Fixes missing renames, thanks Johan Hattne for giving the patches, #314053

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

6 files changed, 176 insertions, 26 deletions

diff --git a/sci-chemistry/ccp4i/ChangeLog b/sci-chemistry/ccp4i/ChangeLog
index a94d1b5c294d..4451beec803f 100644
--- a/sci-chemistry/ccp4i/ChangeLog
+++ b/sci-chemistry/ccp4i/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/ccp4i
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/ChangeLog,v 1.3 2010/04/22 20:19:04 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/ChangeLog,v 1.4 2010/04/25 12:32:54 jlec Exp $
+
+*ccp4i-6.1.3-r2 (25 Apr 2010)
+
+  25 Apr 2010; Justin Lecher <jlec@gentoo.org>
+  files/6.1.3-rename-rapper.patch, +ccp4i-6.1.3-r2.ebuild,
+  files/6.1.3-rename-superpose.patch, files/6.1.3-rename-truncate.patch,
+  -ccp4i-6.1.3-r1.ebuild:
+  Fixes missing renames, thanks Johan Hattne for giving the patches, #314053
 
   22 Apr 2010; Justin Lecher <jlec@gentoo.org> ccp4i-6.1.3-r1.ebuild:
   Fixes for Python ABIs, keyworded for *-linux
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
index d3bb36e3c0a9..41ecfef41dc7 100644
--- a/sci-chemistry/ccp4i/Manifest
+++ b/sci-chemistry/ccp4i/Manifest
@@ -1,10 +1,20 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 6.1.3-fix-baubles.patch 1542 RMD160 c952d16d1e009a9ff345393494bf198fff997934 SHA1 cdc8752026f3cdd96ee0fd6a3f558e0729f88a6a SHA256 37c217f339a46a6b830ce8e791cbd32655e31ab8d58267fb625e841e867402b4
-AUX 6.1.3-rename-rapper.patch 380 RMD160 e8306cec04348a56fbe00026333b27ce2a8544f8 SHA1 f5a87898394add359a1e6f6ceb837530dc53646f SHA256 e15407959e565d32874d2db9003168559b7e9b14f0e68207560d4a5b4db8a728
-AUX 6.1.3-rename-superpose.patch 655 RMD160 6647dc3e0a021f9809d74d5dd785dd6bde456c22 SHA1 485a2e3cd46864769c6cfe10b9b0224ca896d2d6 SHA256 75791921692a603baa88dfa45ff48331ea8b6985a63f04a15ad43dd5be93e52e
-AUX 6.1.3-rename-truncate.patch 810 RMD160 33f8cb14a3bc0f9c6cd249df07f469c9d6601e4d SHA1 ac13f02b6141802e3762efe50a3d270169da0a54 SHA256 5a298cce47726d78ece397affdf1f2d550be520565c7dc5b47a953ab01d23ccd
+AUX 6.1.3-rename-rapper.patch 2404 RMD160 32f69349bac21db4fe3c1d9987931c5592d877a5 SHA1 f3cb8891b8630a98d8fedb0d3d7e6090fef1a69d SHA256 997ed07b06326d63692144f035d09b3bc639cd2eb73e9cfcd4b35a2004eb8a17
+AUX 6.1.3-rename-superpose.patch 1203 RMD160 b0ba4909d23b4aa7e4a7e5175e2511673ef9f442 SHA1 2ede95e06b71391d6f26346e6f6ad05af32684a4 SHA256 e41a5ad1f46f6c0301fa088acc2c8e7c28837342144ff1c2063e21fef6900262
+AUX 6.1.3-rename-truncate.patch 3849 RMD160 44d48f59abbe603940bd21780ace955dd1ac7878 SHA1 ca1a42395cf133a4a9df37c24ee4abb388794cca SHA256 18fe75b6d7dffb838a22e0f38a58823efa635ab3606666d6da912ba08afb3a06
 DIST 6.1.3-oasis4.0.patch.bz2 946 RMD160 b448376114ba41e6999d533929fdb79812476f87 SHA1 7667aca14d28cec01bfa7d2eee9cbce11624f4fa SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
 DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 RMD160 3bf65f26a8635194e69ff9f33a457f9ff7e050d0 SHA1 0172a35d539ed3020228f20f0ddfa82540790cf0 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687
-EBUILD ccp4i-6.1.3-r1.ebuild 2143 RMD160 a107e0af97e88be359d0c0139cb1e14ad8dd18d3 SHA1 e9b7c5b7c7cade35919f6f006da5eed2079ae790 SHA256 b2862e14e8b1c5e36268f79b3cd9e39abeab1f166136a4e2e5380eb61266cc00
-MISC ChangeLog 764 RMD160 ee0c2c9e5ad5a8214a23c24ea32c871f253a118f SHA1 c694e9d78abce31684b283d0847ed0100c44ab9b SHA256 30387d46b532fb13086705dc2ec66052205dbde7dc2fbee02d8d74d5fbbbc0c3
+EBUILD ccp4i-6.1.3-r2.ebuild 2139 RMD160 3ee5efdce5b2373bc76139714cfe6cecf9878c52 SHA1 656f97dc6d3c9c40f010a24329e1357f855671f6 SHA256 3b9e0a3a7ff225c70df2889af731504e3b62bd5a25557fd8e50db9b646c43969
+MISC ChangeLog 1078 RMD160 8eedb944fbd18f7a33a2dab1f5021b71d34d3608 SHA1 fac07f34027e8c0cab2b44753964ee9d7434a52f SHA256 3923520a070569277e8305de9530c98d043655c4130848a8b45d906ebfca3295
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAkvUNnsACgkQgAnW8HDreRZPOACgiQENXoIOuzZOkyKSkdlucRhb
+DWEAnRr99P7a3SU4MvFjef0u9GMZNYmE
+=Srg4
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r1.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r2.ebuild
index e87fe0e6c742..b1b6bd1bb5fc 100644
--- a/sci-chemistry/ccp4i/ccp4i-6.1.3-r1.ebuild
+++ b/sci-chemistry/ccp4i/ccp4i-6.1.3-r2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/ccp4i-6.1.3-r1.ebuild,v 1.3 2010/04/22 22:22:43 arfrever Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/ccp4i-6.1.3-r2.ebuild,v 1.1 2010/04/25 12:32:54 jlec Exp $
 
 EAPI="2"
 PYTHON_DEPEND="2"
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
index a50ae6dbd648..9f5cfb4b635f 100644
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
@@ -1,5 +1,20 @@
---- ccp4i/scripts/rapper.script 2009-02-03 11:49:50.000000000 +0100
-+++ ccp4i/scripts/rapper.script.new     2009-03-12 23:34:47.000000000 +0100
+diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script
+index def44bc..dd4bb7e 100755
+--- a/ccp4i/scripts/check.script
++++ b/ccp4i/scripts/check.script
+@@ -24,7 +24,7 @@
+   if $RUN_RAMPAGE {
+ 
+     # Generate command line
+-    set cmd "[BinPath rapper]"
++    set cmd "[BinPath rappermc]"
+ 
+     set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
+     set paramsfile [FileJoin $rapperdatadir params.xml]
+diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script
+index cdae1e2..faae226 100755
+--- a/ccp4i/scripts/rapper.script
++++ b/ccp4i/scripts/rapper.script
 @@ -17,7 +17,7 @@
  
  #set up command line 
@@ -9,4 +24,38 @@
  
  set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
  set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml]
-
+@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT"
+ 
+ # Run RAPPER to join loop back to framework and out put to defined pdb file
+ # Also need to sort out multimodel files join - FIX ME
+-set cmd2 "[BinPath rapper]"
++set cmd2 "[BinPath rappermc]"
+ append cmd2 " $paramsfile joinpdb "
+ append cmd2 " --pdb2 \"$root\-loop.pdb\" "
+ append cmd2 " --pdb  \"$root\-framework.pdb\" "
+diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl
+index ae88ff2..ee3307b 100755
+--- a/ccp4i/tasks/check.tcl
++++ b/ccp4i/tasks/check.tcl
+@@ -46,7 +46,7 @@ proc check_run { arrayname } {
+  # Check for Rampage program. If it is not found, we switch off the option.
+  # If it was the only option, script will fail with next check.
+  if { $array(RUN_RAMPAGE) == 1 } {
+-   if { [FindExecutable "rapper"] == "" } {
++   if { [FindExecutable "rappermc"] == "" } {
+       WarningMessage "Input Error: Rapper_Rampage program not found in system path."
+       set array(RUN_RAMPAGE) 0
+     }
+diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl
+index e299057..8843a3f 100755
+--- a/ccp4i/tasks/rapper.tcl
++++ b/ccp4i/tasks/rapper.tcl
+@@ -28,7 +28,7 @@ proc rapper_run { arrayname } {
+  # Check for RAPPER program. If it is not found, we switch off the option.
+  # If it was the only option, script will fail with next check.
+   if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} {
+-   if { [FindExecutable "rapper"] == "" } {
++   if { [FindExecutable "rappermc"] == "" } {
+       WarningMessage "Input Error: RAPPER program not found in system path."
+       set build_type 0
+     }
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
index 90480eb8e381..74cd2b946601 100644
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
@@ -1,6 +1,7 @@
-diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/scripts/superpose.script
---- ccp4-6.1.1/ccp4i/scripts/superpose.script	2006-07-26 16:22:49.000000000 +0200
-+++ ccp4-6.1.1.new/ccp4i/scripts/superpose.script	2009-07-05 22:11:59.000000000 +0200
+diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script
+index 3483c97..5027536 100755
+--- a/ccp4i/scripts/superpose.script
++++ b/ccp4i/scripts/superpose.script
 @@ -21,7 +21,7 @@
  
    if { [regexp SSM $SUPERPOSE_MODE ] } {
@@ -10,3 +11,16 @@ diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/script
      set status [Execute $cmd "" program_status report ]
  
    } elseif { [regexp TOP $SUPERPOSE_MODE ] } {
+diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl
+index 748bf6e..c92122a 100755
+--- a/ccp4i/tasks/superpose.tcl
++++ b/ccp4i/tasks/superpose.tcl
+@@ -100,7 +100,7 @@ proc superpose_run { arrayname } {
+ # If user is match equivalent named residues/atoms then fit in the match fields
+   switch [GetValue $arrayname SUPERPOSE_MODE] \
+   SSM {
+-    if { ![file exists [FindExecutable superpose]] } {
++    if { ![file exists [FindExecutable superpose-ccp4]] } {
+        WarningMessage "The program \"superpose\" is not on your path. 
+ Check your installation for \"superpose\" program and \"ssm\" library."
+        return 0
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
index 26f1cda3e381..9af60b7c5152 100644
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
@@ -1,16 +1,85 @@
---- ./ccp4i/templates/truncate.com.orig	2009-03-02 23:31:04.000000000 -0800
-+++ ./ccp4i/templates/truncate.com	2009-03-02 23:31:08.000000000 -0800
-@@ -11,7 +11,7 @@
- $SYMMETRY symmetry $SPACE_GROUP
- $CELL cell $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6
- 
--1 truncate
-+1 ftruncate
-  - { [StringSame $APPLY_TRUNCATE "WILSON" ] } YES | NO
- {[IfSet $ANOMALOUS]} anomalous 
-  - $ANOMALOUS YES | NO
---- ./ccp4i/scripts/truncate.script.orig	2009-03-02 23:39:04.000000000 -0800
-+++ ./ccp4i/scripts/truncate.script	2009-03-02 23:39:41.000000000 -0800
+diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl
+index 7d05905..d01f1dc 100755
+--- a/ccp4i/crank/plugins/prep/crank_prep.tcl
++++ b/ccp4i/crank/plugins/prep/crank_prep.tcl
+@@ -226,7 +226,7 @@ proc run_truncate { i j } {
+     set script "$script\n$labout"
+     set script "$script\nEND\n"
+ 	
+-    set run_command "truncate $command << \"$script\""
++    set run_command "ftruncate $command << \"$script\""
+     puts $run_command
+     catch {eval exec $run_command } output 
+     puts $output
+diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script
+index e74aa0d..a2a1adb 100755
+--- a/ccp4i/scripts/dtrek2mtz.script
++++ b/ccp4i/scripts/dtrek2mtz.script
+@@ -36,7 +36,7 @@
+     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
+ 
+     CreateComScript truncate truncate_script
+-    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
++    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
+     set status [Execute $cmd $truncate_script program_status report]
+ 
+     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
+diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script
+index 90cba83..1c90c33 100755
+--- a/ccp4i/scripts/import.script
++++ b/ccp4i/scripts/import.script
+@@ -144,7 +144,7 @@ if { $FORMAT ==  "MTZ" } {
+ 
+     set truncatemtz [GetTmpFileName -ext mtz ]
+     CreateComScript truncate truncate_script
+-    set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
++    set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
+     set status [Execute $cmd $truncate_script program_status report]
+ 
+ 
+diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script
+index dcc619b..7250513 100755
+--- a/ccp4i/scripts/import_scaled.script
++++ b/ccp4i/scripts/import_scaled.script
+@@ -62,7 +62,7 @@
+ 
+     } else {
+       CreateComScript truncate truncate_script
+-      set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
++      set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
+       set status [Execute $cmd $truncate_script program_status report]
+ 
+       HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
+diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script
+index 6940ccd..bde10d6 100755
+--- a/ccp4i/scripts/scala.script
++++ b/ccp4i/scripts/scala.script
+@@ -275,7 +275,7 @@ END"
+ 
+       } else {
+         CreateComScript truncate truncate_script
+-        set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
++        set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
+         set status [Execute $cmd $truncate_script $LOG_FILE  program_status report  ]
+       }
+           
+diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script
+index 986e06c..a1947a6 100755
+--- a/ccp4i/scripts/scalepack2mtz.script
++++ b/ccp4i/scripts/scalepack2mtz.script
+@@ -35,7 +35,7 @@
+ 
+     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
+     CreateComScript truncate truncate_script
+-    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
++    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
+     set status [Execute $cmd $truncate_script program_status report]
+ 
+     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
+diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script
+index e0e09ce..2d448a2 100755
+--- a/ccp4i/scripts/truncate.script
++++ b/ccp4i/scripts/truncate.script
 @@ -45,7 +45,7 @@
  
    CreateComScript truncate truncate_script