[gentoo-commits] repo/gentoo:master commit in: sci-biology/meme/files/, profiles/, sci-biology/meme/

[Michał Górny]

commit:     d2b309d1c7920bd32c4aa6d4f1c58c70a0201ce8
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Fri Oct  9 07:33:17 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Fri Oct  9 07:34:59 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d2b309d1

sci-biology/meme: Remove last-rited pkg

Closes: https://bugs.gentoo.org/735446
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 profiles/package.mask                              |   1 -
 sci-biology/meme/Manifest                          |   1 -
 .../files/meme-4.11.2_p2-fix-build-system.patch    | 346 -------------------
 sci-biology/meme/files/meme-4.11.2_p2-patch1.patch | 383 ---------------------
 sci-biology/meme/files/meme-4.11.2_p2-patch2.patch |  54 ---
 sci-biology/meme/meme-4.11.2_p2.ebuild             | 109 ------
 sci-biology/meme/metadata.xml                      |   8 -
 7 files changed, 902 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 2845ca18263..0ba68128733 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -516,7 +516,6 @@ net-wireless/mousejack
 net-wireless/python-wifi
 sci-biology/amos
 sci-biology/embassy-meme
-sci-biology/meme
 
 # Arfrever Frehtes Taifersar Arahesis <arfrever.fta@×××××.com> (2020-09-01)
 # Mismatched version (bug #695022). Masked to force upgrade to 2.0.4_pre20200306162733.

diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
deleted file mode 100644
index fd161837618..00000000000
--- 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 b548de5a39a..00000000000
--- 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 30a182f8f43..00000000000
--- 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 498d1df7b66..00000000000
--- 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 0f7d25b4336..00000000000
--- 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 959160fe46b..00000000000
--- 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@g.o</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>