/pkg/freedesktop/harfbuzz/sha256sums       2020-10-04 20:58:31 +0000
@@ -1,2 +0,0 @@
-fed00dc797b7ba3ca943225f0a854baaed4c1640fff8a31d455cd3b5caec855c  
download/harfbuzz-2.5.3.tar.xz
-99a1f1e0654f667bc1b19c53dea9d85c39bd2b24c76ea79c2196c9b84c42d6bd  
download/harfbuzz-2.5.3.tar.xz.sha256