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authorMichał Górny <mgorny@gentoo.org>2020-10-09 09:33:17 +0200
committerMichał Górny <mgorny@gentoo.org>2020-10-09 09:34:59 +0200
commitd2b309d1c7920bd32c4aa6d4f1c58c70a0201ce8 (patch)
treed1761486138bd866831a4f37fb7655534d15e8ae /sci-biology
parentsci-biology/shrimp: Remove last-rited pkg (diff)
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sci-biology/meme: Remove last-rited pkg
Closes: https://bugs.gentoo.org/735446 Signed-off-by: Michał Górny <mgorny@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/meme/Manifest1
-rw-r--r--sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch346
-rw-r--r--sci-biology/meme/files/meme-4.11.2_p2-patch1.patch383
-rw-r--r--sci-biology/meme/files/meme-4.11.2_p2-patch2.patch54
-rw-r--r--sci-biology/meme/meme-4.11.2_p2.ebuild109
-rw-r--r--sci-biology/meme/metadata.xml8
6 files changed, 0 insertions, 901 deletions
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
deleted file mode 100644
index fd161837618b..000000000000
--- a/sci-biology/meme/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST meme_4.11.2.tar.gz 18004930 BLAKE2B accacc7d2422ff6ea3411ff43ea664c94f5d6ba320e1cfec642a88cb6ea5303b2fe8c99a6c35d865c377560118402ab11f869930fd108f02eeaa06321db21655 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
deleted file mode 100644
index b548de5a39a5..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
+++ /dev/null
@@ -1,346 +0,0 @@
-Fix and modernise build system
-* Remove all *FLAGS setting, just append to the user-supplied ones
-* Add --enable-doc and --enable-examples configure flags
-* Install documentation and examples in correct directories
-* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES
-* Install python and perl modules correctly
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -76,61 +76,10 @@
- AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no])
-
- # Check for compiler-specific settings
--LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS`
--if test "${GCC}" = "yes"; then
-- ac_cc_opt="-O3"
-- ac_cc_debug_opt="-O0"
-- ac_cc_warn="-Wall -Wno-unused"
-- ac_cc_debug="-ggdb"
-- # Check for OS X llvm (clang) compiler
-- if `gcc --version |grep llvm >/dev/null`; then
-- ac_cc_debug="-g"
-- fi
-- CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
--else
-- ac_cc_opt="-O"
-- ac_cc_debug_opt=""
-- ac_cc_warn=""
-- ac_cc_debug="-g"
-- CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
--fi
--
--# Set up default libxml2 settings
--# check for installed copy of libxml2
--build_libxml2="yes"
--if test -n "$XML2_CONFIG"; then
-- # Require at least version 2.6
-- required_libxml2_version="2006000"
-- LIBXML2_VERSION="`$XML2_CONFIG --version | \
-- awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`"
-- if test -n "$LIBXML2_VERSION" && \
-- test "$LIBXML2_VERSION" -ge "$required_libxml2_version"; then
-- build_libxml2="no"
-- LIBXML2_LIBS="`$XML2_CONFIG --libs`"
-- LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`"
-- fi
--fi
--if test -z "$LIBXML2_LIBS"; then
-- AC_MSG_WARN([libxml2 library not found])
-- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
-- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
--fi
--
--# Set up default libxslt settings
--# check for installed copy of libxslt
--build_libxslt="yes"
--if test -n "$XSLT_CONFIG"; then
-- build_libxslt="no"
-- LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt"
-- LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`"
--fi
--if test -z "$LIBXSLT_LIBS"; then
-- AC_MSG_WARN([libxslt library not found])
-- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
-- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
-- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
-- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
--fi
-+AC_PROG_MKDIR_P
-+AC_SYS_LARGEFILE
-+CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}"
-+CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}"
-
- # who is installing
- USER=`whoami`
-@@ -279,6 +227,16 @@
- AM_CONDITIONAL(PARALLEL, test ["$parallel" != no])
- AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"])
-
-+dnl Documentation
-+AC_ARG_ENABLE([doc],
-+ AS_HELP_STRING([--enable-doc], [Enable installation of documentation]))
-+AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"])
-+
-+dnl Examples
-+AC_ARG_ENABLE([examples],
-+ AS_HELP_STRING([--enable-examples], [Enable installation of examples]))
-+AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"])
-+
- AC_ARG_ENABLE(
- webservice,
- [ --enable-webservice=deploy_dir Deploy the MEME service on an existing Opal 2.5+ installation],
-@@ -309,24 +267,35 @@
- AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"])
-
- # enable building of included libxml2
--AC_ARG_ENABLE(
-- build_libxml2,
-- [ --enable-build-libxml2 Build included version of libxml2. Default is to use pre-existing locally installed copy.],
-- build_libxml2=$enableval; \
-- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \
-- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , )
--AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes])
-+AC_ARG_ENABLE([build-libxml2],
-+ AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.]))
-+AS_IF([test "x$enable_build_libxml2" = "xyes"], [
-+ dnl Enable building of bundled libs
-+ LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
-+ LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
-+ ],[
-+ dnl Use system libraries
-+ PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6])
-+])
-+AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"])
-+
-
- # enable building of included libxslt
--AC_ARG_ENABLE(
-- build_libxslt,
-- [ --enable-build-libxslt Build included version of libxslt. Default is to use pre-existing locally installed copy.],
-- build_libxslt=$enableval; \
-- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \
-- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \
-- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \
-- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , )
--AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes])
-+AC_ARG_ENABLE([build-libxslt],
-+ AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.]))
-+AS_IF([test "x$enable_build_libxslt" = "xyes"], [
-+ dnl Enable building of bundled libs
-+ LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
-+ LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
-+
-+ LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
-+ LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
-+ ],[
-+ dnl Use system libraries
-+ PKG_CHECK_MODULES([LIBXSLT], [libxslt])
-+ PKG_CHECK_MODULES([LIBEXSLT], [libexslt])
-+])
-+AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"])
-
- # set website url
- AC_ARG_WITH(
-@@ -427,13 +396,13 @@
- [AC_PATH_PROG(PERL, perl)])
- AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] )
-
-+AC_ARG_WITH([perl-dir],
-+ AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"])
-+AC_SUBST([perlmoddir])
-+
-+
- # set path to Python
--AC_ARG_WITH(
-- python,
-- [ --with-python=NAME Set path to Python. Default is to take from user's PATH.],
-- [PYTHON=$withval],
-- [AC_PATH_PROG(PYTHON, python)])
--AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] )
-+AM_PATH_PYTHON
-
- # set path to convert utility
- AC_ARG_WITH(
-@@ -586,13 +555,15 @@
- Configuration parameters
- ========================
-
-- Install path: ${prefix}
-+ Install path (prefix): ${prefix}
- Install UID: ${MEME_USER}
- Version: ${VERSION}
-- C compiler: ${CC}
-- C compiler flags: ${CFLAGS}
-- Linker: ${LD}
-- Special Libs: ${LIBS}
-+ C compiler (CC): ${CC}
-+ C compiler flags (CFLAGS): ${CFLAGS}
-+ C preproc flags (CPPFLAGS): ${CPPFLAGS}
-+ Linker (LD): ${LD}
-+ Linker flags (LDFLAGS): ${LDFLAGS}
-+ Special Libs (LIBS): ${LIBS}
- MPICC ${MPICC}
- MPIRUN ${MPIRUN}
- MPI_CMD ${MPI_CMD}
---- a/doc/css/Makefile.am
-+++ b/doc/css/Makefile.am
-@@ -5,7 +5,7 @@
-
- EXTRA_DIST = $(NORMAL_FILES)
-
--if ! WEBSITE
--doccssdir = $(prefix)/doc/css
-+if ENABLE_DOC
-+doccssdir = $(htmldir)/css
- doccss_DATA = $(NORMAL_FILES)
- endif
---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-@@ -7,8 +7,8 @@
- EXAMPLES = \
- prior.dist.txt
-
--if ! WEBSITE
--exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples/compute_prior_dist_example_output_files
- ex_DATA = $(EXAMPLES)
- endif
-
---- a/doc/examples/Makefile.am
-+++ b/doc/examples/Makefile.am
-@@ -22,8 +22,8 @@
- # load the EXAMPLE_OUTPUT_FILES variable
- include examples.mk
-
--if ! WEBSITE
--exdir = $(prefix)/doc/examples
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples
- nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES)
- endif
-
---- a/doc/examples/sample_opal_scripts/Makefile.am
-+++ b/doc/examples/sample_opal_scripts/Makefile.am
-@@ -15,8 +15,8 @@
- MemeClient.pl \
- MemeClient.py
-
--if ! WEBSITE
--exdir = $(prefix)/doc/examples/sample_opal_scripts
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples/sample_opal_scripts
- ex_DATA = $(EXAMPLES)
- endif
-
---- a/doc/images/Makefile.am
-+++ b/doc/images/Makefile.am
-@@ -30,8 +30,8 @@
-
- MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES)
-
--if ! WEBSITE
--memeimgdir = $(prefix)/doc/images
-+if ENABLE_DOC
-+memeimgdir = $(htmldir)/images
- memeimg_DATA = $(MEME_IMAGES)
- endif
-
---- a/doc/js/Makefile.am
-+++ b/doc/js/Makefile.am
-@@ -41,8 +41,8 @@
-
- BUILT_SOURCES = $(BUILT_FILES)
-
--if ! WEBSITE
--docjsdir = $(prefix)/doc/js
-+if ENABLE_DOC
-+docjsdir = $(htmldir)/js
- docjs_DATA = $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES)
- endif
-
---- a/doc/Makefile.am
-+++ b/doc/Makefile.am
-@@ -129,8 +129,8 @@
- update-sequence-db.html \
- ismb94.pdf
-
--if ! WEBSITE
--memedocdir = $(prefix)/doc
-+if ENABLE_DOC
-+memedocdir = $(htmldir)
- memedoc_DATA = $(NORMAL_FILES)
- endif
-
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -52,7 +52,7 @@
- endif
-
- dbdir:
-- mkdir -p $(MEME_DB)
-+ $(MKDIR_P) $(DESTDIR)/$(MEME_DB)
-
- all-local:
- if WEBSITE
-@@ -64,8 +64,8 @@
- endif
-
- install-data-local:
-- mkdir -p $(MEME_LOGS)
-- chmod a+w $(MEME_LOGS)
-+ $(MKDIR_P) $(DESTDIR)/$(MEME_LOGS)
-+ chmod a+w $(DESTDIR)/$(MEME_LOGS)
-
- distdir = $(PACKAGE)_$(VERSION)
-
---- a/scripts/Makefile.am
-+++ b/scripts/Makefile.am
-@@ -22,8 +22,8 @@
- -e 's%@WHICHJAVA@%$(JAVA)%' \
- -e 's%@WHICHCONVERT@%$(CONVERT)%' \
- -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \
-- -e 's%@PERLLIBDIR@%$(libdir)/perl%' \
-- -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \
-+ -e 's%@PERLLIBDIR@%$(perlmoddir)%' \
-+ -e 's%@PYTHONLIBDIR@%$(pythondir)%' \
- -e 's%@JAVALIBDIR@%$(libdir)/java%' \
- -e 's%@LAM_BIN@%$(LAMBIN)%' \
- -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \
-@@ -62,7 +62,7 @@
- DiffXML.pm \
- HypergeometricDynProg.pm
-
--perlmoddir=$(libdir)/perl
-+perlmoddir = $(exec_prefix)/@perlmoddir@
- perlmod_SCRIPTS = \
- $(BUILT_PERL_MOD) \
- $(NORMAL_PERL_MOD)
-@@ -76,8 +76,7 @@
- hypergeometric.py \
- sequence.py
-
--pythonlibdir=$(libdir)/python
--pythonlib_SCRIPTS = \
-+python_PYTHON = \
- $(BUILT_PYTHON_LIB) \
- $(NORMAL_PYTHON_LIB)
-
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -19,7 +19,13 @@
- ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
- ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE)
-
--SUBDIRS = filters libxml2 libxslt libexslt . parallel
-+SUBDIRS = filters . parallel
-+if BUILD_LIBXML2
-+SUBDIRS += libxml2
-+endif
-+if BUILD_LIBXSLT
-+SUBDIRS += libxslt libexslt
-+endif
-
- BUILT_SOURCES = dir.h projrel.h
-
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
deleted file mode 100644
index 30a182f8f43a..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
+++ /dev/null
@@ -1,383 +0,0 @@
---- a/doc/alphabet-format.html
-+++ b/doc/alphabet-format.html
-@@ -233,7 +233,7 @@
- providing a reference on the meaning of the symbols used. If present, the
- symbol name must be the second field.</p>
- <p>The &quot;<span class="pdat">name</span>&quot; follows the rules of
-- <a href="qstr">quoted text</a>.</p>
-+ <a href="#qstr">quoted text</a>.</p>
- </div>
- <h5>color</h5>
- <div class="indent">
---- a/doc/release-notes.html
-+++ b/doc/release-notes.html
-@@ -14,8 +14,26 @@
- <h2>Motif-based sequence analysis tools</h2>
- </div>
- <h2>MEME Suite Release Notes</h2>
-+ <hr>
-+ <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
-+ <ul>
-+ <li>
-+ <b>Bug fixes</b>
-+ <ul>
-+ <li>
-+ Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate
-+ reading the sequence file.
-+ </li>
-+ <li>
-+ Modified MEME to fall back to a simple Dirichlet prior when
-+ using DNA or a custom alphabet with a prior that requires
-+ a prior library, but no prior libray is specified.
-+ </li>
-+ </ul
-+ </li>
-+ </ul>
-+ <p>
- <hr>
-- <p>
- <b>MEME version 4.11.2 -- May 5 2016</b>
- </p>
- <ul>
---- a/src/fasta-io.c
-+++ b/src/fasta-io.c
-@@ -14,6 +14,7 @@
- #include "alphabet.h"
- #include "fasta-io.h"
- #include "io.h"
-+#include "seq-reader-from-fasta.h"
- #include "prior-reader-from-psp.h"
- #include "seq.h"
-
-@@ -159,61 +160,6 @@
- }
-
- /****************************************************************************
-- * Read raw sequence until a new sequence is encountered or too many letters
-- * are read. The new sequence is appended to the end of the given
-- * sequence.
-- *
-- * Return: Was the sequence read completely?
-- ****************************************************************************/
--static BOOLEAN_T read_raw_sequence_from_reader(
-- DATA_BLOCK_READER_T *fasta_reader, // Sequence source
-- char* name, // Sequence ID (used in error messages).
-- ALPH_T* alph, // Alphabet in use
-- unsigned int offset, // Current position in raw_sequence.
-- unsigned int max_chars, // Maximum chars in raw_sequence.
-- char* raw_sequence // Pre-allocated sequence.
--) {
-- // tlb; change a_char to integer so it will compile on SGI
-- int a_char;
-- int start_update;
-- BOOLEAN_T return_value = TRUE;
--
-- // Start at the end of the given sequence.
-- assert(offset < max_chars);
--
-- DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset);
-- return_value = !fasta_reader->get_next_block(fasta_reader, seq_block);
--
-- char *seq_buffer = get_sequence_from_data_block(seq_block);
-- size_t seq_buffer_size = get_num_read_into_data_block(seq_block);
-- int i;
-- for (i = 0; i < seq_buffer_size; ++i) {
-- a_char = seq_buffer[i];
-- // Skip non-alphabetic characters.
-- if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') {
-- if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) {
-- fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n",
-- a_char, name);
-- }
-- } else {
-- // skip check if unknown alph
-- if (alph != NULL && !alph_is_known(alph, a_char)) {
-- fprintf(stderr, "Warning: Converting illegal character %c to %c ",
-- a_char, alph_wildcard(alph));
-- fprintf(stderr, "in sequence %s.\n", name);
-- a_char = alph_wildcard(alph);
-- }
-- raw_sequence[offset] = (char) a_char;
-- ++offset;
-- }
-- }
--
-- raw_sequence[offset] = '\0';
-- free_data_block(seq_block);
-- return(return_value);
--}
--
--/****************************************************************************
- * Read one sequence from a file in Fasta format.
- *
- * Return: Was a sequence successfully read?
-@@ -320,44 +266,6 @@
- }
-
- /****************************************************************************
-- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-- * and copy them in to the raw sequence in the SEQ_T object starting at the
-- * given buffer offset.
-- ****************************************************************************/
--void read_one_fasta_segment_from_reader(
-- DATA_BLOCK_READER_T *fasta_reader,
-- size_t max_size,
-- size_t buffer_offset,
-- SEQ_T *sequence
--) {
--
-- assert(sequence != NULL);
-- assert(get_seq_length(sequence) <= max_size);
--
-- // Get the raw sequence buffer from the SEQ_T
-- char *raw_sequence = get_raw_sequence(sequence);
-- if (raw_sequence == NULL) {
-- // Allocate space for raw sequence if not done yet.
-- raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
-- raw_sequence[0] = 0;
-- }
--
-- // Read a block of sequence charaters into the
-- // raw sequence buffer for the SEQ_T.
-- char *name = get_seq_name(sequence);
-- BOOLEAN_T is_complete = read_raw_sequence_from_reader(
-- fasta_reader,
-- name,
-- NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable!
-- buffer_offset,
-- max_size,
-- raw_sequence
-- );
-- set_raw_sequence(raw_sequence, is_complete, sequence);
--
--}
--
--/****************************************************************************
- * Read all the sequences from a FASTA file at once.
- Multiple files can be appended by calling this more than once.
- ****************************************************************************/
---- a/src/fasta-io.h
-+++ b/src/fasta-io.h
-@@ -43,19 +43,6 @@
- );
-
- /****************************************************************************
-- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-- * and copy them in to the raw sequence in the SEQ_T object starting at the
-- * given buffer offset.
-- ****************************************************************************/
--void read_one_fasta_segment_from_reader(
-- DATA_BLOCK_READER_T *fasta_reader,
-- size_t max_size,
-- size_t buffer_offset,
-- SEQ_T* sequence
--);
--
--
--/****************************************************************************
- * Read all the sequences from a file in Fasta format.
- ****************************************************************************/
- void read_many_fastas
---- a/src/init.c
-+++ b/src/init.c
-@@ -767,10 +767,16 @@
- if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins
- plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB);
- } else {
-- fprintf(stderr, "The prior library must be specified for DNA or custom "
-- "alphabets when specifiying a prior type of 'dmix', 'mega' "
-- "or 'megap'.");
-- exit(1);
-+ fprintf(
-+ stderr,
-+ "WARNING: When using DNA or a custom alphabet, "
-+ "and specifiying a prior type of\n"
-+ "'dmix', 'mega' or 'megap', a prior library must be provided.\n"
-+ "No prior library was provided, so a simple Dirichlet prior will be used.\n"
-+ );
-+ prior = "dirichlet";
-+ ptype = Dirichlet;
-+ if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet
- }
- }
- }
---- a/src/seq-reader-from-fasta.c
-+++ b/src/seq-reader-from-fasta.c
-@@ -639,11 +639,140 @@
- return fasta_reader->current_position;
- }
-
-+
-+/****************************************************************************
-+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-+ * and copy them in to the raw sequence in the SEQ_T object starting at the
-+ * given buffer offset.
-+ ****************************************************************************/
-+void read_one_fasta_segment_from_reader(
-+ DATA_BLOCK_READER_T *fasta_reader,
-+ size_t max_size,
-+ size_t offset,
-+ SEQ_T *sequence
-+) {
-+
-+
-+ assert(sequence != NULL);
-+ assert(offset < max_size);
-+
-+ // Get the raw sequence buffer from the SEQ_T
-+ char *raw_sequence = get_raw_sequence(sequence);
-+ if (raw_sequence == NULL) {
-+ // Allocate space for raw sequence if not done yet.
-+ raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
-+ raw_sequence[0] = 0;
-+ }
-+
-+ // Read a block of sequence charaters into the
-+ // raw sequence buffer for the SEQ_T, starting at offset.
-+ BOOLEAN_T is_complete = read_raw_sequence_from_reader(
-+ fasta_reader,
-+ max_size - offset,
-+ raw_sequence + offset
-+ );
-+ set_raw_sequence(raw_sequence, is_complete, sequence);
-+}
-+
-+/****************************************************************************
-+ * Read raw sequence until a new sequence is encountered or too many letters
-+ * are read.
-+ *
-+ * Return: Was the sequence read completely?
-+ ****************************************************************************/
-+BOOLEAN_T read_raw_sequence_from_reader(
-+ DATA_BLOCK_READER_T *reader, // Sequence source
-+ unsigned int max_chars, // Maximum chars in raw_sequence.
-+ char* raw_sequence // Pre-allocated sequence buffer.
-+) {
-+
-+ SEQ_READER_FROM_FASTA_T *fasta_reader
-+ = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader);
-+
-+ // Read sequence into temp. buffer from the sequence file.
-+ char buffer[max_chars];
-+ long start_file_pos = ftell(fasta_reader->fasta_file);
-+ size_t seq_index = 0;
-+ size_t total_read = 0;
-+ while (seq_index < max_chars) {
-+
-+ size_t num_char_read = fread(
-+ buffer,
-+ sizeof(char),
-+ max_chars - seq_index,
-+ fasta_reader->fasta_file
-+ );
-+ fasta_reader->current_position += num_char_read;
-+ total_read += num_char_read;
-+
-+ if (feof(fasta_reader->fasta_file)) {
-+ fasta_reader->at_end_of_file = TRUE;
-+ }
-+ else if (num_char_read < (max_chars - seq_index)) {
-+ die(
-+ "Error while reading sequence from file:%s.\nError message: %s\n",
-+ fasta_reader->filename,
-+ strerror(ferror(fasta_reader->fasta_file))
-+ );
-+ }
-+
-+ size_t i;
-+ for(i = 0; i < num_char_read; ++i) {
-+ char c = buffer[i];
-+ assert(c != 0);
-+ if (isspace(c)) {
-+ // Skip over white space
-+ fasta_reader->at_start_of_line = (c == '\n');
-+ }
-+ else if (c == '>' && fasta_reader->at_start_of_line == TRUE) {
-+ // We found the start of a new sequence while trying
-+ // to fill the buffer. Leave the buffer incomplete.
-+ // and wind back the file
-+ fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET);
-+ fasta_reader->current_position = start_file_pos + i - 1;
-+ fasta_reader->at_end_of_seq = TRUE;
-+ fasta_reader->at_start_of_line = FALSE;
-+ fasta_reader->at_end_of_file = FALSE;
-+ break;
-+ }
-+ else {
-+ fasta_reader->at_start_of_line = FALSE;
-+ // Check that character is legal in alphabet.
-+ // If not, replace with wild card character.
-+ if (alph_is_known(fasta_reader->alphabet, c)) {
-+ raw_sequence[seq_index] = c;
-+ }
-+ else {
-+ raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet);
-+ fprintf(
-+ stderr,
-+ "Warning: %c is not a valid character in %s alphabet.\n"
-+ " Converting %c to %c.\n",
-+ c,
-+ alph_name(fasta_reader->alphabet),
-+ c,
-+ raw_sequence[i]
-+ );
-+ }
-+ ++seq_index;
-+ }
-+ }
-+ if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) {
-+ break;
-+ }
-+ }
-+
-+ raw_sequence[seq_index] = '\0';
-+ return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file);
-+}
-+
- /******************************************************************************
-- * Fills in the next data block for the sequence.
-- * During the first call for the sequence it fills in the full data block.
-- * On successive calls, shifts the sequence in the block down one position
-- * and reads one more character.
-+ * Populates the data block for the with the next block of sequence.
-+ *
-+ * During the first call for the sequence it fills in a buffer from a file,
-+ * The sequence pointer in the data block is set to point at the start of the buffer.
-+ * On successive calls, the sequence pointer in the block is shifted down one position
-+ * in the buffer. When the end of the buffer is reached, it is filled again from the file.
- *
- * Returns TRUE if it was able to completely fill the block, FALSE if
- * the next sequence or EOF was reached before the block was filled.
---- a/src/seq-reader-from-fasta.h
-+++ b/src/seq-reader-from-fasta.h
-@@ -37,5 +37,30 @@
- int * end_ptr // end position of sequence (chr:\d+-(\d+))
- );
-
-+/****************************************************************************
-+ * Read raw sequence until a new sequence is encountered or too many letters
-+ * are read.
-+ *
-+ * Return: Was the sequence read completely?
-+ ****************************************************************************/
-+BOOLEAN_T read_raw_sequence_from_reader(
-+ DATA_BLOCK_READER_T *fasta_reader, // Sequence source
-+ unsigned int max_chars, // Maximum chars in raw_sequence.
-+ char* raw_sequence // Pre-allocated sequence.
-+);
-+
-+/****************************************************************************
-+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-+ * and copy them in to the raw sequence in the SEQ_T object starting at the
-+ * given buffer offset.
-+ ****************************************************************************/
-+void read_one_fasta_segment_from_reader(
-+ DATA_BLOCK_READER_T *reader,
-+ size_t max_size,
-+ size_t offset,
-+ SEQ_T *sequence
-+);
-+
-+
- size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader);
- #endif
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
deleted file mode 100644
index 498d1df7b664..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- a/doc/release-notes.html
-+++ b/doc/release-notes.html
-@@ -15,6 +15,21 @@
- </div>
- <h2>MEME Suite Release Notes</h2>
- <hr>
-+ <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b>
-+ <ul>
-+ <li>
-+ <b>Bug fixes</b>
-+ <ul>
-+ <li>
-+ Fixed bug in handling of RNA-like custom alphabets.
-+ </li>
-+ <li>
-+ Fixed bug in MAST -comp option.
-+ </li>
-+ </ul
-+ </li>
-+ </ul>
-+ <hr>
- <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
- <ul>
- <li>
---- a/src/alph-in.c
-+++ b/src/alph-in.c
-@@ -1044,7 +1044,7 @@
- lookup[0] = sym->complement;
- comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup);
- }
-- if (comp1 != comp2) {
-+ if (comp1 && (comp1 != comp2)) {
- add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1,
- "not like %s alphabet as %c complement rules are incorrect",
- ext_name, req_syms[i]));
---- a/src/mast-util.c
-+++ b/src/mast-util.c
-@@ -740,14 +740,14 @@
-
- // create the frequency array
- alph = xlate ? xlate_dest_alph(xlate) : alph;
-- freq = allocate_array(alph_size_core(alph));
-+ freq = allocate_array(alph_size_full(alph));
- init_array(0, freq);
-
- // count the number of letters of each type
- if (xlate) {
- for (n=0; sequence[n]; n++) {
- i = xlate_index(xlate, false, sequence+n);
-- if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq);
-+ if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq);
- }
- } else {
- for (n=0; sequence[n]; n++) {
diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild
deleted file mode 100644
index 0f7d25b43368..000000000000
--- a/sci-biology/meme/meme-4.11.2_p2.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools perl-functions python-single-r1 versionator
-
-MY_PV=$(get_version_component_range 1-3)
-MY_P=${PN}_${MY_PV}
-
-DESCRIPTION="The MEME/MAST system - Motif discovery and search"
-HOMEPAGE="http://meme-suite.org/tools/meme"
-SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz"
-
-LICENSE="meme"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples mpi"
-
-RDEPEND="
- ${PYTHON_DEPS}
- app-shells/tcsh
- dev-libs/libxml2:2
- dev-libs/libxslt
- sys-libs/zlib
- app-text/ghostscript-gpl
- media-gfx/imagemagick
- dev-lang/perl:=
- dev-perl/HTML-Parser
- dev-perl/HTML-Template
- dev-perl/Log-Log4perl
- dev-perl/Math-CDF
- dev-perl/XML-Compile-SOAP
- dev-perl/XML-Compile-WSDL11
- dev-perl/XML-Parser
- dev-perl/XML-Simple
- virtual/perl-Data-Dumper
- virtual/perl-Exporter
- virtual/perl-File-Path
- virtual/perl-File-Spec
- virtual/perl-File-Temp
- virtual/perl-Getopt-Long
- virtual/perl-Scalar-List-Utils
- virtual/perl-Time-HiRes
- mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-S="${WORKDIR}/${MY_P}"
-PATCHES=(
- "${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch
- "${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch
- "${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch
-)
-
-pkg_setup() {
- python-single-r1_pkg_setup
- perl_set_version
-}
-
-src_prepare() {
- default
- eautoreconf
-}
-
-src_configure() {
- econf \
- --sysconfdir="${EPREFIX}"/etc/${PN} \
- --with-logs="${EPREFIX}"/var/log/${PN} \
- --with-perl=perl \
- --with-convert=convert \
- --with-gs=gs \
- --disable-build-libxml2 \
- --disable-build-libxslt \
- $(use_enable debug) \
- $(use_enable doc) \
- $(use_enable examples) \
- $(use_enable !mpi serial) \
- --with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \
- PYTHON="${EPYTHON}"
-
- # delete bundled libs, just to be sure. These need
- # to be removed after econf, else AC_OUTPUT will fail
- rm -r src/{libxml2,lib{,e}xslt} || die
-}
-
-src_test() {
- # bug #297070
- emake -j1 test
-}
-
-src_install() {
- default
- docompress -x /usr/share/doc/${PF}/examples
-
- # prefix all binaries with 'meme-', in order
- # to prevent collisions, bug 455010
- cd "${ED%/}"/usr/bin/ || die
- local i
- for i in *; do
- if [[ $i != meme-* ]]; then
- mv {,meme-}"${i}" || die
- fi
- done
-
- keepdir /var/log/meme
-}
diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/meme/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>