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Remove arb and then-orphaned lesstif93

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Arb has been broken (and marked as such) since the removal of
GCC 4.2 in July 2014. Nothing and no-one uses it. Time to go.
This commit is contained in:
Tobias Geerinckx-Rice 2015-05-25 21:24:57 +02:00
parent 4053dcdace
commit 7b6d9d4cff
8 changed files with 0 additions and 189 deletions
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86
pkgs/applications/science/biology/arb/default.nix
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@ -1,86 +0,0 @@
{ stdenv, fetchurl, glew, mesa, libpng, lesstif, lynx, freeglut
, libtiff, rxp, sablotron, perl, jdk, transfig, gv, gnuplot, xorg }:
# NOTE: This package does not build on 64-bit systems. Because of some faulty
# int->pointer arithmatic. The build scripts are abnormal - but it appears to
# work.
stdenv.mkDerivation {
name = "arb-2007-Dec-07";
src = fetchurl {
url = http://download.arb-home.de/release/2007_12_07/arbsrc.tgz;
sha256 = "04l7qj0wigg1h56a9d70hxhdr343v3dg5dhqrc7fahc1v4h8f1rd";
};
patches = [ ./makefile.patch ];
buildInputs =
[ glew mesa libpng xorg.libXpm lesstif lynx freeglut libtiff rxp
sablotron xorg.libXaw perl jdk transfig xorg.libX11 xorg.libXext
xorg.libXt gv gnuplot
];
unpackPhase = ''
tar xzf $src
'';
buildPhase = ''
echo `make` # avoids error signal
export ARBHOME=`pwd`
export PATH=$ARBHOME/bin:$PATH
make all
'';
installPhase = ''
mkdir -p $out/lib
shareddir=/nix/var/lib/arb
# link out writable shared location lib/pts
mkdir -p $shareddir/lib/pts
cp -vau lib/pts $shareddir/lib
rm -vrf lib/pts
ln -vs $shareddir/lib/pts $out/lib/pts
chmod a+rwx $shareddir/lib/pts
# link out writable shared location lib/nas/
mkdir -p $shareddir/lib/nas
cp -vau lib/nas $shareddir/lib
rm -vrf lib/nas
ln -vs $shareddir/lib/nas $out/lib/nas
chmod a+rwx $shareddir/lib/nas
# link out shared lib/pixmaps (not sure about this, yet):
mkdir -p $shareddir/lib/pixmaps
cp -vau lib/pixmaps $shareddir/lib
rm -vrf lib/pixmaps
ln -vs $shareddir/lib/pixmaps $out/lib/pixmaps
chmod a+rwx $shareddir/lib/pixmaps
# bulk copy
cp -vau * $out
# replace arb script
mv $out/bin/arb $out/bin/arb.orig
cat > $out/bin/arb << ARB
#!/bin/sh
echo Starting Nix compiled arb from $out
echo Shared databases are located in $shareddir
# sometimes local profiles override these:
export ARBHOME=$out
export LD_LIBRARY=$ARBHOME/lib
$out/bin/arb_ntree $*
ARB
chmod +x $out/bin/arb
'';
meta = {
description = "Software for sequence database handling and analysis";
longDescription = ''The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. Note that this package includes its own older versions of clustal etc.'';
license = "non-free";
pkgMaintainer = "http://BioLib.open-bio.org/";
homepage = http://www.arb-home.de/;
priority = "10"; # because it includes binaries of clustal etc.
broken = true;
};
}

12
pkgs/applications/science/biology/arb/makefile.patch
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@ -1,12 +0,0 @@
diff -r a1e04cdafd13 Makefile
--- a/Makefile Thu Sep 25 11:59:19 2008 +0200
+++ b/Makefile Thu Sep 25 11:59:27 2008 +0200
@@ -109,7 +109,7 @@ endif
ALLOWED_GCC_295_VERSIONS=2.95.3
ALLOWED_GCC_3xx_VERSIONS=3.2 3.3.1 3.3.3 3.3.4 3.3.5 3.3.6 3.4.0 3.4.2 3.4.3
-ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3
+ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 4.2.4
ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_295_VERSIONS) $(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion)

13
pkgs/development/libraries/lesstif-0.93/c-bad_integer_cast.patch
View file

@ -1,13 +0,0 @@
--- lesstif2-0.94.4.orig/include/Motif-2.1/XmI/XpmI.h
+++ lesstif2-0.94.4/include/Motif-2.1/XmI/XpmI.h
@@ -217,8 +217,8 @@
FUNC(xpmHashSlot, xpmHashAtom *, (xpmHashTable *table, char *s));
FUNC(xpmHashIntern, int, (xpmHashTable *table, char *tag, void *data));
-#define HashAtomData(i) ((void *)i)
-#define HashColorIndex(slot) ((unsigned int)((*slot)->data))
+#define HashAtomData(i) ((void *)(uintptr_t)i)
+#define HashColorIndex(slot) ((uintptr_t)((*slot)->data))
#define USE_HASHTABLE (cpp > 2 && ncolors > 4)
/* I/O utility */

11
pkgs/development/libraries/lesstif-0.93/c-render_table_crash.patch
View file

@ -1,11 +0,0 @@
--- lesstif2-0.95.0.orig/lib/Xm-2.1/RenderTable.c
+++ lesstif2-0.95.0/lib/Xm-2.1/RenderTable.c
@@ -465,7 +465,7 @@
DEBUGOUT(_LtDebug(__FILE__, w, "_XmRenderTableFinaliseTag(%s)\n", tag));
#if 1
/* Experimental start */
- if (r->dpy == 0)
+ if (r->dpy == 0 && w)
r->dpy = XtDisplay(w);
/* Experimental end */
#endif

24
pkgs/development/libraries/lesstif-0.93/c-xim_chained_list_crash.patch
View file

@ -1,24 +0,0 @@
diff -ru lesstif2-0.94.4-old/lib/Xm-2.1/XmIm.c lesstif2-0.94.4/lib/Xm-2.1/XmIm.c
--- lesstif2-0.94.4-old/lib/Xm-2.1/XmIm.c 2004-10-20 21:32:11.000000000 +0200
+++ lesstif2-0.94.4/lib/Xm-2.1/XmIm.c 2007-03-28 14:39:27.000000000 +0200
@@ -133,7 +133,10 @@
p->next = q->next;
}
- XtFree((char *)stuff);
+ /* if count!=0 then someone uses the stuff as orig_xim
+ so unlink it but not free it */
+ if (!stuff->count)
+ XtFree((char *)stuff);
}
/*
@@ -1060,6 +1063,8 @@
XCloseIM(stuff->xim);
DEBUGOUT(_LtDebug(__FILE__, w, "XCloseIM(%p)\n", stuff->xim));
stuff->orig_xim->xim = NULL;
+ /* stuff->orig_xim is now useless */
+ XtFree(stuff->orig_xim);
} else {
DEBUGOUT(_LtDebug(__FILE__, w, "XmImCloseXIM(%p), count -> %d\n",
stuff->xim, stuff->orig_xim->count));

26
pkgs/development/libraries/lesstif-0.93/default.nix
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@ -1,26 +0,0 @@
{ stdenv, fetchurl, x11, libXp, libXau }:
stdenv.mkDerivation {
name = "lesstif-0.93.94";
src = fetchurl {
url = http://prdownloads.sourceforge.net/lesstif/lesstif-0.93.94.tar.bz2;
sha256 = "0v4l46ill6dhhswsw1hk6rqyng98d85nsr214vhd2k0mfajpig1y";
};
buildInputs = [x11];
propagatedBuildInputs = [libXp libXau];
# This is an older release of lesstif which works with arb.
patches =
[ ./c-bad_integer_cast.patch
./c-xim_chained_list_crash.patch
./c-render_table_crash.patch
./stdint.patch
];
meta = {
priority = "5";
};
}

11
pkgs/development/libraries/lesstif-0.93/stdint.patch
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@ -1,11 +0,0 @@
diff -r 97ac365bfcd6 lesstif-0.93.94/lib/Xm-2.1/Xpm.c
--- lesstif-0.93.94/lib/Xm-2.1/Xpm.c Mon Oct 06 15:52:50 2008 +0200
+++ lesstif-0.93.94/lib/Xm-2.1/Xpm.c Mon Oct 06 15:53:16 2008 +0200
@@ -54,6 +54,7 @@
#include <io.h>
#endif
+#include <stdint.h>
#include <X11/Intrinsic.h> /* Avoid re-definition of Pixel-type */
#include <Xm/XpmP.h>

6
pkgs/top-level/all-packages.nix
View file

@ -6410,8 +6410,6 @@ let
lesstif = callPackage ../development/libraries/lesstif { };
lesstif93 = callPackage ../development/libraries/lesstif-0.93 { };
leveldb = callPackage ../development/libraries/leveldb { };
levmar = callPackage ../development/libraries/levmar { };
@ -13699,10 +13697,6 @@ let
motif = lesstif;
};
arb = callPackage ../applications/science/biology/arb {
lesstif = lesstif93;
};
archimedes = callPackage ../applications/science/electronics/archimedes { };
emboss = callPackage ../applications/science/biology/emboss { };