Debian Patches

Status for r-bioc-rhdf5lib/2.0.0+dfsg-1

Patch	Description	Author	Forwarded	Bugs	Origin	Last update
use_system_hdf5_settings_format.patch	Emit link flags for the shared, Debian-packaged HDF5 library Two Debian-specific adaptations to Rhdf5lib::pkgconfig(): . 1. Link against the shared system library. Upstream links its bundled, static HDF5 build by naming the .a archives directly. The Debian libhdf5.a is not compiled with -fPIC and therefore cannot be linked into the shared objects that reverse dependencies (e.g. r-bioc-rhdf5) produce, failing with "relocation ... can not be used when making a shared object; recompile with -fPIC". Emit "-L<dir> -lhdf5..." instead so the shared libhdf5.so is used. . 2. Parse the Debian libhdf5.settings link flags. pkgconfig() derives the extra HDF5 linker flags from the "Extra libraries" line of libhdf5.settings. Upstream builds HDF5 with CMake, which writes a semicolon-separated list of CMake targets/paths. The Debian libhdf5-dev package is built with autotools and instead writes a space-separated list of ready-to-use flags (e.g. "-lsz -lz -ldl -lm"). Without this change pkgconfig() mangles that line into invalid flags such as "-l-lcrypto ...". Detect the Debian format and pass it through verbatim. . The accompanying test_link_flags.R expectations are updated to match the shared-library flags. ===================================================================	Charles Plessy <plessy@debian.org>	not-needed			2026-07-31