nixpkgs/pkgs/development/r-modules/patches/rhdf5.patch
Justin Bedo 14db22f868
rPackages.rhdf5: fix build
use nixpkgs provided hdf5 instead of vendored library
2023-03-22 09:48:06 +11:00

47 lines
1.2 KiB
Diff

diff --git a/src/Makevars b/src/Makevars
index 713b44c..704ac17 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1,5 +1,5 @@
RHDF5_LIBS = $(shell "$(R_HOME)/bin${R_ARCH_BIN}/Rscript" -e 'Rhdf5lib::pkgconfig("PKG_C_LIBS")')
-PKG_LIBS = $(RHDF5_LIBS)
+PKG_LIBS = $(RHDF5_LIBS) -lhdf5
#PKG_CFLAGS = -Wall
diff --git a/src/h5testLock.c b/src/h5testLock.c
index b326444..5d58b4a 100644
--- a/src/h5testLock.c
+++ b/src/h5testLock.c
@@ -8,16 +8,16 @@ SEXP _h5fileLock(SEXP _file_name) {
int lk = -1;
/* create the temporary file */
- fd = HDopen(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
+ fd = open(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
/* try to lock file */
- lk = HDflock(fd, LOCK_EX | LOCK_NB);
+ lk = flock(fd, LOCK_EX | LOCK_NB);
/* unlock so we can remove */
- HDflock(fd, LOCK_UN);
+ flock(fd, LOCK_UN);
/* close */
- HDclose(fd);
+ close(fd);
/* return value of lock attempt */
PROTECT(Rval = allocVector(INTSXP, 1));
diff --git a/src/h5testLock.h b/src/h5testLock.h
index 2c1c5e4..660c747 100644
--- a/src/h5testLock.h
+++ b/src/h5testLock.h
@@ -1,5 +1,4 @@
#include <fcntl.h>
#include "myhdf5.h"
-#include <H5private.h>
SEXP _h5fileLock();