diff options
| author | Justin Bedo <cu@cua0.org> | 2023-03-22 09:43:03 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2023-03-22 09:47:58 +1100 |
| commit | 442e1b87d1bf0134f0fdea1ca7697e08e0b04627 (patch) | |
| tree | f88eeb6cb8130f7921d2c4c3e866d19b4bed8eef /pkgs/development/r-modules | |
| parent | ccfbc19630465aaa666588417d38b56a557a1bff (diff) | |
rPackages.rhdf5filters: fix build
- use hdf5-blosc from nixpkgs to fix failing vendored build
- add missing build dependencies
Diffstat (limited to 'pkgs/development/r-modules')
| -rw-r--r-- | pkgs/development/r-modules/default.nix | 7 | ||||
| -rw-r--r-- | pkgs/development/r-modules/patches/rhdf5filters.patch | 46 |
2 files changed, 52 insertions, 1 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 8913591d645f..d89a788b5f12 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -582,7 +582,7 @@ let podkat = [ pkgs.zlib.dev ]; qrqc = [ pkgs.zlib.dev ]; rJPSGCS = [ pkgs.zlib.dev ]; - rhdf5filters = [ pkgs.zlib.dev ]; + rhdf5filters = with pkgs; [ zlib.dev bzip2.dev ]; rtk = [ pkgs.zlib.dev ]; scPipe = [ pkgs.zlib.dev ]; seqTools = [ pkgs.zlib.dev ]; @@ -1323,6 +1323,11 @@ let propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5_1_10.dev pkgs.libaec ]; patches = [ ./patches/Rhdf5lib.patch ]; }); + + rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: { + propagatedBuildInputs = with pkgs; attrs.propagatedBuildInputs ++ [ (hdf5-blosc.override {hdf5 = hdf5_1_10;}) ]; + patches = [ ./patches/rhdf5filters.patch ]; + }); }); }; in diff --git a/pkgs/development/r-modules/patches/rhdf5filters.patch b/pkgs/development/r-modules/patches/rhdf5filters.patch new file mode 100644 index 000000000000..39f09f54ceef --- /dev/null +++ b/pkgs/development/r-modules/patches/rhdf5filters.patch @@ -0,0 +1,46 @@ +diff --git a/src/Makevars.in b/src/Makevars.in +index 4441634..665a2dd 100644 +--- a/src/Makevars.in ++++ b/src/Makevars.in +@@ -20,10 +20,9 @@ export PKG_LDFLAGS=@LDFLAGS@ + all: copying $(SHLIB) + + #copy hdf5 library headers to package include +-copying: blosc/libH5Zblosc.so bzip2/libH5Zbz2.so lzf/libH5Zlzf.so ++copying: bzip2/libH5Zbz2.so lzf/libH5Zlzf.so + mkdir -p "${USER_LIB_DIR}" + cp ${BZIP2_LIB} "${USER_LIB_DIR}" +- cp ${BLOSC_LIB} "${USER_LIB_DIR}" + cp ${LZF_LIB} "${USER_LIB_DIR}" + + blosc/libH5Zblosc.so: +diff --git a/src/bzip2/Makefile b/src/bzip2/Makefile +index 449bbe7..154354e 100644 +--- a/src/bzip2/Makefile ++++ b/src/bzip2/Makefile +@@ -1,9 +1,9 @@ + + all: libH5Zbz2.so + +-libH5Zbz2.so: bzip2-1.0.8/libbz2.a +- ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c $(PKG_CPPFLAGS) \ +- -I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a ${PKG_LDFLAGS} -o libH5Zbz2.so ++libH5Zbz2.so: ++ ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c \ ++ -lbz2 -o libH5Zbz2.so + + bzip2-1.0.8/libbz2.a: + $(MAKE) -C bzip2-1.0.8 +diff --git a/src/lzf/Makefile b/src/lzf/Makefile +index 837f80b..eeca0c8 100644 +--- a/src/lzf/Makefile ++++ b/src/lzf/Makefile +@@ -2,7 +2,7 @@ + all: libH5Zlzf.so + + libH5Zlzf.so: lzf/liblzf.a +- ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c $(PKG_CPPFLAGS) \ ++ ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c \ + -I./lzf/ ./lzf/liblzf.a ${PKG_LDFLAGS} -o libH5Zlzf.so + + lzf/liblzf.a: |