From ccc8a397531e1e4e6e82a4097e359666272c62a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= Date: Mon, 20 Jan 2020 11:58:39 +1300 Subject: [PATCH] sci-biology/fsl: credit and detail the patches. Package-Manager: Portage-2.3.79, Repoman-2.3.16 --- sci-biology/fsl/ChangeLog | 5 ++++ .../fsl/files/fsl-6.0.2-fsldir_redux.patch | 28 +++++++++++++++++++ .../fsl/files/fsl-6.0.2-no_xmlpp.patch | 14 ++++++++++ .../fsl/files/fsl-6.0.2-qstring_compat.patch | 17 ++++++++++- sci-biology/fsl/files/fsl-6.0.2-setup.patch | 19 +++++++++++++ 5 files changed, 82 insertions(+), 1 deletion(-) diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index 1d1d42a..f6020cf 100644 --- a/sci-biology/fsl/ChangeLog +++ b/sci-biology/fsl/ChangeLog @@ -1,3 +1,8 @@ + 19 Jan 2020; François Bissey + 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 fsl-6.0.2.ebuild: sci-biology/fsl: final touches. Skip mist-clean. diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch index ffa793d..dc1babd 100644 --- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch +++ b/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 +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 + diff --git a/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch index 47c9120..6eccc43 100644 --- a/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch +++ b/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 +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 + diff --git a/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch index c0e238c..9e6682a 100644 --- a/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch +++ b/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 +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 scratchRow(data.Nrows());//read/write a row at a time for (int64_t row=0;row foo = xml.writeXMLToVector(); +-- +2.24.1 + diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch index 67761e3..39737fd 100644 --- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch +++ b/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 +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 +