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author | Vladimír Čunát <vcunat@gmail.com> | 2018-08-13 20:42:33 +0200 |
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committer | Vladimír Čunát <vcunat@gmail.com> | 2018-08-13 20:43:59 +0200 |
commit | 5b0398dc36ce5746d8d54e04a1dfcab25939484a (patch) | |
tree | 35dbf68b90a8b5e2cbbbbc3ccfbc2529d4c5ca23 /pkgs/applications/science | |
parent | 34baf00b72ad0932f6a2add6cee88d2e8b7bec8e (diff) | |
parent | 249ba3d3ed76e34f61ab7bb2024b013f3feaafb9 (diff) | |
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Merge branch 'master' into staging-next
Conflicts: gobby and libinfinity - I took the hand-edited versions instead of those resuting from the mass-replacement. Hydra: ?compare=1473190
Diffstat (limited to 'pkgs/applications/science')
4 files changed, 37 insertions, 12 deletions
diff --git a/pkgs/applications/science/astronomy/gildas/aarch64.patch b/pkgs/applications/science/astronomy/gildas/aarch64.patch new file mode 100644 index 000000000000..40696a03dec7 --- /dev/null +++ b/pkgs/applications/science/astronomy/gildas/aarch64.patch @@ -0,0 +1,12 @@ +diff -ruN gildas-src-jul18a/admin/define-system.sh gildas-src-jul18a.aarch64/admin/define-system.sh +--- gildas-src-jul18a/admin/define-system.sh 2018-06-12 15:22:32.000000000 +0200 ++++ gildas-src-jul18a.aarch64/admin/define-system.sh 2018-07-21 13:05:52.000000000 +0200 +@@ -174,7 +174,7 @@ + DEFAULT_CONFIG= # Default config is empty + case `uname` in + Linux) +- if [ `uname -m | grep -c "x86_64"` -ne 0 ]; then ++ if [ `uname -m | grep -c "64"` -ne 0 ]; then + GAG_MACHINE=x86_64 + else + GAG_MACHINE=pc diff --git a/pkgs/applications/science/astronomy/gildas/default.nix b/pkgs/applications/science/astronomy/gildas/default.nix index bd4587bf2276..7ede379fb499 100644 --- a/pkgs/applications/science/astronomy/gildas/default.nix +++ b/pkgs/applications/science/astronomy/gildas/default.nix @@ -7,13 +7,13 @@ let in stdenv.mkDerivation rec { - srcVersion = "jun18a"; - version = "20180601_a"; + srcVersion = "jul18a"; + version = "20180701_a"; name = "gildas-${version}"; src = fetchurl { - url = "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.gz"; - sha256 = "0k4x0g69fphb1759cwcw6bbs8imwmq0qwj6zqixxk60skk4n4jvb"; + url = "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.gz"; + sha256 = "0kl3zf6b1kv8hgsfrarsnm2gnrdax3vi8f856249y4nxsa7lbv2i"; }; enableParallelBuilding = true; @@ -22,20 +22,16 @@ stdenv.mkDerivation rec { buildInputs = [ gtk2-x11 lesstif cfitsio python27Env ]; - patches = [ ./wrapper.patch ./return-error-code.patch ./clang.patch ]; + patches = [ ./wrapper.patch ./return-error-code.patch ./clang.patch ./mod.patch ./aarch64.patch ]; configurePhase='' substituteInPlace admin/wrapper.sh --replace '%%OUT%%' $out substituteInPlace admin/wrapper.sh --replace '%%PYTHONHOME%%' ${python27Env} + substituteInPlace utilities/main/gag-makedepend.pl --replace '/usr/bin/perl' ${perl}/bin/perl source admin/gildas-env.sh -c gfortran -o openmp echo "gag_doc: $out/share/doc/" >> kernel/etc/gag.dico.lcl ''; - buildPhase='' - make depend - make - ''; - postInstall='' mkdir -p $out/bin cp -a ../gildas-exe-${srcVersion}/* $out diff --git a/pkgs/applications/science/astronomy/gildas/mod.patch b/pkgs/applications/science/astronomy/gildas/mod.patch new file mode 100644 index 000000000000..c917b4674f13 --- /dev/null +++ b/pkgs/applications/science/astronomy/gildas/mod.patch @@ -0,0 +1,17 @@ +diff -ruN gildas-src-jul18a/admin/Makefile.build gildas-src-jul18a.mod/admin/Makefile.build +--- gildas-src-jul18a/admin/Makefile.build 2018-06-14 14:36:54.000000000 +0200 ++++ gildas-src-jul18a.mod/admin/Makefile.build 2018-07-06 13:31:46.000000000 +0200 +@@ -291,6 +291,13 @@ + win-$(LIB_IDENTITY)-und.def -o $@ $(FLDLIBS) $(LIB_DEPENDS) $(ADD_LIBS) $(SYS_LIBS)) + endif + ++# Dummy rules for modules just so that make consider the module a ++# valid dependency when first parsing the makefiles. This rule should ++# never be applied as the modules are a by-product of the compilation ++# of the object ++$(builddir)/%.mod: ++ echo "dummy" > /dev/null ++ + # Fortran executables + $(bindir)/% : $(builddir)/%.o | $(bindir) + $(FC) $(ALL_FLDFLAGS) $< $(OBJECTS) -o $@ \ diff --git a/pkgs/applications/science/biology/vcftools/default.nix b/pkgs/applications/science/biology/vcftools/default.nix index 394973692dca..a6f52ae97b59 100755 --- a/pkgs/applications/science/biology/vcftools/default.nix +++ b/pkgs/applications/science/biology/vcftools/default.nix @@ -3,13 +3,13 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "vcftools"; - version = "0.1.15"; + version = "0.1.16"; src = fetchFromGitHub { repo = pname; owner = "vcftools"; rev = "v${version}"; - sha256 = "15yxr4kidqb42gkbd6rjra6b07wpl6rgivlh9q73yavh5myafqk4"; + sha256 = "0msb09d2cnm8rlpg8bsc1lhjddvp3kf3i9dsj1qs4qgsdlzhxkyx"; }; buildInputs = [ autoreconfHook pkgconfig zlib perl ]; |