[R-pkg-team] Bug#1087826: r-bioc-rhdf5: FTBFS with HDF5 1.14: ‘H5I_REFERENCE’ undeclared (first use in this function)

[Michael R. Crusoe]

Control: forwarded -1 https://github.com/grimbough/rhdf5/issues/147

I've confirmed that the latest release of rhdf5 still FTBFS with libhdf4 1.14 and I've informed upstream about the issue.

I uploaded the patch, and while it did work for amd64, mips64el, and ppc64el; the build failed for arm64, riscv64 and s390x where it did not before.

I made the following adjustment to the patch, which seems to have worked. Many thanks!

diff --git a/debian/patches/hdf5-1.14.patch b/debian/patches/hdf5-1.14.patch
index 87bbcb7..fd37cc8 100644
--- a/debian/patches/hdf5-1.14.patch
+++ b/debian/patches/hdf5-1.14.patch
@@ -3,13 +3,14 @@ Description: Support HDF5 1.14
  Forwarded: https://github.com/grimbough/rhdf5/issues/147#issuecomment-2535565591
  Last-Update: 2024-11-19
  
-Index: r-bioc-rhdf5-2.48.0+dfsg/src/H5constants.c
-===================================================================
---- r-bioc-rhdf5-2.48.0+dfsg.orig/src/H5constants.c
-+++ r-bioc-rhdf5-2.48.0+dfsg/src/H5constants.c
-@@ -153,11 +153,11 @@ SEXP _H5constants( ) {
+--- r-bioc-rhdf5.orig/src/H5constants.c
++++ r-bioc-rhdf5/src/H5constants.c
+@@ -151,15 +151,15 @@
+   const char *name_H5T_CSET[] = { "H5T_CSET_ASCII", "H5T_CSET_UTF8" };
+   addVector_int(i++, Rval, groupnames, "H5T_CSET", 2, const_H5T_CSET, name_H5T_CSET);
   
-   int const_H5I_TYPE[15]       = { H5I_FILE, H5I_GROUP, H5I_DATATYPE, H5I_DATASPACE, H5I_DATASET, H5I_ATTR,
+-  int const_H5I_TYPE[15]       = { H5I_FILE, H5I_GROUP, H5I_DATATYPE, H5I_DATASPACE, H5I_DATASET, H5I_ATTR,
++  int const_H5I_TYPE[]         = { H5I_FILE, H5I_GROUP, H5I_DATATYPE, H5I_DATASPACE, H5I_DATASET, H5I_ATTR,
   				   H5I_BADID, H5I_UNINIT,
  -				   H5I_REFERENCE, H5I_VFL, H5I_GENPROP_CLS, H5I_GENPROP_LST,
  +				   H5I_VFL, H5I_GENPROP_CLS, H5I_GENPROP_LST,
@@ -19,12 +20,13 @@ Index: r-bioc-rhdf5-2.48.0+dfsg/src/H5constants.c
  -				   "H5I_REFERENCE", "H5I_VFL", "H5I_GENPROP_CLS", "H5I_GENPROP_LST",
  +				   "H5I_VFL", "H5I_GENPROP_CLS", "H5I_GENPROP_LST",
   				   "H5I_ERROR_CLASS", "H5I_ERROR_MSG", "H5I_ERROR_STACK" };
-   addVector_int(i++, Rval, groupnames, "H5I_TYPE", 15, const_H5I_TYPE, name_H5I_TYPE);
+-  addVector_int(i++, Rval, groupnames, "H5I_TYPE", 15, const_H5I_TYPE, name_H5I_TYPE);
++  addVector_int(i++, Rval, groupnames, "H5I_TYPE", 14, const_H5I_TYPE, name_H5I_TYPE);
   
-Index: r-bioc-rhdf5-2.48.0+dfsg/src/Makevars
-===================================================================
---- r-bioc-rhdf5-2.48.0+dfsg.orig/src/Makevars
-+++ r-bioc-rhdf5-2.48.0+dfsg/src/Makevars
+   hid_t const_H5P[16]      = {  H5P_OBJECT_CREATE, H5P_FILE_CREATE, H5P_FILE_ACCESS, H5P_DATASET_CREATE, H5P_DATASET_ACCESS, H5P_DATASET_XFER,
+ 			      H5P_FILE_MOUNT, H5P_GROUP_CREATE, H5P_GROUP_ACCESS, H5P_DATATYPE_CREATE, H5P_DATATYPE_ACCESS, H5P_STRING_CREATE,
+--- r-bioc-rhdf5.orig/src/Makevars
++++ r-bioc-rhdf5/src/Makevars
  @@ -1,7 +1,7 @@
   RHDF5_LIBS="/usr/lib/`dpkg-architecture -qDEB_HOST_MULTIARCH`/hdf5/serial/"
   PKG_LIBS=/usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so -L$(RHDF5_LIBS) -lhdf5
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