From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/maqview/files/0.2.5-ldflags.patch | 46 ++++++++++++++++++++++ sci-biology/maqview/files/0.2.5-zlib.patch | 33 ++++++++++++++++ .../maqview/files/maqview-0.2.5-gcc4.7.patch | 16 ++++++++ 3 files changed, 95 insertions(+) create mode 100644 sci-biology/maqview/files/0.2.5-ldflags.patch create mode 100644 sci-biology/maqview/files/0.2.5-zlib.patch create mode 100644 sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch (limited to 'sci-biology/maqview/files') diff --git a/sci-biology/maqview/files/0.2.5-ldflags.patch b/sci-biology/maqview/files/0.2.5-ldflags.patch new file mode 100644 index 000000000000..92b9a3ed58ac --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-ldflags.patch @@ -0,0 +1,46 @@ + configure.ac | 18 +++--------------- + 1 files changed, 3 insertions(+), 15 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 90e612b..5a00d15 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -9,17 +9,10 @@ AC_PROG_INSTALL + AC_STDC_HEADERS + + is_static=0 +-case ${prefix} in +- NONE);; +- *) is_static=1 +- AC_MSG_WARN([Library libglut will be statically linked.]) +- LDFLAGS="-L${prefix}/lib" +- CPPFLAGS="-I${prefix}/include";; +-esac + + # set CFLAGS and LDFLAGS + +-true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS" ++true_CFLAGS="-DMAQ_LONGREADS" + case "${host_os}" in + darwin*) + GLLIBS="-framework OpenGL -framework GLUT" +@@ -30,17 +23,12 @@ case "${host_os}" in + i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";; + esac + AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"]) +- AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)], +- [is_static=1]) +- case $is_static in +- 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";; +- 0) GLLIBS="-lGL -lglut -lm";; +- esac ++ GLLIBS="-lGL -lglut -lm -lGLU" + AC_SUBST([GLLIBS]);; + # *) AC_MSG_ERROR([OS is not supported]);; + esac + AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1]) +-CFLAGS=$true_CFLAGS ++CFLAGS="${CFLAGS} $true_CFLAGS" + + AC_CONFIG_FILES([Makefile]) + AC_OUTPUT diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch new file mode 100644 index 000000000000..cd35273de66b --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-zlib.patch @@ -0,0 +1,33 @@ + Makefile.am | 6 +++--- + zrio.c | 2 +- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index dad515a..9617eb7 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,8 +1,8 @@ + bin_PROGRAMS = zrio maqindex maqview maqindex_socks +-zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \ +- infback.c inftrees.c trees.c uncompr.c zutil.c +-generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src) ++generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c ++LIBS = -lz + zrio_SOURCES = zrio_main.c $(generic_src) ++zrio_LDADD = -lz + maqindex_SOURCES = maqmap_index_main.c $(generic_src) + maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \ + $(generic_src) +diff --git a/zrio.c b/zrio.c +index ffed00a..fe744df 100644 +--- a/zrio.c ++++ b/zrio.c +@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void + totin += strm.avail_in; + totout += strm.avail_out; + tmp = strm.avail_out; +- ret = inflate_zr(&strm, Z_BLOCK); /* return at end of block */ ++ ret = inflate(&strm, Z_BLOCK); /* return at end of block */ + totin -= strm.avail_in; + totout -= strm.avail_out; + if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout); diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch new file mode 100644 index 000000000000..043208bb79b5 --- /dev/null +++ b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch @@ -0,0 +1,16 @@ + stdhash.hh | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/stdhash.hh b/stdhash.hh +index eaf98af..f22c5a6 100644 +--- a/stdhash.hh ++++ b/stdhash.hh +@@ -493,7 +493,7 @@ public: + inline bool insert(const keytype_t &key, const valtype_t &val) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + vals[i] = val; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } -- cgit v1.2.3