Reworked the solution for the netperf collision, dropped the 'find all executable files' method of installing tools for 'emake install', added missing deps; resolves bug 546566

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0x2B6559ED

4 files changed, 194 insertions, 22 deletions

diff --git a/sci-mathematics/snns/ChangeLog b/sci-mathematics/snns/ChangeLog
index d97797f47199..b4607cf9ef85 100644
--- a/sci-mathematics/snns/ChangeLog
+++ b/sci-mathematics/snns/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-mathematics/snns
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/snns/ChangeLog,v 1.27 2015/04/10 20:09:40 axs Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/snns/ChangeLog,v 1.28 2015/04/14 15:10:59 axs Exp $
+
+*snns-4.3-r2 (14 Apr 2015)
+
+  14 Apr 2015; Ian Stakenvicius (_AxS_) <axs@gentoo.org>
+  +files/4.3-snns-netperf.patch, +snns-4.3-r2.ebuild, -snns-4.3-r1.ebuild:
+  Reworked the solution for the netperf collision, dropped the 'find all
+  executable files' method of installing tools for 'emake install', added
+  missing deps; resolves bug 546566
 
   10 Apr 2015; Ian Stakenvicius (_AxS_) <axs@gentoo.org> snns-4.3-r1.ebuild:
   added REQUIRED_USE to properly support the python-optional distutils-r1
diff --git a/sci-mathematics/snns/Manifest b/sci-mathematics/snns/Manifest
index da8ac2d0d382..32a0327f4e56 100644
--- a/sci-mathematics/snns/Manifest
+++ b/sci-mathematics/snns/Manifest
@@ -4,6 +4,7 @@ Hash: SHA256
 AUX 4.2-fPIC-python.patch 498 SHA256 175ae2fa3ceebb288d5a634b2f65f778f6cced9f35f369b0dbda20011fb3c8c6 SHA512 49969f9ef6d7da2c7175afdfbc03d95bf2973c3af67002e56cd146792fc2c85b68592e69e1d3e6a27d75a0741be7ce488d8c762e74d5b761b3d6ce9aad92d48d WHIRLPOOL f7f81a47433dbd94cca092afde6743338c6fe7f501d33bd9cbdef2b34e6a85b0efb6d983b191706f79f028fb6ee0b4e1eb9ef992d23a7b1c7d847bae38f469f8
 AUX 4.2-ldflags.patch 1109 SHA256 5cebf78bf106ae055bb556004dc285b5ae5362e9a1f4eea296c666be6014265b SHA512 274da0d037922c7bec246cb47a57cf63ca700345073ae0159d5636921a51370e02ed4dd18618e657477c513b2141c87a40c7082abe4fdaeb287ce42b33907033 WHIRLPOOL e206c3e530a17b0548bcb30855691f433e4802cbe1a8e2a2a793c4337281fc3d063485039771091bd1580882819edb075669398a0365ab36ec54f94cf5317e75
 AUX 4.3-bison-version.patch 463 SHA256 db71246207e413f56fbc1e673b61f09a0310d6e1e8a40eb2688da87c772c8e6b SHA512 5ad60b931e1bf79ccc023ca6fdde4ded155cf5d5d47216fec4811dc7689c95b0147dbc3210507c20ca59086f9d0e0df30b5c0a42daada549919c473176338344 WHIRLPOOL bdf02e266680efb9ec690ca19b87583b9fc8217369ace023a0a630dfefbcf7554ab9448dc807e8ce7b83bd1e3f2ade17b2e6d369c041d3ceb33848a6e7e97ae9
+AUX 4.3-snns-netperf.patch 4398 SHA256 76a022ba90dc69b1b78a0c4824c9b5a41709e9152abe5813d38a2d555863da7a SHA512 316c1121e7269adc142a0dd7b7dc9882605bc4c01cb5fa15e5b1d3de93ece31e4ff27894439e54fce6c174d763133bf7cd69b2142bfb3f030609e5e9ba5d41c1 WHIRLPOOL 93bc9758bbd87f5fb2fc284f25c2dbee8386e5be5923fb96d64372b0cfc10d2a3a450ad396495c037d1ae726566dfb93ebb0927837c69b9b56daf058f8547a03
 AUX 4.3-unstrip.patch 260 SHA256 4efb6e5fcbb130eb850bc5d0c837db6b37e78466068cf2c472082d8dd8f334d9 SHA512 9fb6826160850c4de977367a16ebfcd49667ee5bb5647a3a0441a32e58ce5e7649e25c03d4c43b71eab037ad13bdefe1668bedde691fc9883ed2e5e743856b16 WHIRLPOOL 462ad2fc58d837b92a6fafe9d7c8a34e539ae39a3074396ae0665dc6b3be846df5b6fc62a0fb95186cd0f84f715b8e76189a62e3aca47bf2ab490391caaf31a7
 DIST PySNNS-20040605.tar.gz 20158 SHA256 c2dff5a88faa756546dac1c850d5196d8bba39f793537c5ebcaa61e21f0db317
 DIST PythonFunctionSupport-20050210.patch.gz 15728 SHA256 c507c70aa158ffb1422aeef693d45f2e8486b1fc7056142736796dd4273f4869
@@ -15,13 +16,13 @@ DIST snns-4.2-20040227.patch.gz 55476 SHA256 08a5fa51552b33e5e981d68cbf05792d40d
 DIST snns-4.2-patched.tar.gz 2188658 SHA256 d0fc25dcb82979a46bfdfd24a090ec113b039d0f144f8f7c10404775acd129a7
 EBUILD snns-4.2-r8.ebuild 2884 SHA256 9757e21c848595dd87e937f0210732cdbdda90aca67f50403ef51c479095b3d3 SHA512 66486c9c3fc4f9263e47cf7e77dd7a34e98526e751ecbbc8ada750830b444596c398931cf727b26264cfb8dc3bd06356ef97bb3fb14531b9a6a9fd1b29794a2a WHIRLPOOL 3f7d7aa234f92c140dd4fe64671cc9cb052e56c9a5c6bd07f39b7834b1ce3035cb43af0be44e47734ca114e96e7c5af2c7ec4ca75634549acc037b8ed87bf919
 EBUILD snns-4.2-r9.ebuild 2463 SHA256 0c91a05b6aa5a8fd51378843b0e7edf855887c199ec1222e2feaa42d74b43517 SHA512 b586d06836b45c7d59d714259f36d44cc4340fa22362a5241663037b8100bcb07da83117a83173a2ac0b38c365fbe08c040087109603eda419319086c8f9b6a0 WHIRLPOOL 52c3adffbe6d695cac4d032f50fe0d96a9358a9350ab1619c57646eee29c5c15975aa010c93fa4f8b99cf45edbed1eef9f31e3fe4fdf5b1cc8efa6de86738784
-EBUILD snns-4.3-r1.ebuild 2847 SHA256 44e71fa998d6696acaee0aa1587d2119a4c19ad1b7109bb537021fb8bdd178e7 SHA512 ac75815cc578436674f5955deabe60b53c549dfd05b03f49d08f55825e191947eed3453e86dcc0089f8d22ae5c50b5e66d8566af44df666f2fad847476bc4024 WHIRLPOOL 1ebf5443391a5e5360b35b64dcd0b314933555702e00e384802bce84d4ce4743de8eefa7bb41aa22d74b9b5ec835477ec0db81761f0eac8761bc1bb7a972d27b
-MISC ChangeLog 6153 SHA256 72379e0afe43c8ff1427d5a03d887e6510d2328a051daeeab2e604285cae1ac3 SHA512 970c3d8a11df5ae91a2f6eabb86f6d9138d16455e20d038298089c368b5ff9fe233a8092ec0603ce02a03fba9e4029dbe0bb5868c0af17f632ce882db5f25930 WHIRLPOOL 4854af2ea627dc250e4cd59267f2912c2907e1949899f30c52d007219b84a1e53f59b18f19e84c721ede64c087e975927f3cffd91ec8f582f434040d3703b172
+EBUILD snns-4.3-r2.ebuild 2931 SHA256 55b23561765e1ebebe61664609d02c5e3113ad2c8ba6b6b7c5af0f3baadf7ecd SHA512 d1532695a38b42169ad94fb99c1ba69c179b447f424c3d6f6c98513a4406d675d0b647c4812cd894acf4444c586729c295b3226c6fd42453153f83a19378421d WHIRLPOOL 58dcd61606ce710f28f7cca877e7cec9a33f128029482cd4a2ad3812206b94bfe1f1c9c7c4c172db28c7f7d2c0887ac0355de8269b722417cc7abc460ed7a9df
+MISC ChangeLog 6497 SHA256 7fae9e1502614d953eecda1505207d4b0ee076dc2ec956dcd9a1d3bfcf25815b SHA512 50bf8afa509f15e3cff6b3b3606ab98ecbd04bc7f65259e46e8c4d89f41874502eb6cb51b5c132b9fa9a9c7dbd10ccd2e175457f707d0ae8d32f99826989cde2 WHIRLPOOL a9c90a71c4dc3bed32d8279976b49f21ab777b24f384872e9a82a0f2b2ccbd61544d767fdd8b672f4476a1e071e9b9a02227db7e079099b83eee226251adfd9a
 MISC metadata.xml 257 SHA256 d3f26a7e161752ba8d618621c4b35de7071842e19e89b551f151fab5b2828c61 SHA512 fd666ef2ec77fe174951826bf8dbcbee21eae3bb79ee3a23e712501db1809ec2d0810c0c20d841b2cbe9831741939ce7da3c48275c2dc882ecdfd5669babf35b WHIRLPOOL d5499683a990792452d6b65cb2d9e74fd86ee8946645ae3b5b55489fe12cc110e754594a36bc9b55bb074e0a02d30ecc080c355874bfbe49c453bbe0a7b52547
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diff --git a/sci-mathematics/snns/files/4.3-snns-netperf.patch b/sci-mathematics/snns/files/4.3-snns-netperf.patch
new file mode 100644
index 000000000000..f154a538b2d9
--- /dev/null
+++ b/sci-mathematics/snns/files/4.3-snns-netperf.patch
@@ -0,0 +1,164 @@
+--- a/examples/nettalk.README	2008-04-21 03:55:43.000000000 -0400
++++ b/examples/nettalk.README	2015-04-14 09:38:23.836014999 -0400
+@@ -60,7 +60,7 @@
+ Hints:
+ ======
+ 
+-We usually call nettalk.net from the tool 'netperf', a benchmarking
++We usually call nettalk.net from the tool 'snns-netperf', a benchmarking
+ version of SNNS without graphical user interface but with the full and
+ current SNNS kernel. It is supplied with SNNS in the tools directory.
+ We usually train and test nettalk for 10 cycles. Since convergence is
+--- a/man/man1/snns.1	2008-04-21 03:56:05.000000000 -0400
++++ b/man/man1/snns.1	2015-04-14 09:36:27.406012874 -0400
+@@ -111,7 +111,7 @@
+ .BR netlearn (1)
+ backpropagation test program
+ 
+-.BR netperf (1)
++.BR snns-netperf (1)
+ benchmark program
+ 
+ .BR pat_sel (1)
+@@ -132,4 +132,4 @@
+ yet. 
+ 
+ .SH AUTHOR
+-Guenter W. Mamier 
+\ No newline at end of file
++Guenter W. Mamier 
+--- a/tools/doc/netperf.doc	2008-04-21 03:56:06.000000000 -0400
++++ b/tools/doc/netperf.doc	1969-12-31 19:00:00.000000000 -0500
+@@ -1,49 +0,0 @@
+-                  ===============================
+-                  Description of the tool NETPERF
+-                  ===============================
+-
+-This is a benchmark program for SNNS. Propagtion and
+-backpropagation tests are performed.
+-
+-synopsis: netperf
+-
+-
+-example:
+-
+-unix >netperf
+-
+-produces
+-
+-  SNNS 3D-Kernel V3.1000
+-  -----  Benchmark Test  -----
+-
+-  Filename of the network file: ../../../examples/nettalk.net
+-  Loading the network ...
+-
+-  Network name: nettalk1
+-  No. of units       : 349
+-  No. of input units : 203
+-  No. of output units: 26
+-  No. of sites: 0
+-  No. of links: 27480
+-
+-  Learning function: Std_Backpropagation
+-  Update function  : Topological_Order
+-
+-  Do you want to benchmark
+-  Propagation [1] or
+-  Backpropagation [2] ?
+-  Input: 1
+-
+-  Choose no. of cycles: 100
+-
+-  Begin propagation ...
+-
+-
+-  No. of units updated: 34900
+-  No. of sites updated: 0
+-  No. of links updated: 2748000
+-  CPU Time used: 3.05 seconds
+-
+-  No. of connection per second (CPS): 9.0098e+05
+-
+--- a/tools/doc/snns-netperf.doc	1969-12-31 19:00:00.000000000 -0500
++++ b/tools/doc/snns-netperf.doc	2015-04-14 09:37:21.126013855 -0400
+@@ -0,0 +1,49 @@
++                ====================================
++                Description of the tool SNNS-NETPERF
++                ====================================
++
++This is a benchmark program for SNNS. Propagtion and
++backpropagation tests are performed.
++
++synopsis: snns-netperf
++
++
++example:
++
++unix >snns-netperf
++
++produces
++
++  SNNS 3D-Kernel V3.1000
++  -----  Benchmark Test  -----
++
++  Filename of the network file: ../../../examples/nettalk.net
++  Loading the network ...
++
++  Network name: nettalk1
++  No. of units       : 349
++  No. of input units : 203
++  No. of output units: 26
++  No. of sites: 0
++  No. of links: 27480
++
++  Learning function: Std_Backpropagation
++  Update function  : Topological_Order
++
++  Do you want to benchmark
++  Propagation [1] or
++  Backpropagation [2] ?
++  Input: 1
++
++  Choose no. of cycles: 100
++
++  Begin propagation ...
++
++
++  No. of units updated: 34900
++  No. of sites updated: 0
++  No. of links updated: 2748000
++  CPU Time used: 3.05 seconds
++
++  No. of connection per second (CPS): 9.0098e+05
++
+--- a/tools/sources/Makefile	2015-04-14 09:34:31.386010756 -0400
++++ b/tools/sources/Makefile	2015-04-14 09:35:50.526012201 -0400
+@@ -89,7 +89,7 @@
+ 
+ TOOLS_PRG          = $(TOOLS_SOURCES_C:.c=)
+ KRTOOLS_PRG        = snns2c pat_sel netlearn td_bignet ff_bignet \
+-                     netperf snnsbat feedback-gennet convert2snns \
++                     snns-netperf snnsbat feedback-gennet convert2snns \
+                      isnns linknets
+ BATCH_PRG          = batchman
+ 
+@@ -110,7 +110,7 @@
+ tools:       $(TOOLS_PRG) $(KRTOOLS_PRG) $(BATCH_PRG)
+ 
+ $(TOOLSBINDIR):
+-	-mkdir $(TOOLSBINDIR)
++	-mkdir -p $(TOOLSBINDIR)
+ 
+ install: tools $(TOOLSBINDIR)
+ 	for tooltarget in $(TOOLS_PRG) $(KRTOOLS_PRG) $(BATCH_PRG) ; do \
+@@ -191,8 +191,8 @@
+ ff_bignet: ff_bignet.o $(KERNELLIBS)
+ 	$(CC) $(LDFLAGS) ff_bignet.o $(KERNELALLLIBS) -o ff_bignet
+ 
+-netperf: netperf.o $(KERNELLIBS)
+-	$(CC) $(LDFLAGS) netperf.o $(KERNELALLLIBS) -o netperf
++snns-netperf: netperf.o $(KERNELLIBS)
++	$(CC) $(LDFLAGS) netperf.o $(KERNELALLLIBS) -o snns-netperf
+ 
+ snnsbat: snnsbat.o $(KERNELLIBS)
+ 	$(CC) $(LDFLAGS) snnsbat.o $(KERNELALLLIBS) -o snnsbat
diff --git a/sci-mathematics/snns/snns-4.3-r1.ebuild b/sci-mathematics/snns/snns-4.3-r2.ebuild
index 5c385e6ff90f..f7a025874a08 100644
--- a/sci-mathematics/snns/snns-4.3-r1.ebuild
+++ b/sci-mathematics/snns/snns-4.3-r2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/snns/snns-4.3-r1.ebuild,v 1.2 2015/04/10 20:09:40 axs Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/snns/snns-4.3-r2.ebuild,v 1.1 2015/04/14 15:10:59 axs Exp $
 
 EAPI=5
 PYTHON_COMPAT=( python2_7 )
@@ -18,14 +18,16 @@ KEYWORDS="~amd64 ~ppc ~x86"
 SLOT="0"
 IUSE="X doc python"
 
-RDEPEND="X? ( x11-libs/libXaw3d )
-	python? ( ${PYTHON_DEPS} )"
-DEPEND=">=sys-devel/bison-1.2.2
-	X? (
+RDEPEND="X? (
+		x11-libs/libX11
 		x11-libs/libXaw3d
-		x11-proto/xproto
+		x11-libs/libXt
 	)"
+DEPEND="${RDEPEND}
+	X? ( x11-proto/xproto )
+	>=sys-devel/bison-1.2.2"
 
+RDEPEND+=" python? ( ${PYTHON_DEPS} )"
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
 S="${WORKDIR}/${MY_P}"
@@ -34,6 +36,7 @@ src_prepare() {
 	epatch "${FILESDIR}"/4.3-unstrip.patch
 	epatch "${FILESDIR}"/4.3-bison-version.patch
 	epatch "${FILESDIR}"/4.2-ldflags.patch
+	epatch "${FILESDIR}"/4.3-snns-netperf.patch # bug 248322
 
 	# change all references of Xaw to Xaw3d
 	cd "${S}"/xgui/sources
@@ -41,7 +44,9 @@ src_prepare() {
 		sed -e "s:X11/Xaw/:X11/Xaw3d/:g" -i "${file}"
 	done
 
-	# clean up files that apparently are not removed by any clean rules
+	# clean up the dirty dist sources and remove files that apparently
+	# are not removed by any clean rules
+	emake clean
 	rm -Rf "${S}"/{tools,xgui}/bin \
 		"${S}"/{Makefile.def,config.h} \
 		"${S}"/configuration/config.{guess,log}
@@ -70,9 +75,6 @@ src_compile() {
 	local compileopts=( compile-kernel compile-tools )
 	use X && compileopts+=( compile-xgui )
 
-	# tarball is sometimes left dirty
-	emake clean
-
 	# parallel make sometimes fails (phosphan)
 	# so emake each phase separately (axs)
 	for tgt in "${compileopts[@]}"; do
@@ -87,12 +89,9 @@ src_compile() {
 }
 
 src_install() {
-	for file in `find tools -type f -perm +100`; do
-		dobin $file
-	done
-
-	# bug 248322
-	mv "${ED}"/usr/bin/{,snns-}netperf || die
+	pushd "${S}"/tools/sources > /dev/null || die
+	emake TOOLSBINDIR="${ED}"usr/bin install
+	popd > /dev/null || die
 
 	if use X; then
 		newbin xgui/sources/xgui snns