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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/mustang/files | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-chemistry/mustang/files')
-rw-r--r-- | sci-chemistry/mustang/files/mustang-3-gcc43.patch | 55 | ||||
-rw-r--r-- | sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch | 16 |
2 files changed, 71 insertions, 0 deletions
diff --git a/sci-chemistry/mustang/files/mustang-3-gcc43.patch b/sci-chemistry/mustang/files/mustang-3-gcc43.patch new file mode 100644 index 000000000000..ef2818b92ed8 --- /dev/null +++ b/sci-chemistry/mustang/files/mustang-3-gcc43.patch @@ -0,0 +1,55 @@ +diff -u MUSTANG_v.3.orig/src/ew_2.cpp MUSTANG_v.3/src/ew_2.cpp +--- MUSTANG_v.3.orig/src/ew_2.cpp 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/ew_2.cpp 2008-12-09 10:47:22.000000000 -0700 +@@ -36,6 +36,7 @@ + using std::ifstream; + + #include<math.h> ++#include <cstdlib> + #include "macros.h" + #include "globals.h" + #include "ew.h" +diff -u MUSTANG_v.3.orig/src/multiple_superposition.cpp MUSTANG_v.3/src/multiple_superposition.cpp +--- MUSTANG_v.3.orig/src/multiple_superposition.cpp 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/multiple_superposition.cpp 2008-12-09 10:49:00.000000000 -0700 +@@ -51,6 +51,7 @@ + #include "alloc_routines.h" + #include "de_alloc_routines.h" + #include <cmath> ++#include <cstdlib> + #define THRESH 0.0001 + + void MOVE_TO_CENTER_OF_GRAVITY( int NSTRUC , int NRES , float ***R , float **CMs ) +diff -u MUSTANG_v.3.orig/src/multiple_superposition.h MUSTANG_v.3/src/multiple_superposition.h +--- MUSTANG_v.3.orig/src/multiple_superposition.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/multiple_superposition.h 2008-12-09 10:48:11.000000000 -0700 +@@ -25,3 +25,4 @@ + #define MULT_SUPERPOSE + void M_SUPERPOSE( int , int , float***, float** , float*** ) ; + #endif ++#include <cstdlib> +diff -u MUSTANG_v.3.orig/src/pdb_ripper.h MUSTANG_v.3/src/pdb_ripper.h +--- MUSTANG_v.3.orig/src/pdb_ripper.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/pdb_ripper.h 2008-12-09 10:46:47.000000000 -0700 +@@ -29,4 +29,5 @@ + void PARSE_ENTIRE_PDB_STRUCTURE( char * , int ) ; + + #endif ++#include <cstdlib> + +diff -u MUSTANG_v.3.orig/src/progress_align.h MUSTANG_v.3/src/progress_align.h +--- MUSTANG_v.3.orig/src/progress_align.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/progress_align.h 2008-12-09 10:47:50.000000000 -0700 +@@ -25,3 +25,4 @@ + #define PROG_ALGN_H + void PROGRESSIVE_ALIGNMENT_USING_EXTENDED_EDGE_WEIGHTS() ; + #endif ++#include <cstdlib> +diff -u MUSTANG_v.3.orig/src/read_structures.h MUSTANG_v.3/src/read_structures.h +--- MUSTANG_v.3.orig/src/read_structures.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/read_structures.h 2008-12-09 10:46:22.000000000 -0700 +@@ -26,3 +26,4 @@ + void READ_STRUCTURES( char **paths ); + void READ_ENTIRE_PDBS( char **paths) ; + #endif ++#include <cstdlib> diff --git a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch new file mode 100644 index 000000000000..9e5dea85afeb --- /dev/null +++ b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch @@ -0,0 +1,16 @@ + src/superpose_on_core_2.cpp | 2 ++ + 1 files changed, 2 insertions(+), 0 deletions(-) + +diff --git a/src/superpose_on_core_2.cpp b/src/superpose_on_core_2.cpp +index ae137de..059dfe3 100644 +--- a/src/superpose_on_core_2.cpp ++++ b/src/superpose_on_core_2.cpp +@@ -55,6 +55,8 @@ using std::ofstream ; + #include "multiple_superposition.h" + #include "3D_manip_functions.h" + ++#include <unistd.h> ++ + int **core_columns ; + int *core_columns_2 , NCORE = 0 ; + int **algn_to_seq_hash ; |