diff --git a/pkgs/applications/science/biology/arb/default.nix b/pkgs/applications/science/biology/arb/default.nix deleted file mode 100644 index 2f622e94057..00000000000 --- a/pkgs/applications/science/biology/arb/default.nix +++ /dev/null @@ -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 $out/bin/arb - ''; - - meta = { - description = "Software for sequence database handling and analysis"; - longDescription = ''The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. Note that this package includes its own older versions of clustal etc.''; - license = "non-free"; - pkgMaintainer = "http://BioLib.open-bio.org/"; - homepage = http://www.arb-home.de/; - priority = "10"; # because it includes binaries of clustal etc. - broken = true; - }; -} diff --git a/pkgs/applications/science/biology/arb/makefile.patch b/pkgs/applications/science/biology/arb/makefile.patch deleted file mode 100644 index 8e7962511af..00000000000 --- a/pkgs/applications/science/biology/arb/makefile.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -r a1e04cdafd13 Makefile ---- a/Makefile Thu Sep 25 11:59:19 2008 +0200 -+++ b/Makefile Thu Sep 25 11:59:27 2008 +0200 -@@ -109,7 +109,7 @@ endif - - ALLOWED_GCC_295_VERSIONS=2.95.3 - ALLOWED_GCC_3xx_VERSIONS=3.2 3.3.1 3.3.3 3.3.4 3.3.5 3.3.6 3.4.0 3.4.2 3.4.3 --ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 -+ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 4.2.4 - ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_295_VERSIONS) $(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS) - - GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion) diff --git a/pkgs/development/libraries/lesstif-0.93/c-bad_integer_cast.patch b/pkgs/development/libraries/lesstif-0.93/c-bad_integer_cast.patch deleted file mode 100644 index 620d702f0f0..00000000000 --- a/pkgs/development/libraries/lesstif-0.93/c-bad_integer_cast.patch +++ /dev/null @@ -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 */ diff --git a/pkgs/development/libraries/lesstif-0.93/c-render_table_crash.patch b/pkgs/development/libraries/lesstif-0.93/c-render_table_crash.patch deleted file mode 100644 index 1699dbe1908..00000000000 --- a/pkgs/development/libraries/lesstif-0.93/c-render_table_crash.patch +++ /dev/null @@ -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 diff --git a/pkgs/development/libraries/lesstif-0.93/c-xim_chained_list_crash.patch b/pkgs/development/libraries/lesstif-0.93/c-xim_chained_list_crash.patch deleted file mode 100644 index 10bdf8d0b97..00000000000 --- a/pkgs/development/libraries/lesstif-0.93/c-xim_chained_list_crash.patch +++ /dev/null @@ -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)); diff --git a/pkgs/development/libraries/lesstif-0.93/default.nix b/pkgs/development/libraries/lesstif-0.93/default.nix deleted file mode 100644 index e8ec3d5e659..00000000000 --- a/pkgs/development/libraries/lesstif-0.93/default.nix +++ /dev/null @@ -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"; - }; -} diff --git a/pkgs/development/libraries/lesstif-0.93/stdint.patch b/pkgs/development/libraries/lesstif-0.93/stdint.patch deleted file mode 100644 index 8b202704abd..00000000000 --- a/pkgs/development/libraries/lesstif-0.93/stdint.patch +++ /dev/null @@ -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 - #endif - -+#include - #include /* Avoid re-definition of Pixel-type */ - - #include diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index c9dc30d9f0a..46f73556894 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -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 { };