added fixes by jlec, bumped lapack to 3.3.1

4 files changed, 91 insertions, 7 deletions

diff --git a/sci-libs/atlas/ChangeLog b/sci-libs/atlas/ChangeLog
index d8f7da4..66f201c 100644
--- a/sci-libs/atlas/ChangeLog
+++ b/sci-libs/atlas/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Apr 2011; Justin Lecher <jlec@gentoo.org> atlas-3.9.39.ebuild:
+  Correct syntax for cpufrq check being all CPUs under performance controll
+
+*atlas-3.9.39 (21 Mar 2011)
+
   21 Mar 2011; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.9.39.ebuild:
   Version bump. Seriously refactored the ebuild. Now choose posix threads over
   openmp when the two are enabled
diff --git a/sci-libs/atlas/Manifest b/sci-libs/atlas/Manifest
index cfceed8..ff83e1e 100644
--- a/sci-libs/atlas/Manifest
+++ b/sci-libs/atlas/Manifest
@@ -1,7 +1,9 @@
+AUX 3.9.39-bfr-overflow.patch 2755 RMD160 4f8204eee5b429e9d3db1c211af80396a575fc87 SHA1 9b59bd8a7bb55e7ed4138731262d17532949ece0 SHA256 19cdab39e50e06de0bdc2a080642388fec3a16c826657621f15fc294268d3438
 DIST atlas3.8.3.tar.bz2 2527756 RMD160 0425e630d9d0c5b7aae81427a41b7eaa18447e90 SHA1 c7546210df4796457d9e96a00444adc4c0f2e77f SHA256 e537168f2022db98b9029c8064815b5581620c12d782016138b1bf0bbb01f473
 DIST atlas3.9.39.tar.bz2 5493831 RMD160 118ad28a6dab1633b55a4654a2b67688177dedb7 SHA1 025a62a6577035552cb48aeb45bb4270c3d66580 SHA256 ddb3804d3b2dada955f3b07f8c3b26aff274aaaa2de2211a15309aa892bc5c83
 DIST lapack-3.3.0.tgz 6064824 RMD160 cc72e7c93ab13464fd892d684b00b910cbbd3b3e SHA1 4f0b103da52110e7f60d1d7676727103aca9785e SHA256 bc531761287156e17476395c42664a15373723f54a6f80f192cda47771ec1225
+DIST lapack-3.3.1.tgz 4945204 RMD160 5e9d90122110045e07351f3ab30dc4e2b43d52db SHA1 3ce437e05f0e9a3c8148ec41922f6efeef0ebdac SHA256 56821ab51c29369a34e5085728f92c549a9aa926f26acf7eeac87b61eed329e4
 EBUILD atlas-3.8.3.ebuild 6019 RMD160 10c7b3937ec41c2c182f1faecbcf7c2e8901befe SHA1 15ebfd302a3764880fc599a7d1cdc59a214e3a27 SHA256 cc3139e44d2da073767df95280be90413fe39f5e02e0ce5243ff2267891d3e16
-EBUILD atlas-3.9.39.ebuild 5879 RMD160 702b18e5546453b51ce7155dc1fb145c60b29a92 SHA1 000fcea4b916cf09e8d7c6a042af3843ab70af97 SHA256 b78b9706318fb7ad30828b37c07ad697a8ce3e1be929f3d0c72268b74ac27908
-MISC ChangeLog 621 RMD160 755eab85fb123a94aa51ad5cd331f2a51191f1d0 SHA1 123bb45ac67e3048c72d06505fc665923cabce03 SHA256 0baa2873a98dc52777c96696648f06ad7b51473fa08b6fa0ca03964ab54af3b7
+EBUILD atlas-3.9.39.ebuild 5979 RMD160 caba82a1f3259acf11cab3380b0efcd04c2755c3 SHA1 df8d5999f89e492fc0462da867b50da69a726394 SHA256 c2e78d76e2498816fa940ff5655a28e240dfc9649b17abdc1be083ba99e87a3b
+MISC ChangeLog 795 RMD160 8d5ba909af2ad30226cc74243d68497841ee82e9 SHA1 81879222c36b0ad11c06fa51eada79606982a4e6 SHA256 7dac35dba3918fd328766170dcab030be67648abe1c32952ffd65a62994254bb
 MISC metadata.xml 726 RMD160 e43f5ea9c594bbe2174f6640bbfdccd8b17d4a68 SHA1 0ab8c05e7925b4716d8c94acd952bf3ab85165cb SHA256 27ef4eee7e645ad923644830d057db45d32342ad250ad903ff10915a9ca068fd
diff --git a/sci-libs/atlas/atlas-3.9.39.ebuild b/sci-libs/atlas/atlas-3.9.39.ebuild
index ff66b88..02feaa9 100644
--- a/sci-libs/atlas/atlas-3.9.39.ebuild
+++ b/sci-libs/atlas/atlas-3.9.39.ebuild
@@ -5,7 +5,7 @@
 EAPI=4
 inherit eutils toolchain-funcs multilib versionator alternatives-2
 
-LAPACKP=lapack-3.3.0
+LAPACKP=lapack-3.3.1
 
 DESCRIPTION="Automatically Tuned Linear Algebra Software"
 HOMEPAGE="http://math-atlas.sourceforge.net/"
@@ -17,8 +17,9 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="fortran doc lapack openmp static-libs threads"
 
-RDEPEND=""
-DEPEND="${RDEPEND}"
+RDEPEND="fortran? ( virtual/fortran )"
+DEPEND="${RDEPEND}
+	sys-power/cpufrequtils"
 
 S="${WORKDIR}/ATLAS"
 
@@ -165,9 +166,9 @@ pkg_setup() {
 		local ncpu=$(LANG=C cpufreq-info | grep -c "analyzing CPU")
 		local cpu=0
 		while [[ ${cpu} -lt ${ncpu} ]]; do
-			if "$(LANG=C cpufreq-info -p -c ${cpu} | grep -q performance)"; then
+			if ! $(LANG=C cpufreq-info -p -c ${cpu} | grep -q performance); then
 				ewarn "CPU $cpu is not set to performance"
-				ewarn "Run sudo cpufreq-set -g performance -c <CPU #> for all CPUs"
+				ewarn "Run cpufreq-set -r -g performance as root"
 				die "${PN} needs all cpu set to performance"
 			fi
 			cpu=$(( cpu + 1 ))
@@ -181,6 +182,10 @@ pkg_setup() {
 	fi
 }
 
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-bfr-overflow.patch
+}
+
 src_configure() {
 	atlas_configure shared "-Fa alg -fPIC"
 	use static-libs && atlas_configure static
diff --git a/sci-libs/atlas/files/3.9.39-bfr-overflow.patch b/sci-libs/atlas/files/3.9.39-bfr-overflow.patch
new file mode 100644
index 0000000..a4ae52a
--- /dev/null
+++ b/sci-libs/atlas/files/3.9.39-bfr-overflow.patch
@@ -0,0 +1,72 @@
+ ATLAS/tune/blas/level1/axpysrch.c  |    2 +-
+ ATLAS/tune/blas/level1/copysrch.c  |    2 +-
+ ATLAS/tune/blas/level1/iamaxsrch.c |    2 +-
+ ATLAS/tune/blas/level1/scalsrch.c  |    2 +-
+ ATLAS/tune/blas/level1/swapsrch.c  |    2 +-
+ 5 files changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/ATLAS/tune/blas/level1/axpysrch.c b/ATLAS/tune/blas/level1/axpysrch.c
+index 48bd756..f7f7845 100644
+--- a/ATLAS/tune/blas/level1/axpysrch.c
++++ b/ATLAS/tune/blas/level1/axpysrch.c
+@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
+ {
+    FILE *fpin;
+    FILENODE *fbase, *fn, *fp=NULL;
+-   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
++   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
+    char *pcc, *pccflags;
+    int i, n, ID, alpha, beta, incX, incY;
+ 
+diff --git a/ATLAS/tune/blas/level1/copysrch.c b/ATLAS/tune/blas/level1/copysrch.c
+index 3a9fcfc..736f501 100644
+--- a/ATLAS/tune/blas/level1/copysrch.c
++++ b/ATLAS/tune/blas/level1/copysrch.c
+@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
+ {
+    FILE *fpin;
+    FILENODE *fbase, *fn, *fp=NULL;
+-   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
++   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
+    char *pcc, *pccflags;
+    int i, n, ID, alpha, beta, incX, incY;
+ 
+diff --git a/ATLAS/tune/blas/level1/iamaxsrch.c b/ATLAS/tune/blas/level1/iamaxsrch.c
+index e9e766a..91b3acd 100644
+--- a/ATLAS/tune/blas/level1/iamaxsrch.c
++++ b/ATLAS/tune/blas/level1/iamaxsrch.c
+@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
+ {
+    FILE *fpin;
+    FILENODE *fbase, *fn, *fp=NULL;
+-   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
++   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
+    char *pcc, *pccflags;
+    int i, n, ID, alpha, beta, incX, incY;
+ 
+diff --git a/ATLAS/tune/blas/level1/scalsrch.c b/ATLAS/tune/blas/level1/scalsrch.c
+index 48be97e..35d724d 100644
+--- a/ATLAS/tune/blas/level1/scalsrch.c
++++ b/ATLAS/tune/blas/level1/scalsrch.c
+@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
+ {
+    FILE *fpin;
+    FILENODE *fbase, *fn, *fp=NULL;
+-   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
++   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
+    char *pcc, *pccflags;
+    int i, n, ID, alpha, beta, incX, incY;
+ 
+diff --git a/ATLAS/tune/blas/level1/swapsrch.c b/ATLAS/tune/blas/level1/swapsrch.c
+index 776d2d7..5281ae5 100644
+--- a/ATLAS/tune/blas/level1/swapsrch.c
++++ b/ATLAS/tune/blas/level1/swapsrch.c
+@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
+ {
+    FILE *fpin;
+    FILENODE *fbase, *fn, *fp=NULL;
+-   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
++   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
+    char *pcc, *pccflags;
+    int i, n, ID, alpha, beta, incX, incY;
+