commit: 9bb544d96f49c7012fc75eb9a82495df39e7e6cf Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Fri Mar 19 11:14:25 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Fri Mar 19 11:14:25 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9bb544d9
sci-biology/autoeditor: remove masked package Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 5 -- sci-biology/autoeditor/autoeditor-1.20.ebuild | 41 ---------- sci-biology/autoeditor/files/Makefile.patch | 100 ----------------------- sci-biology/autoeditor/files/sample_expected.out | 22 ----- sci-biology/autoeditor/metadata.xml | 25 ------ 5 files changed, 193 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 5ff181a3b..dbd59dd0c 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,11 +30,6 @@ #--- END OF EXAMPLES --- -# Andrew Ammerlaan <[email protected]> (05 March 2021) -# Does not compile, last update in 2009 -# Masked for removal in 14 days, if you need this please complain -sci-biology/autoeditor - # Andrew Ammerlaan <[email protected]> (06 March 2021) # Python2 only # Masked for removal in 14 days, if you need this please complain diff --git a/sci-biology/autoeditor/autoeditor-1.20.ebuild b/sci-biology/autoeditor/autoeditor-1.20.ebuild deleted file mode 100644 index 229058fe6..000000000 --- a/sci-biology/autoeditor/autoeditor-1.20.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION="Automatic correct of discrepancies in multiple sequence alignments" -HOMEPAGE="https://sourceforge.net/projects/amos/"; -SRC_URI=" - ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-${PV}.tar.gz - test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-${PV}-sample.tar.gz )" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND=" - >=sci-libs/io_lib-1.8.11 - sci-biology/tigr-foundation-libs - sys-libs/zlib" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/autoEditor-1.20 - -src_prepare(){ - epatch "${FILESDIR}"/Makefile.patch - rm -rf TigrFoundation-2.0 || die "Failed to drop TigrFoundation-2.0/" -} - -# TODO: -# * QA Notice: Package has poor programming practices which may compile -# * fine but exhibit random runtime failures. -# * getConsQV.c:1051: warning: implicit declaration of function 'memset' - -src_test(){ - emake sample > sample.out - diff -u -w "${FILESDIR}"/sample_expected.out sample.out || die -} diff --git a/sci-biology/autoeditor/files/Makefile.patch b/sci-biology/autoeditor/files/Makefile.patch deleted file mode 100644 index 643b1e452..000000000 --- a/sci-biology/autoeditor/files/Makefile.patch +++ /dev/null @@ -1,100 +0,0 @@ ---- Makefile 2009-11-23 23:29:24.000000000 +0100 -+++ /tmp/Makefile 2010-12-05 15:06:53.000000000 +0100 -@@ -3,7 +3,7 @@ - - # $Id: Makefile,v 1.2 2009/11/23 22:29:24 mschatz Exp $ - --INSTALL_DIR = /usr/local/bin -+INSTALL_DIR = $(DESTDIR)/bin - - PROG_NAME = autoEditor - all: $(PROG_NAME) -@@ -56,10 +56,9 @@ - RAWCOBJS = $(SRCS:.c=.o) - OBJS = $(RAWCOBJS:.cc=.o) - --TF_ROOT = TigrFoundation-2.0 - LIBSLICE = libSlice-1.0 - --IOLIB = ${PWD}/io_lib-1.8.11/install -+IOLIB = /usr - IO_LIB_INC = $(IOLIB)/include/io_lib - IO_LIB_LIB = $(IOLIB)/lib - -@@ -68,8 +67,6 @@ - - DEFINES = -DUSE_ZLIB -DUSE_CPP_FRONTEND - --DEBUG = -O2 -g -- - LFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - - ifeq ($(HOSTTYPE), alpha) -@@ -96,32 +93,12 @@ - endif - - CFLAGS = -Wall $(DEBUG) $(DEFINES) $(INC) ${LFS} --CPPFLAGS = $(CFLAGS) -I$(TF_ROOT) -L$(TF_ROOT) -D_HAS_GETOPT --LDLIBS = -lSlice -lTigrFoundation -lm -lread -lz -- -+CPPFLAGS = $(CFLAGS) -D_HAS_GETOPT -+LDLIBS = -lSlice -lTigrFoundation -lm -lstaden-read -lz - --${IOLIB}/lib/libread.la: -- cd io_lib-1.8.11; \ -- rm -Rf ${IOLIB}; \ -- if [ -e Makefile ] ; then make distclean; fi; \ -- ./configure --prefix=${IOLIB}; \ -- make; \ -- make install; \ -- cp os.h ${IOLIB}/include/io_lib; \ -- cp config.h ${IOLIB}/include/io_lib; \ -- if [ -e ${IOLIB}/lib/libread.so ]; \ -- then mv ${IOLIB}/lib/libread.so ${IOLIB}/lib/libread-so.so; \ -- fi; - - libSlice-1.0/libSlice.a: - cd libSlice-1.0; \ -- CXXFLAGS="-I../TigrFoundation-2.0 -L../TigrFoundation-2.0" \ -- CC=$(CC) \ -- CXX=$(CXX) \ -- make; -- --TigrFoundation-2.0/libTigrFoundation.a: -- cd TigrFoundation-2.0; \ - CC=$(CC) \ - CXX=$(CXX) \ - make; -@@ -129,9 +106,7 @@ - - - # Rule for linking all of the objects into the program --$(PROG_NAME): ${IOLIB}/lib/libread.la \ -- TigrFoundation-2.0/libTigrFoundation.a \ -- libSlice-1.0/libSlice.a \ -+$(PROG_NAME): libSlice-1.0/libSlice.a \ - $(OBJS) - $(CXX) $(CPPFLAGS) -o $@ $(OBJS) $(LDLIBS); \ - echo; \ -@@ -144,18 +119,13 @@ - cd libSlice-1.0; \ - make clean; \ - cd ..; \ -- cd TigrFoundation-2.0; \ -- make clean; \ -- cd ..; \ -- cd io_lib-1.8.11; \ -- rm -Rf install; \ -- if [ -e Makefile ]; then make distclean; fi; - - sample: ${PROG_NAME} - ./${PROG_NAME} -v -c sample/29713/chromo sample/29713/29713 - - install: ${PROG_NAME} -- cp ${PROG_NAME} ${INSTALL_DIR} -+ mkdir -p $(DESTDIR)/bin || exit -+ cp ${PROG_NAME} $(DESTDIR)/bin/ - - uninstall: -- rm ${INSTALL_DIR}/${PROG_NAME} -+ rm ${DESTDIR}/${PROG_NAME} diff --git a/sci-biology/autoeditor/files/sample_expected.out b/sci-biology/autoeditor/files/sample_expected.out deleted file mode 100644 index e792b8455..000000000 --- a/sci-biology/autoeditor/files/sample_expected.out +++ /dev/null @@ -1,22 +0,0 @@ -./autoEditor -v -c sample/29713/chromo sample/29713/29713 -Creating index of offsets of seq_ids in sample/29713/29713.seq ... done -Creating index of offsets of seq_ids in sample/29713/29713.qual ... done -Creating index of offsets of seq_ids in sample/29713/29713.pos ... done -ENTERING THE MAIN LOOP ... -Processing asmbl 29713 44 reads - Parsing sample/29713/29713.qual file ... done - Aligning sequences to the consensus sequence ... done - Parsing sample/29713/29713.seq file ... done - Parsing sample/29713/29713.pos file ... done - Correcting errors ... done - Freeing tiling data ... done - Aligning sequences to the consensus sequence ... done - Recalling consensus sequence values and their quality classes ... done - Correcting gap slices ... done - Freeing tiling data ... done - Aligning sequences to the consensus sequence ... done - Creating new contig, qual, and seq files ... done - Freeing tiling data ... done - Freeing sequence data ... done - Flushing Trace Cache ... done -DONE WITH THE MAIN LOOP in 0min 1sec diff --git a/sci-biology/autoeditor/metadata.xml b/sci-biology/autoeditor/metadata.xml deleted file mode 100644 index a9237cbcc..000000000 --- a/sci-biology/autoeditor/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription>AutoEditor is a program that can automatically correct discrepancies in a -multiple alignment by reanalyzing the chromatograms of the discrepant bases. -The input to AutoEditor is the multiple alignment in contig form, the sequence -and quality values in FASTA format, and the base call positions in -"SEQNAME basecallpositions\n" format where the basecall positions are written -in hex (4 nibbles per basecall position) concatentated together. The path -to the chromatograms for the sequences should be specified with the -c option. -More help is available with -h. - -The output is to a timestamped autoEditor directory that has the input files -edited along with other TIGR specific file formats. Sample input data is -provided with the distribution in the sample directory. -</longdescription> -</pkgmetadata>
