diff options
| -rw-r--r-- | profiles/package.mask | 1 | ||||
| -rw-r--r-- | sci-biology/meme/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch | 346 | ||||
| -rw-r--r-- | sci-biology/meme/files/meme-4.11.2_p2-patch1.patch | 383 | ||||
| -rw-r--r-- | sci-biology/meme/files/meme-4.11.2_p2-patch2.patch | 54 | ||||
| -rw-r--r-- | sci-biology/meme/meme-4.11.2_p2.ebuild | 109 | ||||
| -rw-r--r-- | sci-biology/meme/metadata.xml | 8 |
7 files changed, 0 insertions, 902 deletions
diff --git a/profiles/package.mask b/profiles/package.mask index 2845ca182633..0ba681287335 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@gmail.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 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 "<span class="pdat">name</span>" 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> |