sci-biology/fsl: credit and detail the patches.

Package-Manager: Portage-2.3.79, Repoman-2.3.16

sci-biology/fsl/ChangeLog

@@ -1,3 +1,8 @@
+  19 Jan 2020; François Bissey <frp.bissey@gmail.com>
+  files/fsl-6.0.2-fsldir_redux.patch, files/fsl-6.0.2-no_xmlpp.patch,
+  files/fsl-6.0.2-qstring_compat.patch, files/fsl-6.0.2-setup.patch:
+  sci-biology/fsl: credit and detail the patches.
+
   08 Nov 2019; François Bissey <frp.bissey@gmail.com> fsl-6.0.2.ebuild:
   sci-biology/fsl: final touches. Skip mist-clean.
 

sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch

@@ -1,3 +1,28 @@
+From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:40:53 +1300
+Subject: [PATCH] Making sure fsl code and executable can find other executable
+ and data in standard location.
+
+---
+ src/fast4/fast_two.cc              |  8 ++++----
+ src/feat5/feat_model.cc            |  8 +++-----
+ src/feat5/tsplot.cc                |  7 +++----
+ src/first/first_utils.cc           |  4 ++--
+ src/fnirt/fnirtfns.cpp             | 11 ++++-------
+ src/fslsurface/fslsurface_first.cc |  6 ++----
+ src/fslsurface/fslsurfacemaths.cpp | 12 ------------
+ src/libvis/miscpic.h               |  7 +------
+ src/melodic/meldata.cc             |  4 ++--
+ src/melodic/meloptions.cc          |  8 --------
+ src/melodic/meloptions.h           |  1 -
+ src/melodic/melreport.cc           | 12 ++++++------
+ src/melodic/melreport.h            | 20 ++++++++++----------
+ src/mm/mixture_model.cc            |  4 ++--
+ src/siena/siena_diff.cc            | 28 +++++++++++++---------------
+ src/topup/topupfns.cpp             |  3 +--
+ 16 files changed, 53 insertions(+), 90 deletions(-)
+
 diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
 index 592b5df..b525444 100644
 --- a/src/fast4/fast_two.cc
@@ -465,3 +490,6 @@ index 6873758..9e8b956 100644
      if (TOPUP::check_exist(ecfname)) return(ecfname);
      else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
        ecfname += string(".cnf");
+-- 
+2.24.1
+

sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch

@@ -1,3 +1,14 @@
+From 9de29e5141afa43c06f347ca158b67168fbb0031 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:46:52 +1300
+Subject: [PATCH] Build without xmlpp since we use an external ciftilib that
+ doesnt require it. Replace it and other ciftilib flags with CIFTICFLAGS.
+
+---
+ src/flameo/Makefile  | 4 ++--
+ src/melodic/Makefile | 4 ++--
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
 diff --git a/src/flameo/Makefile b/src/flameo/Makefile
 index d22eb965..e967e682 100644
 --- a/src/flameo/Makefile
@@ -42,3 +53,6 @@ index 50666517..0c356a2d 100644
  
  TEST_OBJS = test.o 
  
+-- 
+2.24.1
+

sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch

@@ -1,3 +1,15 @@
+From 5a5ab3c80eaaea1fe9a43659e2ea5b773b587bb0 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:51:52 +1300
+Subject: [PATCH] Because we use qstrings in ciftilib, calls to ciftilib file
+ function have to be made into compatible c strings.
+
+---
+ src/flameo/gsa.cc      | 4 ++--
+ src/melodic/meldata.cc | 2 +-
+ src/melodic/meldata.h  | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
 diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
 index 70f8f385..16167abe 100644
 --- a/src/flameo/gsa.cc
@@ -21,7 +33,7 @@ index 70f8f385..16167abe 100644
        vector<float> scratchRow(data.Nrows());//read/write a row at a time
        for (int64_t row=0;row<data.Ncols();row++) {	    
 diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
-index 1749a459..b76f052d 100644
+index c4ad2349..1515e702 100644
 --- a/src/melodic/meldata.cc
 +++ b/src/melodic/meldata.cc
 @@ -118,7 +118,7 @@ namespace Melodic{
@@ -46,3 +58,6 @@ index 49774003..f5326bdd 100644
  	  cifti::CiftiXML xml(inputCifti.getCiftiXML());
  	  cifti::CiftiScalarsMap scalarsMap;
  	  std::vector<char> foo = xml.writeXMLToVector();
+-- 
+2.24.1
+

sci-biology/fsl/files/fsl-6.0.2-setup.patch

@@ -1,3 +1,19 @@
+From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:54:37 +1300
+Subject: [PATCH] Adjust the build system so it doesnt build packages
+ externally provided by portage. Make the compilation flags more generic and
+ easily adjustable. Make the build system stop at the first fault.
+
+---
+ build                   |  6 +++---
+ config/buildSettings.mk | 20 ++++++++++----------
+ config/common/buildproj |  8 +++++---
+ config/common/vars.mk   | 10 +++++-----
+ extras/build            |  8 ++++----
+ src/mist-clean/Makefile |  2 +-
+ 6 files changed, 28 insertions(+), 26 deletions(-)
+
 diff --git a/build b/build
 index 05dac06c..d90e407b 100755
 --- a/build
@@ -177,3 +193,6 @@ index 20402cca..6918bee4 100755
 +			rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
  
  .PHONY:		all clean installdata
+-- 
+2.24.1
+