Version bump and removed old ebuilds.

(Portage version: 2.2_rc1/cvs/Linux 2.6.25-SENTINEL-4 i686)

4 files changed, 92 insertions, 31 deletions

diff --git a/sci-libs/blas-atlas/files/atlas-3.9.0-decl-fix.patch b/sci-libs/blas-atlas/files/atlas-3.9.0-decl-fix.patch
new file mode 100644
index 000000000000..1ec44fcf7884
--- /dev/null
+++ b/sci-libs/blas-atlas/files/atlas-3.9.0-decl-fix.patch
@@ -0,0 +1,71 @@
+diff -Naur ATLAS/bin/atlas_waitfile.c ATLAS-new/bin/atlas_waitfile.c
+--- ATLAS/bin/atlas_waitfile.c	2007-10-07 09:48:56.000000000 -0400
++++ ATLAS-new/bin/atlas_waitfile.c	2007-10-09 10:57:13.000000000 -0400
+@@ -1,3 +1,4 @@
++#include <stdlib.h>
+ #include <stdio.h>
+ 
+ void PrintUsage(char *nam)
+diff -Naur ATLAS/src/auxil/ATL_buildinfo.c ATLAS-new/src/auxil/ATL_buildinfo.c
+--- ATLAS/src/auxil/ATL_buildinfo.c	2007-10-07 09:49:03.000000000 -0400
++++ ATLAS-new/src/auxil/ATL_buildinfo.c	2007-10-09 10:56:10.000000000 -0400
+@@ -1,3 +1,4 @@
++#include <stdio.h>
+ #include "atlas_buildinfo.h"
+ #include "atlas_cacheedge.h"
+ 
+diff -Naur ATLAS/tune/blas/gemm/usercomb.c ATLAS-new/tune/blas/gemm/usercomb.c
+--- ATLAS/tune/blas/gemm/usercomb.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/gemm/usercomb.c	2007-10-09 10:58:53.000000000 -0400
+@@ -29,6 +29,7 @@
+  */
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <string.h>
+ #include <assert.h>
+ 
+ int LineIsCont(char *ln)
+diff -Naur ATLAS/tune/blas/gemv/gemvtune.c ATLAS-new/tune/blas/gemv/gemvtune.c
+--- ATLAS/tune/blas/gemv/gemvtune.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/gemv/gemvtune.c	2007-10-09 11:00:29.000000000 -0400
+@@ -36,6 +36,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <assert.h>
++#include <string.h>
+ 
+ struct FA_allocs
+ {
+diff -Naur ATLAS/tune/blas/gemv/mvsearch.c ATLAS-new/tune/blas/gemv/mvsearch.c
+--- ATLAS/tune/blas/gemv/mvsearch.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/gemv/mvsearch.c	2007-10-09 10:59:56.000000000 -0400
+@@ -32,6 +32,7 @@
+ #include <stdlib.h>
+ #include <ctype.h>
+ #include <assert.h>
++#include <string.h>
+ #include "atlas_fopen.h"
+ 
+ #define ATL_MVIsMM(iflag_) ( ((iflag_) | 8) == (iflag_) )
+diff -Naur ATLAS/tune/blas/ger/ger1tune.c ATLAS-new/tune/blas/ger/ger1tune.c
+--- ATLAS/tune/blas/ger/ger1tune.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/ger/ger1tune.c	2007-10-09 11:01:15.000000000 -0400
+@@ -36,6 +36,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <assert.h>
++#include <string.h>
+ 
+ struct FA_allocs
+ {
+diff -Naur ATLAS/tune/blas/ger/r1search.c ATLAS-new/tune/blas/ger/r1search.c
+--- ATLAS/tune/blas/ger/r1search.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/ger/r1search.c	2007-10-09 11:00:58.000000000 -0400
+@@ -31,6 +31,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <ctype.h>
++#include <string.h>
+ #include <assert.h>
+ #include "atlas_fopen.h"
+ 
diff --git a/sci-libs/blas-atlas/files/atlas-3.9.0-upstream-fixes.patch b/sci-libs/blas-atlas/files/atlas-3.9.0-upstream-fixes.patch
new file mode 100644
index 000000000000..a0e548f10d73
--- /dev/null
+++ b/sci-libs/blas-atlas/files/atlas-3.9.0-upstream-fixes.patch
@@ -0,0 +1,21 @@
+diff -Naur ATLAS/src/auxil/ATL_ptflushcache.c ATLAS.new/src/auxil/ATL_ptflushcache.c
+--- ATLAS/src/auxil/ATL_ptflushcache.c	2008-07-17 21:24:53.000000000 -0400
++++ ATLAS.new/src/auxil/ATL_ptflushcache.c	2008-07-18 18:40:37.000000000 -0400
+@@ -88,7 +88,7 @@
+      }
+      fct[i].N = N;
+      fct[i].dp = cache+i*N;
+-     ATL_ptCF(fct+i);
++     ATL_ptCF(fct+i-1);
+      dret = fct[i].dret;
+      for (i=0; i < ATL_NTHREADS-1; i++)
+      {
+@@ -133,7 +133,7 @@
+    {
+       ATL_assert(!pthread_create(tp+i, &attr, ATL_ptCLF, fp));
+    }
+-   ATL_FlushAreaByCL(fp);   /* should be redundant, do to be safe */
++   ATL_FlushAreasByCL(fp);   /* should be redundant, do to be safe */
+    for (i=0; i < ATL_NTHREADS; i++)
+    {
+       ATL_assert(!pthread_join(tp[i], NULL));
diff --git a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-fix.patch b/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-fix.patch
deleted file mode 100644
index 9409f90c8a07..000000000000
--- a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-fix.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff -Naur ATLAS/src/blas/gemm/ATL_cmmJITcp.c ATLAS.new/src/blas/gemm/ATL_cmmJITcp.c
---- ATLAS/src/blas/gemm/ATL_cmmJITcp.c	2008-02-22 11:38:58.000000000 -0500
-+++ ATLAS.new/src/blas/gemm/ATL_cmmJITcp.c	2008-05-23 18:07:34.000000000 -0400
-@@ -264,8 +264,11 @@
-       NBmm1 = Mjoin(PATLU,pMBmm_b1);
-       NBmmX = Mjoin(PATLU,pMBmm_bX);
-    }
--   else  /* two or more dim < NB, requires generated cleanup */
--      NBmm0 = NBmm1 = NBmmX = Mjoin(PATLU,pKBmm);
-+   else 
-+   { 
-+     NBmm0 = NBmm1 = NBmmX = Mjoin(PATLU,pKBmm);
-+     if (SCALAR_IS_ZERO(beta)) Mjoin(PATL,gezero)(M, N, C, ldc); 
-+   }
-    if (nblk)
-    {
-       if (B)
diff --git a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-perf-fix.patch b/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-perf-fix.patch
deleted file mode 100644
index 8afa7c7692c9..000000000000
--- a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-perf-fix.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff -Naur ATLAS/src/blas/gemm/ATL_gemmXX.c ATLAS.new/src/blas/gemm/ATL_gemmXX.c
---- ATLAS/src/blas/gemm/ATL_gemmXX.c	2008-02-22 11:38:58.000000000 -0500
-+++ ATLAS.new/src/blas/gemm/ATL_gemmXX.c	2008-06-06 16:32:31.000000000 -0400
-@@ -188,10 +188,6 @@
-             mm2 = mm1;
-             mm1 = Mjoin(PATL,mmJITcp);
-          }
--         {
--            mm2 = mm1;
--            mm1 = Mjoin(PATL,mmJITcp);
--         }
-    #endif
-    #ifdef SMALLK_MM
-       if (ATL_OOM Mjoin(PATL,mmJKI)(ETA, ETB, M, N, K, alpha, A, lda, B, ldb,