Installation failed from Github on 32-bit ARM

[SebastienGrall]

Hi,

building package from Github failed with error "undefined symbol: __atomic_store_8"

platform/architecture:
Linux raspberrypi 5.15.36-v7l+ #1549 SMP Thu Apr 28 19:51:34 BST 2022 armv7l GNU/Linux
PRETTY_NAME="Raspbian GNU/Linux 10 (buster)"
NAME="Raspbian GNU/Linux"

Error :

g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o s2.so absl/base/internal/cycleclock.o absl/base/internal/exponential_biased.o absl/base/internal/low_level_alloc.o absl/base/internal/periodic_sampler.o absl/base/internal/raw_logging.o absl/base/internal/scoped_set_env.o absl/base/internal/spinlock_wait.o absl/base/internal/spinlock.o absl/base/internal/strerror.o absl/base/internal/sysinfo.o absl/base/internal/thread_identity.o absl/base/internal/throw_delegate.o absl/base/internal/unscaledcycleclock.o absl/base/log_severity.o absl/container/internal/hashtablez_sampler_force_weak_definition.o absl/container/internal/hashtablez_sampler.o absl/container/internal/raw_hash_set.o absl/debugging/failure_signal_handler.o absl/debugging/internal/address_is_readable.o absl/debugging/internal/demangle.o absl/debugging/internal/elf_mem_image.o absl/debugging/internal/examine_stack.o absl/debugging/internal/stack_consumption.o absl/debugging/internal/vdso_support.o absl/debugging/leak_check_disable.o absl/debugging/leak_check.o absl/debugging/stacktrace.o absl/debugging/symbolize.o absl/numeric/int128.o absl/strings/ascii.o absl/strings/charconv.o absl/strings/cord.o absl/strings/escaping.o absl/strings/internal/charconv_bigint.o absl/strings/internal/charconv_parse.o absl/strings/internal/cord_internal.o absl/strings/internal/cord_rep_ring.o absl/strings/internal/escaping.o absl/strings/internal/memutil.o absl/strings/internal/ostringstream.o absl/strings/internal/pow10_helper.o absl/strings/internal/str_format/arg.o absl/strings/internal/str_format/bind.o absl/strings/internal/str_format/extension.o absl/strings/internal/str_format/float_conversion.o absl/strings/internal/str_format/output.o absl/strings/internal/str_format/parser.o absl/strings/internal/utf8.o absl/strings/match.o absl/strings/numbers.o absl/strings/str_cat.o absl/strings/str_replace.o absl/strings/str_split.o absl/strings/string_view.o absl/strings/substitute.o absl/synchronization/barrier.o absl/synchronization/blocking_counter.o absl/synchronization/internal/create_thread_identity.o absl/synchronization/internal/graphcycles.o absl/synchronization/internal/per_thread_sem.o absl/synchronization/internal/waiter.o absl/synchronization/mutex.o absl/synchronization/notification.o absl/time/civil_time.o absl/time/clock.o absl/time/duration.o absl/time/format.o absl/time/internal/cctz/src/civil_time_detail.o absl/time/internal/cctz/src/time_zone_fixed.o absl/time/internal/cctz/src/time_zone_format.o absl/time/internal/cctz/src/time_zone_if.o absl/time/internal/cctz/src/time_zone_impl.o absl/time/internal/cctz/src/time_zone_info.o absl/time/internal/cctz/src/time_zone_libc.o absl/time/internal/cctz/src/time_zone_lookup.o absl/time/internal/cctz/src/time_zone_posix.o absl/time/internal/cctz/src/zone_info_source.o absl/time/time.o absl/types/bad_any_cast.o absl/types/bad_optional_access.o absl/types/bad_variant_access.o cpp-compat.o s2-accessors.o s2-bounds.o s2-cell.o s2-cell-union.o s2-constructors-formatters.o s2-predicates.o s2-transformers.o init.o RcppExports.o s2-geography.o s2-lnglat.o s2-matrix.o s2-point.o s2-xptr.o wk-impl.o wk-c-utils.o tessellator.o s2-geography/accessors.o s2-geography/accessors-geog.o s2-geography/linear-referencing.o s2-geography/distance.o s2-geography/build.o s2-geography/coverings.o s2-geography/geography.o s2-geography/predicates.o s2/base/stringprintf.o s2/base/strtoint.o s2/encoded_s2cell_id_vector.o s2/encoded_s2point_vector.o s2/encoded_s2shape_index.o s2/encoded_string_vector.o s2/id_set_lexicon.o s2/mutable_s2shape_index.o s2/r2rect.o s2/s1angle.o s2/s1chord_angle.o s2/s1interval.o s2/s2boolean_operation.o s2/s2builder_graph.o s2/s2builder.o s2/s2builderutil_closed_set_normalizer.o s2/s2builderutil_find_polygon_degeneracies.o s2/s2builderutil_lax_polygon_layer.o s2/s2builderutil_s2point_vector_layer.o s2/s2builderutil_s2polygon_layer.o s2/s2builderutil_s2polyline_layer.o s2/s2builderutil_s2polyline_vector_layer.o s2/s2builderutil_snap_functions.o s2/s2builderutil_testing.o s2/s2cap.o s2/s2cell_id.o s2/s2cell_index.o s2/s2cell_union.o s2/s2cell.o s2/s2centroids.o s2/s2closest_cell_query.o s2/s2closest_edge_query.o s2/s2closest_point_query.o s2/s2contains_vertex_query.o s2/s2convex_hull_query.o s2/s2coords.o s2/s2crossing_edge_query.o s2/s2debug.o s2/s2earth.o s2/s2edge_clipping.o s2/s2edge_crosser.o s2/s2edge_crossings.o s2/s2edge_distances.o s2/s2edge_tessellator.o s2/s2error.o s2/s2furthest_edge_query.o s2/s2latlng_rect_bounder.o s2/s2latlng_rect.o s2/s2latlng.o s2/s2lax_loop_shape.o s2/s2lax_polygon_shape.o s2/s2lax_polyline_shape.o s2/s2loop_measures.o s2/s2loop.o s2/s2max_distance_targets.o s2/s2measures.o s2/s2metrics.o s2/s2min_distance_targets.o s2/s2padded_cell.o s2/s2point_compression.o s2/s2point_region.o s2/s2pointutil.o s2/s2polygon.o s2/s2polyline_alignment.o s2/s2polyline_measures.o s2/s2polyline_simplifier.o s2/s2polyline.o s2/s2predicates.o s2/s2projections.o s2/s2r2rect.o s2/s2region_coverer.o s2/s2region_intersection.o s2/s2region_term_indexer.o s2/s2region_union.o s2/s2region.o s2/s2shape_index_buffered_region.o s2/s2shape_index_measures.o s2/s2shape_index.o s2/s2shape_measures.o s2/s2shapeutil_build_polygon_boundaries.o s2/s2shapeutil_coding.o s2/s2shapeutil_contains_brute_force.o s2/s2shapeutil_edge_iterator.o s2/s2shapeutil_get_reference_point.o s2/s2shapeutil_range_iterator.o s2/s2shapeutil_visit_crossing_edge_pairs.o s2/s2testing.o s2/s2text_format.o s2/s2wedge_relations.o s2/strings/ostringstream.o s2/strings/serialize.o s2/util/bits/bit-interleave.o s2/util/bits/bits.o s2/util/coding/coder.o s2/util/coding/varint.o s2/util/math/exactfloat/exactfloat.o s2/util/math/mathutil.o s2/util/units/length-units.o -l:libssl.so.1.1 -l:libcrypto.so.1.1 -L/usr/local/lib/R/lib -lR
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘s2’ in dyn.load(file, DLLpath = DLLpath, ...):
impossible de charger l'objet partagé '/tmp/RtmpZyLtMm/Rinst29ed7913fa8c/00LOCK-s2/00new/s2/libs/s2.so':
/tmp/RtmpZyLtMm/Rinst29ed7913fa8c/00LOCK-s2/00new/s2/libs/s2.so: undefined symbol: __atomic_store_8
Erreur : le chargement a échoué
Exécution arrêtée
ERROR: loading failed

• removing ‘/tmp/RtmpZyLtMm/Rinst29ed7913fa8c/s2’
  -----------------------------------
  ERROR: package installation failed
  STDERR:
  Erreur : Failed to install 's2' from GitHub:
  Failed to R CMD build package, try build = FALSE.
  Exécution arrêtée

[SebastienGrall]

May be the same problem than https://gitlab.kitware.com/cmake/cmake/-/issues/21174

[paleolimbot]

Thank you for doing some digging there! I will do tiny bit of digging and see if I can't fix this.

[paleolimbot]

Thanks for being patient here...is there any chance I could trouble you to run remotes::install_github("r-spatial/s2#171") on your Raspberry Pi to see if that fixes the issue?

[SebastienGrall]

Yes, thanks a lot!