Remove packages slated for QA removal today.

6 files changed, 0 insertions, 614 deletions

diff --git a/sci-chemistry/maid/ChangeLog b/sci-chemistry/maid/ChangeLog
deleted file mode 100644
index 7ff8a32a47fe..000000000000
--- a/sci-chemistry/maid/ChangeLog
+++ /dev/null
@@ -1,56 +0,0 @@
-# ChangeLog for sci-chemistry/maid
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/ChangeLog,v 1.14 2008/07/27 15:02:08 markusle Exp $
-
-  27 Jul 2008; Markus Dittrich <markusle@gentoo.org>
-  +files/maid-gcc4.3.patch, maid-20011112.ebuild:
-  Added gcc-4.3 compatibility patch.
-
-  27 Jun 2008; Ulrich Mueller <ulm@gentoo.org> maid-20011112.ebuild:
-  Change dependency from virtual/motif to x11-libs/openmotif, bug 224749.
-
-  22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; maid-20011112.ebuild:
-  Drop virtual/x11 references.
-
-  22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog:
-  Redigest for Manifest2
-
-  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  (#148281) Change herd to sci-chemistry from sci.
-
-  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  Remove myself as maintainer, anyone feel free to work on this, although I'll
-  continue to do so as well.
-
-  09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; maid-20011112.ebuild:
-  x86 stable.
-
-  07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  Update to my new email address.
-
-  23 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>; maid-20011112.ebuild:
-  Remove redundant src_compile(), reported by ciaranm.
-
-  23 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>;
-  -files/fix-compilation.patch:
-  Forgot to cvs rm it.
-
-  23 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>; maid-20011112.ebuild:
-  (#123634) Push big patch to mirrors.
-
-  15 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>; maid-20011112.ebuild:
-  Fix SRC_URI.
-
-  15 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>; maid-20011112.ebuild:
-  Fix license. The author informed me by email that it's intended to be freely
-  distributed, modified and redistributed.
-
-*maid-20011112 (15 Dec 2005)
-
-  15 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>;
-  +files/fix-compilation.patch, +files/fix-warnings.patch, +metadata.xml,
-  +maid-20011112.ebuild:
-  MAID does automatic fitting of protein X-ray crystallography electron
-  density maps. It can correctly build about 60% of alpha carbons on
-  medium-resolution maps and about 80% on high-resolution maps.
-
diff --git a/sci-chemistry/maid/Manifest b/sci-chemistry/maid/Manifest
deleted file mode 100644
index 76f5472fbe74..000000000000
--- a/sci-chemistry/maid/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX fix-warnings.patch 17141 RMD160 b10d94b75c684b3ac506c28dfdd70ec8fb000fc1 SHA1 07ee353194663a69168618c711f80cc7fde64e07 SHA256 338e595a56ea1592221f833ab368afa672b4571460a9d46667871ded7cf8e5c1
-AUX maid-gcc4.3.patch 2568 RMD160 2e5eed95ee819d3e17536fb161bde072966bdf8d SHA1 bf2f34dc8e6492a28c92f3f42fdc3ccbb83a9e21 SHA256 e410d7eca3c0446a99fdd3b8d7dfcf01798a92c88b690700c3c3b566c80cd97f
-DIST maid-fix-compilation.patch.bz2 5044 RMD160 fd196923baff07836bebd8cdd463b4f72a12cc87 SHA1 2a705ca79b7500ec4d2a66f4fdfff3dec97da2f8 SHA256 17a2dda71af96d45f57c1cbf500bad1d1aca596cc4da4eee481b4bb62207d7be
-DIST maid_unix_12nov01.tar.gz 480609 RMD160 fcfcd63e2c68afb43ba576430aac23d5fbee419d SHA1 962c459faa2855f73eba7bed6411d7ae984a32ce SHA256 4dcf2c2945a97efa7dcea8e89a2b3d65c8daf0f44705e11305c426854db5eaa0
-EBUILD maid-20011112.ebuild 1394 RMD160 6497dfd686b814bf58bd0d2a503ccb4c6455d59a SHA1 733dd6466935dbbb447483cb5a8971a66e87b03e SHA256 73db7505642e1de7e869a235a614181a7e179f887deaa897c4373fb8ad7f01e8
-MISC ChangeLog 2231 RMD160 1f28bdbf2bff69f30ac4f3219c897920b8f12ea5 SHA1 66aeb13db8a6d08a2153bd280b03cad79e401e40 SHA256 2b1e840c3312a241b5d62dfead5f698b86527aa98bd63219689e74af6f03382a
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/maid/files/fix-warnings.patch b/sci-chemistry/maid/files/fix-warnings.patch
deleted file mode 100644
index b4f48d244a69..000000000000
--- a/sci-chemistry/maid/files/fix-warnings.patch
+++ /dev/null
@@ -1,419 +0,0 @@
-diff -ur glmaid_dist.orig/assignseq.c++ glmaid_dist/assignseq.c++
---- glmaid_dist.orig/assignseq.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/assignseq.c++	2005-12-15 08:36:47.000000000 -0800
-@@ -2630,9 +2630,9 @@
-    if(ibestden <= 1) // 0.8 or 1.0
-        *maxngap = geo.maxngap;
-    else if(ibestden ==2) // 1.2
--       *maxngap = 1.5*geo.maxngap;
-+       *maxngap = (int) (1.5*geo.maxngap);
-    else if (ibestden >2) // 1.4 or 1.6
--       *maxngap = 2.0 *geo.maxngap;   
-+       *maxngap = (int) (2.0 *geo.maxngap);   
-  }
- #endif
- 
-diff -ur glmaid_dist.orig/bone.c++ glmaid_dist/bone.c++
---- glmaid_dist.orig/bone.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/bone.c++	2005-12-15 08:31:26.000000000 -0800
-@@ -815,7 +815,7 @@
-    }
- 
- 
--   bonemin = bone1.minden*maidfile.denscale;  // lower limit  used to make bone (round down) 
-+   bonemin = (int) (bone1.minden*maidfile.denscale);  // lower limit  used to make bone (round down) 
- fprintf(fpout,"bonemin = %d\n",bonemin);
-    defineiden(bone1,iden,den1,bonemin); // set point on boundary = REMOVE
-    bsort(den1,bone1,sortv,bonemin,sortnum,&maxsize);  // sort density into bins; sort[i] is vector of 1 ..... max
-diff -ur glmaid_dist.orig/checkfit.c++ glmaid_dist/checkfit.c++
---- glmaid_dist.orig/checkfit.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/checkfit.c++	2005-12-15 08:22:14.000000000 -0800
-@@ -2977,7 +2977,7 @@
-    *maxden = -1000.0;
-    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
-    for(k=0;k<=2;k++)
--       ir[k]=fd[k]+0.5; /*round  to integer*/
-+       ir[k]=(int) (fd[k]+0.5); /*round  to integer*/
-    for(ii=ir[0]-2;ii<=ir[0]+2;ii++){
-      if( (ii>=1)&& (ii<=den1.amax[0]-den1.amin[0]-1) )
-         for(jj=ir[1]-2;jj<=ir[1]+2;jj++)
-diff -ur glmaid_dist.orig/extend2.c++ glmaid_dist/extend2.c++
---- glmaid_dist.orig/extend2.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/extend2.c++	2005-12-15 08:24:45.000000000 -0800
-@@ -363,7 +363,7 @@
-    nend[3]=geo.nend[1]+3;
- #if 1  // Works well in most cases
-    mrot[0]= 2*nrot;
--   mrot[1]= 1.5*nrot;
-+   mrot[1]= (int) (1.5*nrot);
-    mrot[2]= nrot;
-    mrot[3]= nrot;
- #endif
-diff -ur glmaid_dist.orig/extendfit.c++ glmaid_dist/extendfit.c++
---- glmaid_dist.orig/extendfit.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/extendfit.c++	2005-12-15 08:26:43.000000000 -0800
-@@ -4024,7 +4024,7 @@
- ext.usenfits = 3;//  I do not think this makes any difference since it reset in other routines -Number of unassigned connected that must be linked to assigne seq. value
-    geo.deldist = sqrt( dot(den1.delx,den1.delx) ); // length of den1.delx vector = 1.445 for shad , res = 2.5
-    if(geo.deldist < 1.445)
--      geo.gnmax = 7*(1.445/geo.deldist) +1;
-+      geo.gnmax = (int) (7*(1.445/geo.deldist) +1);
-    else
-       geo.gnmax = 7;
-    geo.maxugap = 8;  //Maximum gap allowed to connect unassigned fits
-diff -ur glmaid_dist.orig/fit.c++ glmaid_dist/fit.c++
---- glmaid_dist.orig/fit.c++	2005-12-15 08:15:43.000000000 -0800
-+++ glmaid_dist/fit.c++	2005-12-15 08:36:24.000000000 -0800
-@@ -65,7 +65,7 @@
- tordata.torconst=torconstorig;
- tordata2.torconst=torconstorig;   
- tordata.rfor=rfororig; //-BE CAREFUL - MUST BE SURE rfororig defined/geo.maxside = origmaxside;   
--geo.maxside = origmaxside;   
-+geo.maxside = (int) origmaxside;   
-     if (&client_data) {
-         XtRemoveWorkProc (work_id);
-     }
-diff -ur glmaid_dist.orig/initialize.c++ glmaid_dist/initialize.c++
---- glmaid_dist.orig/initialize.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/initialize.c++	2005-12-15 08:34:02.000000000 -0800
-@@ -300,7 +300,7 @@
-                            nless=nless+1;
-                            dds= -MAXCHAR+1;
-                       }
--                      den1.den[i][j][k]=dds;
-+                      den1.den[i][j][k]=(signed) dds;
- 		     }
- 		}
- 	}
-Files glmaid_dist.orig/initialize.o and glmaid_dist/initialize.o differ
-diff -ur glmaid_dist.orig/mapmenu.c++ glmaid_dist/mapmenu.c++
---- glmaid_dist.orig/mapmenu.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/mapmenu.c++	2005-12-15 08:35:53.000000000 -0800
-@@ -430,7 +430,7 @@
- {
-   int i;
-      for(i=0;i<3;i++)
--     map.crange[i] = fcontradius[item_no]/map.delx[i];
-+     map.crange[i] = (int) (fcontradius[item_no]/map.delx[i]);
- //printf("map radius = %d\n",map.crange[0]);
- }
- 
-diff -ur glmaid_dist.orig/math.c++ glmaid_dist/math.c++
---- glmaid_dist.orig/math.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/math.c++	2005-12-15 08:31:55.000000000 -0800
-@@ -51,9 +51,9 @@
-   z=xx[2]/den1.cvz;
-   y=(xx[1]-z*den1.cvy)/den1.singam;
-   x=xx[0]-y*den1.cosgam-z*den1.cosbe;
--  ijk[0]=x/den1.delx[0] - den1.amin[0];
--  ijk[1]=y/den1.delx[1] - den1.amin[1];
--  ijk[2]=z/den1.delx[2] - den1.amin[2];
-+  ijk[0]=(int) (x/den1.delx[0] - den1.amin[0]);
-+  ijk[1]=(int) (y/den1.delx[1] - den1.amin[1]);
-+  ijk[2]=(int) (z/den1.delx[2] - den1.amin[2]);
- }
- 
- void imcv(struct griddata& den1,int xi[3],float sx[3])  /*convert from  integer xi,xj (grid point)
-diff -ur glmaid_dist.orig/menu.c++ glmaid_dist/menu.c++
---- glmaid_dist.orig/menu.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/menu.c++	2005-12-15 08:35:15.000000000 -0800
-@@ -321,7 +321,7 @@
- {
-    int i;  
-    sc.cubecol[0] += 0.01;
--   i= sc.cubecol[0];
-+   i= (int) sc.cubecol[0];
-    sc.cubecol[0]= sc.cubecol[0]-i;;
-    draw_screen(client_data);
-     return False; // Runs continually
-@@ -987,14 +987,14 @@
-     int i;
- 
-     for(i=0;i<=2;i++) // Use default contour radius
--          den1.crange[i]=sc.contourradius/den1.delx[i];
-+          den1.crange[i]=(int) (sc.contourradius/den1.delx[i]);
-     den1.contonoff = -1;
-     den1.selectcontonoff = -1;
-     for(i=0;i<3;i++)
-        den1.color[i]=bluev[i];
-     den1.conlevel = sc.conlevel*maidfile.denscale;  // Set contourleve to default value
-     // Allocate arrays for contour routines
--    den1.ntri = NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2]); // Scale ntri relative del = 1
-+    den1.ntri = (int) (NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2])); // Scale ntri relative del = 1
- printf("Allocating arrays for contour routines  ntriangles = %d\n",den1.ntri);
-     imat2(den1.tri,den1.ntri,9);
- printf("   Done\n");
-diff -ur glmaid_dist.orig/pdbtolev.c++ glmaid_dist/pdbtolev.c++
---- glmaid_dist.orig/pdbtolev.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/pdbtolev.c++	2005-12-15 08:27:19.000000000 -0800
-@@ -645,7 +645,7 @@
- {
-     int i,j,natot,bi;
-     float  bsqr;
--    natot=subst[snum].pos[0][0]; /*total # of atoms*/
-+    natot=(int) subst[snum].pos[0][0]; /*total # of atoms*/
-     bsqr=tsqr(bondlength);
-     for(i=1;i<=natot;i++)
-        cmat[i][0]=0; /*initally no connections to i*/
-diff -ur glmaid_dist.orig/rankside.c++ glmaid_dist/rankside.c++
---- glmaid_dist.orig/rankside.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/rankside.c++	2005-12-15 08:33:32.000000000 -0800
-@@ -201,13 +201,13 @@
- #endif
-      tbad = fit.ibad[resn][a1] + fit.ibad[resn][a2] +fit.ibad[resn][a3];
-      if(tbad==0)
--         return 0+iadd;    
-+         return 0+(int) iadd;    
-      if(tbad ==1)
--         return 1+iadd;
-+         return 1+(int) iadd;
-      if(tbad==2)  
--         return 2+iadd;
-+         return 2+(int) iadd;
-      if(tbad==3)  
--         return 4+iadd;
-+         return 4+(int) iadd;
-      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
-          return 3;
-      else
-@@ -245,11 +245,11 @@
-         iadd = iadd+1;
- #endif
-      if(fit.ibad[resn][a1]==0 ) 
--         return 0+iadd;    
-+         return 0+(int) iadd;    
-      else if( fit.ibad[resn][a2]==0 )
--         return 1+iadd;
-+         return 1+(int) iadd;
-      else if( fit.ibad[resn][a3]==0 )
--         return 1+iadd;
-+         return 1+(int) iadd;
-      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
-          return 3;
-      else
-@@ -285,11 +285,11 @@
-         iadd = iadd+1;
- #endif
-      if(fit.ibad[resn][a1]==0 ) 
--         return 0+iadd;    
-+         return 0+(int) iadd;    
-      else if( fit.ibad[resn][a2]==0 )
--         return 1+iadd;
-+         return 1+(int) iadd;
-      else if( fit.ibad[resn][a3]==0 )
--         return 1+iadd;
-+         return 1+(int) iadd;
-      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
-          return 3;
-      else
-@@ -316,11 +316,11 @@
-      if(valden> 1.1*ringden) //change2
-         iadd = iadd+1;
-      if(fit.ibad[resn][a1]==0 ) 
--         return 0+iadd;    
-+         return 0+(int) iadd;    
-      else if( fit.ibad[resn][a2]==0 )
--         return 1+iadd;
-+         return 1+(int) iadd;
-      else if( fit.ibad[resn][a3]==0 )
--         return 1+iadd;
-+         return 1+(int) iadd;
-      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
-          return 3;
-      else
-Files glmaid_dist.orig/rankside.o and glmaid_dist/rankside.o differ
-diff -ur glmaid_dist.orig/refine.c++ glmaid_dist/refine.c++
---- glmaid_dist.orig/refine.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/refine.c++	2005-12-15 08:26:15.000000000 -0800
-@@ -67,8 +67,8 @@
- */
- {
-    int ix,rnd;
--   ix = floor(x);
--   rnd = nn*(x-ix) + 0.5;
-+   ix = (int) floor(x);
-+   rnd = (int) (nn*(x-ix) + 0.5);
-    printf("nn = %d x = %5.3f  rnd = %d  Grid point %5.3f\n",nn,x,rnd,ix+(float)rnd/nn);
-    return rnd;
- }
-@@ -82,8 +82,8 @@
-    int k;
- 
-    for(k=0;k<=2;k++){
--      ivec[k] = floor(fvec[k]);
--      ival[k] = nn*(fvec[k]-ivec[k]) + 0.5;
-+      ivec[k] = (int) floor(fvec[k]);
-+      ival[k] = (int) (nn*(fvec[k]-ivec[k]) + 0.5);
-    }
- }   
- 
-@@ -115,9 +115,9 @@
-    }
-    for(k=0;k<=2;k++)
-        gzd.dvec[gzd.num][k] =ivec[k];
--   gzd.den[gzd.num] = scalechar* exp(-rad*rad/bfact) +0.5; // mult by 100 and round
-+   gzd.den[gzd.num] = (int) (scalechar* exp(-rad*rad/bfact) +0.5); // mult by 100 and round
-    for(k=0;k<=2;k++)
--       gzd.forv[gzd.num][k] = 4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact;   
-+       gzd.forv[gzd.num][k] = (int) (4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact);   
- }
- 
- void assignforce(gzdhead)
-@@ -421,7 +421,7 @@
-    gzd[0].num = 0; 
-    oneatomgrid(den1,geo,ivec0,cenpos,gzd[0],bfact,countfunc);
-    printf("totnum = %d\n",gzd[0].num);
--   maxgzd = gzd[0].num = 1.5*gzd[0].num; // increase by 15%
-+   maxgzd = gzd[0].num = (int) (1.5*gzd[0].num); // increase by 15%
-    allocategzd(gzd[0].num);
-    del = 1.0/NDIV;
-    for(i=0;i<=NDIV;i++){
-diff -ur glmaid_dist.orig/sphere.c++ glmaid_dist/sphere.c++
---- glmaid_dist.orig/sphere.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/sphere.c++	2005-12-15 08:36:06.000000000 -0800
-@@ -95,7 +95,7 @@
-        fclose(fp);
-     } // spherefile opened
-     sc.isphere = maidfile.nsphere; // set active sphere to last read
--    sc.drawspheres =1.0;
-+    sc.drawspheres =1;
-     if (widget = XtNameToWidget (spheremenu,"button_0")) //DEFAULT:  Turn off check box for label on/off button
-             XtVaSetValues (widget, XmNset,TRUE, NULL);
- }
-diff -ur glmaid_dist.orig/tordyn.c++ glmaid_dist/tordyn.c++
---- glmaid_dist.orig/tordyn.c++	2005-12-15 08:13:32.000000000 -0800
-+++ glmaid_dist/tordyn.c++	2005-12-15 08:28:27.000000000 -0800
-@@ -337,8 +337,8 @@
-     xtof(den1,apos,fd);
- /* New version, interpolates all neighbors*/
-     for(k=0;k<=2;k++){
--       ir[k]=fd[k]; /*round down*/
--       irh[k]=fd[k]+0.5; /*round to next 1/2*/
-+       ir[k]=(int) fd[k]; /*round down*/
-+       irh[k]=(int) (fd[k]+0.5); /*round to next 1/2*/
-        if( (ir[k]<1)|| (irh[k]>den1.amax[k]-den1.amin[k]-1) ){
- //         if(verbose>=1)
-          if(verbose>=2) // 30nov00 - do not print this line
-@@ -683,7 +683,7 @@
-    atomden = 0;
-    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
-    for(kc=0;kc<=2;kc++)
--       ir[kc]=fd[kc]; /*round down to integer*/
-+       ir[kc]=(int) fd[kc]; /*round down to integer*/
-    for(k=0;k<=2;k++){ // check if pos in density range
-       if( (ir[k]<2)|| (ir[k]>den1.amax[k]-den1.amin[k]-2) ){
-          if(verbose>=2)
-@@ -2898,7 +2898,7 @@
- //printf("oneside = %d geopos6(x) = geo.pos[geo.nend[0]+oneside][6][0] = %5.3f\n",geo.oneside,geo.pos[geo.nend[0]+geo.oneside][6][0]);
-    }
-    *returnden = bestden;  // return best cterm density
--   *returnbad = bestbad;
-+   *returnbad = (int) bestbad;
-  }// quitcont <5
-  quitrout:;
-  geo.fixend = origfixend; // set back to original value
-diff -ur glmaid_dist.orig/trace.c++ glmaid_dist/trace.c++
---- glmaid_dist.orig/trace.c++	2005-12-15 08:09:55.000000000 -0800
-+++ glmaid_dist/trace.c++	2005-12-15 08:31:07.000000000 -0800
-@@ -1079,7 +1079,7 @@
- 
-    xtoi(den1,pos[resnum][atomnum],ig);
-    for(k=0;k<=2;k++)
--     ig[k]=ig[k]+0.5; /*rounds to  nearest grid point*/
-+     ig[k]=(int) (ig[k]+0.5); /*rounds to  nearest grid point*/
-    for(k=0;k<=2;k++){ // check if pos in density range
-       if( (ig[k]<2)|| (ig[k]>den1.amax[k]-den1.amin[k]-2) )
-          return 0;
-@@ -1099,7 +1099,7 @@
- 
-    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
-    for(k=0;k<=2;k++)
--     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
-+     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
-    for(k=0;k<=2;k++){ // check if pos in density range
-       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
-          if(verbose>=2)
-@@ -1127,7 +1127,7 @@
- 
-    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
-    for(k=0;k<=2;k++)
--     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
-+     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
-    for(k=0;k<=2;k++){ // check if pos in density range
-       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
-          if(verbose>=2)
-@@ -1204,7 +1204,7 @@
- 
-    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
-    for(k=0;k<=2;k++)
--     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
-+     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
-    for(k=0;k<=2;k++){ // check if pos in density range
-       if( ((ig[k]-geo.setrad)<0)|| ((ig[k]+geo.setrad)>den1.griddim[k]-1) ){
-          if(verbose>=2)
-@@ -2543,7 +2543,7 @@
-    atomden = 0;
-    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
-    for(kc=0;kc<=2;kc++)
--       ir[kc]=fd[kc]; /*round down to integer*/
-+       ir[kc]=(int) fd[kc]; /*round down to integer*/
-    for(k=0;k<=2;k++){ // check if pos in density range
-       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
- //if(verbose>=2)
-@@ -2569,7 +2569,7 @@
-    atomden = 0;
-    xtof(den1,pos[inum][itype],fd); /* convert from double word to float sccreen*/
-    for(kc=0;kc<=2;kc++)
--       ir[kc]=fd[kc]; /*round down to integer*/
-+       ir[kc]=(int) fd[kc]; /*round down to integer*/
-    for(k=0;k<=2;k++){ // check if pos in density range
-       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
-         if(verbose>=2)
-@@ -3438,7 +3438,7 @@
-     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
- dist = dist/2.0;
-     thdel = rotdel/dist; // step size of theta rotation
--    mth =1+ thtot/thdel; // max # of theta steps  - round up
-+    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
-     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
-     maxden = -10000.0;
- for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
-@@ -3455,7 +3455,7 @@
-        }
-        else{
-          delph = rotdel/(dist*sin(th));//the delta phi angle step
--         mphi = phitot/delph +1; // round up
-+         mphi = (int) (phitot/delph) +1; // round up
-          delph = phitot/mphi; // make phitot = mphi*delph 
-        }
-        for(iph = 0;iph<=mphi;iph++){ // the phi step 
-@@ -3545,7 +3545,7 @@
-     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
- dist = dist/2.0;
-     thdel = rotdel/dist; // step size of theta rotation
--    mth =1+ thtot/thdel; // max # of theta steps  - round up
-+    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
-     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
-     maxden = -10000.0;
- for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
-@@ -3562,7 +3562,7 @@
-        }
-        else{
-          delph = rotdel/(dist*sin(th));//the delta phi angle step
--         mphi = phitot/delph +1; // round up
-+         mphi = (int) (phitot/delph) +1; // round up
-          delph = phitot/mphi; // make phitot = mphi*delph 
-        }
-        for(iph = 0;iph<=mphi;iph++){ // the phi step 
-@@ -6905,8 +6905,8 @@
-   for(i=0;i<=2;i++)
-     avegrid = avegrid+den1.delx[i];
-   avegrid = avegrid/3.0;
--  geo.nihel = 0.5 + geo.curdist[1]/(1.414*avegrid); // 0.5 so that rounds to nearest int
--  geo.nisheet = geo.curdist[2]/(1.414*avegrid);
-+  geo.nihel = (int) (0.5 + geo.curdist[1]/(1.414*avegrid)); // 0.5 so that rounds to nearest int
-+  geo.nisheet = (int) (geo.curdist[2]/(1.414*avegrid));
- printf("\nGRID SIZE:  %5.3f %5.3f %5.3f avegrid = %5.3f  nihel = %d\n", 
-       den1.delx[0],den1.delx[1],den1.delx[2],avegrid,geo.nihel);
- 
-Files glmaid_dist.orig/trace.o and glmaid_dist/trace.o differ
diff --git a/sci-chemistry/maid/files/maid-gcc4.3.patch b/sci-chemistry/maid/files/maid-gcc4.3.patch
deleted file mode 100644
index 6b793541b837..000000000000
--- a/sci-chemistry/maid/files/maid-gcc4.3.patch
+++ /dev/null
@@ -1,67 +0,0 @@
-diff -Naur glmaid_dist/bone.c++ glmaid_dist.new/bone.c++
---- glmaid_dist/bone.c++	2001-11-12 08:35:49.000000000 -0500
-+++ glmaid_dist.new/bone.c++	2008-07-27 10:52:35.000000000 -0400
-@@ -15,7 +15,7 @@
-    2) Set value that are going to be revoved equal to -MARCHAR rather then +MAXCHAR so can use MAXCHAR as a real value
-    3) Set removed value = REMOVE (- =100), rather then 0
- */
--
-+#include <cstring>
- #include "drawwindow.h"
- //#include "screen.h"
- #include "math.h"
-diff -Naur glmaid_dist/checkfit.c++ glmaid_dist.new/checkfit.c++
---- glmaid_dist/checkfit.c++	2001-11-12 08:35:49.000000000 -0500
-+++ glmaid_dist.new/checkfit.c++	2008-07-27 10:52:05.000000000 -0400
-@@ -1,7 +1,7 @@
- /* checkfit.c++   Moved routines used to check and cut the final fit
-    for trace.c++ to here
- */
--
-+#include <cstring>
- #include "drawwindow.h"
- #include "math.h"
- #include "trace.h"
-diff -Naur glmaid_dist/combine.c++ glmaid_dist.new/combine.c++
---- glmaid_dist/combine.c++	2001-11-12 08:35:50.000000000 -0500
-+++ glmaid_dist.new/combine.c++	2008-07-27 10:52:12.000000000 -0400
-@@ -22,6 +22,7 @@
-    6) Next - run combinefit:
-        This looks through fits to find fits with some overlap of seq. assighment.
- */
-+#include <cstring>
- #include "drawwindow.h"
- #include "math.h"
- #include "trace.h" // includes a number of "extern .... " lines
-diff -Naur glmaid_dist/fittopdb.c++ glmaid_dist.new/fittopdb.c++
---- glmaid_dist/fittopdb.c++	2001-11-12 08:35:50.000000000 -0500
-+++ glmaid_dist.new/fittopdb.c++	2008-07-27 10:52:48.000000000 -0400
-@@ -56,6 +56,7 @@
-    strcpy(aaname[2],"SER");
- VIII) in maid - each fit is a separate file, in maid - one file
- */
-+#include <cstring>
- #include "peptide.h"
- #include "drawwindow.h"  // also calls global.h
- #include "trace.h"
-diff -Naur glmaid_dist/initialize.c++ glmaid_dist.new/initialize.c++
---- glmaid_dist/initialize.c++	2001-11-12 08:35:50.000000000 -0500
-+++ glmaid_dist.new/initialize.c++	2008-07-27 10:52:42.000000000 -0400
-@@ -1,4 +1,5 @@
- // Initial values called from main
-+#include <cstring>
- #include "tordyn.h" // routines for torsiondynamics
- #include "peptide.h"  // routines for peptide creation and drawing
- #include "drawwindow.h"  // also calls global.h
-diff -Naur glmaid_dist/trace.c++ glmaid_dist.new/trace.c++
---- glmaid_dist/trace.c++	2001-11-12 08:35:49.000000000 -0500
-+++ glmaid_dist.new/trace.c++	2008-07-27 10:52:22.000000000 -0400
-@@ -3,7 +3,7 @@
- SEE:  trace.notes
- 1=ca,2=c,3=o;4=n,5=cb; 6=cb2 in pos
- */
--      
-+#include <cstring>      
- #include "drawwindow.h"
- #include "math.h"
- #include "trace.h"
diff --git a/sci-chemistry/maid/maid-20011112.ebuild b/sci-chemistry/maid/maid-20011112.ebuild
deleted file mode 100644
index 127276b9e26a..000000000000
--- a/sci-chemistry/maid/maid-20011112.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/maid-20011112.ebuild,v 1.9 2008/07/27 15:02:08 markusle Exp $
-
-inherit eutils toolchain-funcs
-
-MY_PN="${PN}_unix"
-MY_PV="${PV:6:2}nov${PV:2:2}"
-MY_P="${MY_PN}_${MY_PV}"
-DESCRIPTION="Automates the fitting of protein X-ray crystallographic electron density maps"
-HOMEPAGE="http://www.msi.umn.edu/~levitt/"
-SRC_URI="http://www.msi.umn.edu/~levitt/${MY_P}.tar.gz
-	mirror://gentoo/maid-fix-compilation.patch.bz2"
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="x86"
-IUSE="X"
-DEPEND="X? ( x11-libs/openmotif
-		virtual/glu
-		virtual/opengl
-		x11-libs/libXt
-	)"
-S="${WORKDIR}/glmaid_dist"
-
-src_unpack() {
-	if best_version virtual/opengl | grep mesa; then
-		if ! built_with_use media-libs/mesa motif; then
-			msg="Build media-libs/mesa with USE=motif"
-			eerror "${msg}"
-			die "${msg}"
-		fi
-	fi
-
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${DISTDIR}"/maid-fix-compilation.patch.bz2
-	epatch "${FILESDIR}"/fix-warnings.patch
-	epatch "${FILESDIR}"/${PN}-gcc4.3.patch
-
-	if use X; then
-		ln -s makefile_graphics makefile
-	else
-		ln -s makefile_batch makefile
-	fi
-
-	sed -i \
-		-e "s:^Cgeneric = .*:Cgeneric = $(tc-getCXX):g" \
-		-e "s:\(Copt.*\)-O:\1${CFLAGS}:g" \
-		makefile
-}
-
-src_install() {
-	dodoc MANUAL*
-	if use X; then
-		dobin maid
-	else
-		dobin maidbatch
-	fi
-}
diff --git a/sci-chemistry/maid/metadata.xml b/sci-chemistry/maid/metadata.xml
deleted file mode 100644
index 9ac9ffdb3a41..000000000000
--- a/sci-chemistry/maid/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
-</pkgmetadata>