From b9fafb8302a511ddfcd908a0abf892354b4f22af Mon Sep 17 00:00:00 2001 From: "Michael Mair-Keimberger (asterix)" Date: Sun, 29 Jan 2017 09:40:28 +0100 Subject: sci-biology/meme: remove unused patches Closes: https://github.com/gentoo/gentoo/pull/3708 --- .../meme/files/meme-3.5.4-Makefile.am.patch | 17 -- sci-biology/meme/files/meme-3.5.4-patch1.patch | 198 --------------------- sci-biology/meme/files/meme-3.5.4-patch2.patch | 70 -------- .../meme/files/meme-4.0.0-Makefile.am.patch | 17 -- 4 files changed, 302 deletions(-) delete mode 100644 sci-biology/meme/files/meme-3.5.4-Makefile.am.patch delete mode 100644 sci-biology/meme/files/meme-3.5.4-patch1.patch delete mode 100644 sci-biology/meme/files/meme-3.5.4-patch2.patch delete mode 100644 sci-biology/meme/files/meme-4.0.0-Makefile.am.patch (limited to 'sci-biology') diff --git a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch deleted file mode 100644 index 1293de0ea080..000000000000 --- a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400 -+++ Makefile.am 2007-04-24 10:37:37.000000000 -0400 -@@ -57,11 +57,11 @@ - endif - - dbdir: -- mkdir -p $(MEME_DB) -+ mkdir -p $(DESTDIR)$(MEME_DB) - - 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) - diff --git a/sci-biology/meme/files/meme-3.5.4-patch1.patch b/sci-biology/meme/files/meme-3.5.4-patch1.patch deleted file mode 100644 index b072d7edc527..000000000000 --- a/sci-biology/meme/files/meme-3.5.4-patch1.patch +++ /dev/null @@ -1,198 +0,0 @@ ---- meme_3.5.4/website/cgi-bin/process_request.pl 2006-09-21 19:46:29.000000000 +0000 -+++ trunk/website/cgi-bin/process_request.pl 2007-05-30 01:35:02.000000000 +0000 -@@ -1,6 +1,6 @@ - #!@WHICHPERL@ - ## --## $Id: process_request.pl 1339 2006-09-21 19:46:28Z tbailey $ -+## $Id: process_request.pl 1807 2007-05-30 01:34:31Z tbailey $ - ## - ## $Log: process_request.pl,v $ - ## Revision 1.6.6.1 2006/02/16 23:22:35 nadya -@@ -55,7 +55,8 @@ - $blocks_url = "http://blocks.fhcrc.org/blocks-bin/process_blocks.pl"; - # - # You can change this if you wish to use a different JASPAR server --$jaspar_root = "http://mordor.cgb.ki.se"; -+#$jaspar_root = "http://mordor.cgb.ki.se"; -+$jaspar_root = "http://asp.ii.uib.no:8090"; - $jaspar_url = "$jaspar_root/cgi-bin/jaspar2005/jaspar_db.pl"; - # - # You can change this if you wish to use a different Meta-MEME server -@@ -221,7 +222,7 @@ - - $fasta = ""; # return value - @lines = split(/\n/, $block); # split block into lines -- for ($i = 1; $i<$#lines; $i++) { -+ for ($i = 2; $i<$#lines; $i++) { - last if $lines[$i] =~ /^\/\//; - @words = split(/\s+/, $lines[$i]); # split line into words - # get sequence line -@@ -239,7 +240,7 @@ - - $fasta = ""; # return value - @lines = split(/\n/, $block); # split block into lines -- for ($i = 1; $i<$#lines; $i++) { -+ for ($i = 2; $i<$#lines; $i++) { - last if $lines[$i] =~ /^\/\//; - @words = split(/\s+/, $lines[$i]); # split line into words - # get id line and sequence line -@@ -311,7 +312,8 @@ - $content = $request->content; - - # fix bug in JASPAR output; add database field to view buttons -- $content =~ s/rm=present/rm=present&db=$sub_db/g; -+ # remove fix: JASPAR fixed the bug -+ # $content =~ s/rm=present/rm=present&db=$sub_db/g; - - # display the page - print $content; ---- meme_3.5.4/src/ureadseq.c 2006-09-21 19:46:28.000000000 +0000 -+++ trunk/src/ureadseq.c 2007-05-18 08:18:05.000000000 +0000 -@@ -1,5 +1,5 @@ - /* -- * $Id: ureadseq.c 1339 2006-09-21 19:46:28Z tbailey $ -+ * $Id: ureadseq.c 1787 2007-05-18 08:17:28Z tbailey $ - * - * $Log$ - * Revision 1.2 2006/03/08 20:50:11 nadya -@@ -206,10 +206,9 @@ - - Local void addinfo(char *s, struct ReadSeqVars *V) - { -- char s2[256], *si; -+ char *si = (char *) malloc((strlen(s) + 40) * sizeof(char)); - boolean saveadd; - -- si = s2; - while (*s == ' ') s++; - sprintf(si, " %d) %s\n", V->nseq, s); - -@@ -217,6 +216,7 @@ - V->addit = true; - V->isseqchar = isAnyChar; - addseq( si, V); -+ free(si); - V->addit = saveadd; - V->isseqchar = isSeqChar; - } -@@ -966,7 +966,6 @@ - } while ((l == 0) && !feof(V->f)); - - if (feof(V->f)) V->err = eNoData; -- - else switch (format_) { - case kPlain : readPlain(V); break; - case kIG : readIG(V); break; -@@ -1181,7 +1180,7 @@ - int nlines= 0, k=0, splen= 0, otherlines= 0, aminolines= 0, dnalines= 0; - char sp[MAXLINE]; - long linestart=0; -- int maxlines2check=500; -+ int maxlines2check=5000; - - #define ReadOneLine(sp) \ - { done |= (feof(fseq)); \ ---- meme_3.5.4/src/include/ureadseq.h 2006-09-21 19:46:28.000000000 +0000 -+++ trunk/src/ureadseq.h 2007-05-18 08:18:05.000000000 +0000 -@@ -1,5 +1,5 @@ - /* -- * $Id: ureadseq.h 1339 2006-09-21 19:46:28Z tbailey $ -+ * $Id: ureadseq.h 1048 2006-07-06 20:07:44Z cegrant $ - * - * $Log$ - * Revision 1.1 2005/07/29 19:12:07 nadya -@@ -15,7 +15,7 @@ - #include "config.h" - #include "macros.h" - --#define MAXLINE 1024 -+#define MAXLINE 10240 - - typedef char boolean; - #define NEWLINE '\n' ---- meme_3.5.4/src/read_seq_file.c 2006-09-21 19:46:28.000000000 +0000 -+++ ./read_seq_file.c 2007-05-18 06:51:06.000000000 +0000 -@@ -433,6 +433,7 @@ - name[i++] = c; /* non-blank: add to name */ - } - } -+ Resize(name, i+1, char); - name[i] = '\0'; - - /* read in description */ ---- meme_3.5.4/website/html/meme-install.html 2006-09-21 19:46:29.000000000 +0000 -+++ fred/meme-install.html 2007-05-30 02:00:56.000000000 +0000 -@@ -208,42 +208,39 @@ -

Getting and installing the patches

-

The distribution may have patches associated with it. They are available - from http://meme.nbcr.net/downloads/. --The patch file name is filename.VERSION.patch. In addition, a --patched file is distributed as well and can be used as a drop-in substitute --for the original file. The drop-in file is filename.VERSION. --It is necessary to download only one of the two files depending on the method used for --patching. All patches for a specific version should be installed. The list --below provides instructions for installation of availble patches for specific --version. -+Patch files are located in a directory named -+VERSION.patches, -+for example, meme_3.5.4.patches. -+Patch file have names like: -+VERSION.patch_SERIAL_NO, for example, meme_3.5.4.patch_3. -+

To install a patch, download the patch file from the URL given above. -+Then perform the following commands to install it: -+
$ cp PATCH_FILE VERSION
$ cd VERSION -+
$ patch -p1 < PATCH_FILE -+
$ make install -+
$ make test -+

-+

-+For example, to install the first patch to version meme_3.5.4, you would perform the following commands: -+
$ cp meme_3.5.4.patch_1 meme_3.5.4 -+
$ cd meme_3.5.4 -+
$ patch -p1 < meme_3.5.4.patch_1 -+
$ make install -+
$ make test -+

-+

-+You must install all of the patches for a specific version in serial -+number order. For example, if you wish to install patch number 3, -+you must first have installed patches number 1 and 2 for that version. -+This is easy to do. Just download all the patches for your current -+version, copy them to your current versions's directory, and then -+install them in order by repeating the patch, -+command above, with each patch file. You only need to run the -+install and -+make test commands once, after -+the last patch command. -

- --
-- -- -- -- -- -- -- -- -- -- -- --
VersionPatch listInstallation
3.5.0mast-client.txt --
    --
  1. If downloaded a patch file mast-client.txt.3.5.0.patch: --
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/ --
    # cd meme_3.5.0/scripts/ --
    # patch -p0 < mast-client.txt.3.5.0.patch --
    --
    2. --
  2. If downloaded a patched file mast-client.txt.3.5.0: --
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt --
    3. --
--
--
-- -

-

[ Top ]

- diff --git a/sci-biology/meme/files/meme-3.5.4-patch2.patch b/sci-biology/meme/files/meme-3.5.4-patch2.patch deleted file mode 100644 index cc07a98307f2..000000000000 --- a/sci-biology/meme/files/meme-3.5.4-patch2.patch +++ /dev/null @@ -1,70 +0,0 @@ ---- meme_3.5.4/website/cgi-bin/meme.pl 2006-09-21 19:46:29.000000000 +0000 -+++ trunk/website/cgi-bin/meme.pl 2007-09-10 00:28:33.000000000 +0000 -@@ -1,6 +1,6 @@ - #!@WHICHPERL@ - ## --## $Id: meme.pl 1339 2006-09-21 19:46:28Z tbailey $ -+## $Id: meme.pl 2054 2007-09-10 00:27:42Z tbailey $ - ## - ## $Log$ - ## Revision 1.12 2006/03/07 23:30:19 nadya -@@ -467,21 +467,21 @@ - - # check against allowed dna letters - $x = $_; -- $x =~ tr/ABCDGHKMNRSTUVWY//cd; -+ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; - $new = length $x; - if ($old == $new) { - "dna"; - } else { - # check against allowed protein letters - $x = $_; -- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; -+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; - $new = length $x; - if ($old == $new) { - "protein"; - } else { - # get the unknown letters - $x = $_; -- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; -+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; - &whine(" - Your sequences contained the following unrecognized letters: $x. -
---- meme_3.5.4/website/cgi-bin/mast.pl 2006-09-21 19:46:29.000000000 +0000 -+++ trunk/website/cgi-bin/mast.pl 2007-09-10 00:38:14.000000000 +0000 -@@ -1,6 +1,6 @@ - #!@WHICHPERL@ - ## --## $Id: mast.pl 1339 2006-09-21 19:46:28Z tbailey $ -+## $Id: mast.pl 2055 2007-09-10 00:37:11Z tbailey $ - ## - ## $Log$ - ## Revision 1.8 2006/03/07 23:30:19 nadya -@@ -479,21 +479,21 @@ - - # check against allowed nucleotide letters - $x = $_; -- $x =~ tr/ABCDGHKMNRSTUVWY//cd; -+ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; - $new = length $x; - if ($old == $new) { - return("DNA"); - } else { - # check against allowed protein letters - $x = $_; -- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; -+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; - $new = length $x; - if ($old == $new) { - return("PROTEIN"); - } else { - # get the unknown letters - $x = $_; -- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; -+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; - &whine(" - Your sequences contained the following unrecognized letters: $x. -
diff --git a/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch b/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch deleted file mode 100644 index 1293de0ea080..000000000000 --- a/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400 -+++ Makefile.am 2007-04-24 10:37:37.000000000 -0400 -@@ -57,11 +57,11 @@ - endif - - dbdir: -- mkdir -p $(MEME_DB) -+ mkdir -p $(DESTDIR)$(MEME_DB) - - 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) - -- cgit v1.2.3-65-gdbad