[R] Link-time optimization reports violations of one-definition rule in the R package

[paleolimbot]

Describe the bug, including details regarding any error messages, version, and platform.

The warning:

* checking whether package ‘arrow’ can be installed ... [18m/17m] WARNING
Found the following significant warnings:
  /arrow/cpp/src/arrow/type.h:323: warning: virtual table of type ‘struct NestedType’ violates one definition rule [-Wodr]
  /arrow/cpp/src/arrow/type.h:288: warning: virtual table of type ‘struct FixedWidthType’ violates one definition rule [-Wodr]
See ‘/arrow/r/check/arrow.Rcheck/00install.out’ for details.

‘/arrow/r/check/arrow.Rcheck/00install.out’ (for details): https://dev.azure.com/ursacomputing/crossbow/_build/results?buildId=42712&view=logs&j=0da5d1d9-276d-5173-c4c4-9d4d4ed14fdb&t=6c939d89-0d1a-51f2-8b30-091a7a82e98c&l=1591

/arrow/cpp/src/arrow/type.h:323: warning: virtual table of type ‘struct NestedType’ violates one definition rule [-Wodr]
  323 | class ARROW_EXPORT NestedType : public DataType, public ParametricType {
      | 
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:323:20: note: the conflicting type defined in another translation unit
  323 | class ARROW_EXPORT NestedType : public DataType, public ParametricType {
      |                    ^
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:177:22: note: virtual method ‘storage_id’
  177 |   virtual Type::type storage_id() const { return id_; }
      |                      ^
<built-in>: note: ought to match virtual method ‘__cxa_pure_virtual’ but does not
/arrow/cpp/src/arrow/type.h:288: warning: virtual table of type ‘struct FixedWidthType’ violates one definition rule [-Wodr]
  288 | class ARROW_EXPORT FixedWidthType : public DataType {
      | 
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:288:20: note: the conflicting type defined in another translation unit
  288 | class ARROW_EXPORT FixedWidthType : public DataType {
      |                    ^
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:177:22: note: virtual method ‘storage_id’
  177 |   virtual Type::type storage_id() const { return id_; }
      |                      ^
<built-in>: note: ought to match virtual method ‘__cxa_pure_virtual’ but does not

I think this is an R package problem...somehow we are mixing up the includes or the linking in such a way that we're picking up includes outside of the package directory (which we really don't want in case there's a user install of Arrow that's a different version!).

Component(s)

R

[paleolimbot]

@assignUser could that be an sccache thing? Like...the cache hit generates a .o file where identical definitions from different filenames are treated identically?

[assignUser]

Hm, maybe? But I feel it's unlikely because the cached file would have to be successful build before being cached... Maybe it's some weird transitive thing?

[assignUser]

You could modify the workflow to remove the sccache envvars which will disable it.

[paleolimbot]

In the context of:

arrow/dev/tasks/tasks.yml

Lines 1357 to 1367 in fa2f45d

	# This is with R built with --enable-lto
	# CRAN also does R CMD INSTALL --use-LTO
	# which overrides the UseLTO field in r/DESCRIPTION
	test-r-rhub-debian-gcc-devel-lto-latest:
	ci: azure
	template: r/azure.linux.yml
	params:
	r_org: rhub
	r_image: debian-gcc-devel-lto
	r_tag: latest
	flags: '-e NOT_CRAN=false -e INSTALL_ARGS=--use-LTO'

...how would I do that?

[assignUser]

Remove https://github.com/apache/arrow/blob/master/dev/tasks/r/azure.linux.yml#L66

[paleolimbot]

Hmm...not transient and not cache-related. Somehow there are includes from two different Arrow source trees making their way into the .o files.

[paleolimbot]

Or one of the libraries is coming from a system install. I can't find anything wrong with the install output:

g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include -DARROW_STATIC   -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_JSON -I'/opt/R-devel/lib/R/library/cpp11/include' -I/usr/local/include    -fpic  -Wall -pedantic -flto -c RTasks.cpp -o RTasks.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include -DARROW_STATIC   -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_JSON -I'/opt/R-devel/lib/R/library/cpp11/include' -I/usr/local/include    -fpic  -Wall -pedantic -flto -c altrep.cpp -o altrep.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include -DARROW_STATIC   -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_JSON -I'/opt/R-devel/lib/R/library/cpp11/include' -I/usr/local/include    -fpic  -Wall -pedantic -flto -c array.cpp -o array.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include -DARROW_STATIC   -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_JSON -I'/opt/R-devel/lib/R/library/cpp11/include' -I/usr/local/include    -fpic  -Wall -pedantic -flto -c array_to_vector.cpp -o array_to_vector.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include -DARROW_STATIC   -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_JSON -I'/opt/R-devel/lib/R/library/cpp11/include' -I/usr/local/include    -fpic  -Wall -pedantic -flto -c threadpool.cpp -o threadpool.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include -DARROW_STATIC   -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_JSON -I'/opt/R-devel/lib/R/library/cpp11/include' -I/usr/local/include    -fpic  -Wall -pedantic -flto -c type_infer.cpp -o type_infer.o
g++ -std=gnu++17 -shared -Wall -pedantic -flto -fpic -L/opt/R-devel/lib/R/lib -L/usr/local/lib -o arrow.so RTasks.o altrep.o array.o array_to_vector.o arraydata.o arrowExports.o bridge.o buffer.o chunkedarray.o compression.o compute-exec.o compute.o config.o csv.o dataset.o datatype.o expression.o extension-impl.o feather.o field.o filesystem.o io.o json.o memorypool.o message.o parquet.o r_to_arrow.o recordbatch.o recordbatchreader.o recordbatchwriter.o safe-call-into-r-impl.o scalar.o schema.o symbols.o table.o threadpool.o type_infer.o -L/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/lib -larrow_dataset -lparquet -larrow -larrow_bundled_dependencies -L/opt/R-devel/lib/R/lib -lR
/arrow/cpp/src/arrow/type.h:323: warning: virtual table of type ‘struct NestedType’ violates one definition rule [-Wodr]
  323 | class ARROW_EXPORT NestedType : public DataType, public ParametricType {
      | 
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:323:20: note: the conflicting type defined in another translation unit
  323 | class ARROW_EXPORT NestedType : public DataType, public ParametricType {
      |                    ^
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:177:22: note: virtual method ‘storage_id’
  177 |   virtual Type::type storage_id() const { return id_; }
      |                      ^
<built-in>: note: ought to match virtual method ‘__cxa_pure_virtual’ but does not
/arrow/cpp/src/arrow/type.h:288: warning: virtual table of type ‘struct FixedWidthType’ violates one definition rule [-Wodr]
  288 | class ARROW_EXPORT FixedWidthType : public DataType {
      | 
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:288:20: note: the conflicting type defined in another translation unit
  288 | class ARROW_EXPORT FixedWidthType : public DataType {
      |                    ^
/arrow/r/check/arrow.Rcheck/00_pkg_src/arrow/libarrow/arrow-10.0.1.9000/include/arrow/type.h:177:22: note: virtual method ‘storage_id’
  177 |   virtual Type::type storage_id() const { return id_; }
      |                      ^
<built-in>: note: ought to match virtual method ‘__cxa_pure_virtual’ but does not
lto-wrapper: warning: using serial compilation of 128 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information