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rPackages.Rhdf5lib: fix build

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This commit is contained in:
Justin Bedo
2026-05-29 09:02:09 +10:00
parent 8ee070ca0c
commit a4664b8196
2 changed files with 37 additions and 47 deletions
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pkgs/development/r-modules/default.nix
+14 -2
View File
@@ -765,7 +765,9 @@ let
];
RGtk2 = [ pkgs.gtk2.dev ];
rhdf5 = [ pkgs.zlib ];
Rhdf5lib = with pkgs; [ zlib.dev ];
Rhdf5lib = with pkgs; [
cmake
];
Rhpc = with pkgs; [
zlib
bzip2.dev
@@ -1252,6 +1254,10 @@ let
fftw.dev
pkg-config
];
Rhdf5lib = with pkgs; [
curl
zlib.dev
];
GRAB = [ pkgs.zlib.dev ];
jqr = [ pkgs.jq.out ];
kza = [ pkgs.pkg-config ];
@@ -3109,7 +3115,13 @@ let
Rhdf5lib =
let
hdf5 = pkgs.hdf5_1_10;
hdf5 = pkgs.hdf5.overrideAttrs (attrs: {
cmakeFlags = attrs.cmakeFlags ++ [ "-DHDF5_ENABLE_ROS3_VFD:BOOL=TRUE" ];
buildInputs = attrs.buildInputs ++ [ pkgs.curl.dev ];
postInstall = attrs.postInstall or "" + ''
cp src/libhdf5.settings $dev/lib
'';
});
in
old.Rhdf5lib.overrideAttrs (attrs: {
propagatedBuildInputs = attrs.propagatedBuildInputs ++ [
pkgs/development/r-modules/patches/Rhdf5lib.patch
+23 -45
View File
@@ -1,8 +1,8 @@
diff --git a/R/zzz.R b/R/zzz.R
index 97becd7..803ca39 100644
index 2af2b3e..21ddc00 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -20,7 +20,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
@@ -22,7 +22,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
path <- Sys.getenv(
x = "RHDF5LIB_RPATH",
@@ -10,70 +10,48 @@ index 97becd7..803ca39 100644
+ unset = ""
)
if (nzchar(.Platform$r_arch)) {
@@ -59,7 +59,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5 %s',
sysname <- Sys.info()['sysname']
@@ -47,7 +47,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5 %s',
patharch, winlibs)
}, {
- sprintf('"%s/libhdf5.a"%s%s',
+ sprintf('-lhdf5',
patharch, .getSzipLoc(patharch), .getDynamicLinks())
+ sprintf('-lhdf5',
patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
}
)
@@ -70,7 +70,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5_cpp -lhdf5 %s',
@@ -58,7 +58,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5_cpp -lhdf5 %s',
patharch, winlibs)
}, {
- sprintf('"%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
+ sprintf('-lhdf5_cpp -lhdf5',
patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
}
)
@@ -81,7 +81,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5_hl -lhdf5 %s',
@@ -69,7 +69,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5_hl -lhdf5 %s',
patharch, winlibs)
}, {
- sprintf('"%s/libhdf5_hl.a" "%s/libhdf5.a"%s%s',
+ sprintf('-lhdf5_hl -lhdf5',
patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+ sprintf('-lhdf5_hl -lhdf5',
patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
}
)
@@ -92,7 +92,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s',
@@ -80,7 +80,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s',
patharch, winlibs)
}, {
- sprintf('"%s/libhdf5_hl_cpp.a" "%s/libhdf5_hl.a" "%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
+ sprintf('-lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5',
patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
}
)
@@ -124,6 +124,7 @@ getHdf5Version <- function() {
#'
@@ -113,6 +113,7 @@ getHdf5Version <- function() {
#' @noRd
#' @keywords internal
.getDynamicLinks <- function() {
.getDynamicLinks <- function(path) {
+ return("")
sysname <- Sys.info()['sysname']
if(sysname == "Windows") {
links <- "-lz"
diff --git a/src/Makevars.in b/src/Makevars.in
index addb6a0..590784a 100644
--- a/src/Makevars.in
+++ b/src/Makevars.in
@@ -18,7 +18,7 @@ USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
PKG_CPPFLAGS = -I${USER_INCLUDE_DIR} ${ZLIB_INCLUDE}
PKG_CFLAGS = ${ZLIB_LIB}
-PKG_LIBS = "${USER_LIB_DIR}libhdf5.a" @SZIP_LIB@ -lz
+PKG_LIBS = -lhdf5 -lsz
@@ -26,7 +26,7 @@ all: $(SHLIB)
$(SHLIB): Rhdf5lib.o
-Rhdf5lib.o: copy-hdf5 @COPY_SZIP@
+Rhdf5lib.o:
copy-szip: copy-hdf5
cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "${USER_LIB_DIR}"
settings_file <- file.path(path, "libhdf5.settings")
libhdf5_settings <- readLines(settings_file)
libstr <- grep("Extra libraries", x = libhdf5_settings, fixed = TRUE, value = TRUE) |>