[R-pkg-team] Bug#1078921: r-cran-hdf5r: FTBFS against HDF5 1.14

[Gilles Filippini]

Source: r-cran-hdf5r
Version: 1.3.9+dfsg-1
Severity: important

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Hi,

The r-cran-hdf5r package fails to build from source in a test rebuild against
hdf5 1.14 currently in experimental:

gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/hdf5/serial  -I/usr/include/hdf5/serial     -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.1=. 
- -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c convert.c -o convert.o
convert.c: In function ‘R_reorder’:
convert.c:1586:24: error: initialization of ‘hsize_t *’ {aka ‘long unsigned int *’} from incompatible pointer type ‘long long unsigned int *’ [-Wincompatible-pointer-types]
 1586 |   hsize_t* new_order = (unsigned long long *) VOIDPTR(R_helper);
      |                        ^
make[1]: *** [/usr/lib/R/etc/Makeconf:195: convert.o] Error 1


The patch below fixes the issue:

Index: r-cran-hdf5r-1.3.9+dfsg/src/convert.c
===================================================================
- --- r-cran-hdf5r-1.3.9+dfsg.orig/src/convert.c
+++ r-cran-hdf5r-1.3.9+dfsg/src/convert.c
@@ -1583,7 +1583,7 @@ SEXP R_reorder(SEXP R_src, SEXP R_num_ro
   hsize_t item_size = SEXP_to_longlong(R_item_size, 0);
 
   SEXP R_helper = PROTECT(RToH5(R_new_order, H5T_NATIVE_ULLONG, num_rows));
- -  hsize_t* new_order = (unsigned long long *) VOIDPTR(R_helper);
+  hsize_t* new_order = (hsize_t *) VOIDPTR(R_helper);
   
   SEXP R_dst = PROTECT(duplicate(R_src));
   reorder(VOIDPTR(R_dst), VOIDPTR(R_src), num_rows, num_cols, item_size, new_order);


Best,
_g.

- -- System Information:
Debian Release: 12.0
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-21-amd64 (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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