Update vendored abseil-cpp

[paleolimbot]

This extracts the abseil component of #249 an uses it to update the vendored Abseil version.

The current code vendors a bunch of source files from an old version of abseil-cpp...this has resulted in some challenges since abseil-cpp is not really intended to be built in this way (although it has been delightfully stable for many years). Unfortunately, this prevents us from updating S2 because updated S2 won't build against our very old version of Abseil ( #257 ).

This PR updates the code to use (1) abseil via pkg-config (works on MacOS, Linux, and Windows), and (2) by using CMake to build the vendored abseil-cpp. This also works on MacOS, Linux, and Windows, (although it requires cmake). Abseil is available on MacOS via brew install abseil, apt-get install libabsl-dev on Ubuntu (maybe only since 22.04 LTS), and abseil-cpp-devel on Fedora (Haven't tested yet).

On Windows specifically, the checks that CRAN performs will always use abseil-cpp from RTools. For older versions, it will use cmake to do build the local version (may need some workshopping...it currently works but I am not sure of the details).

[paleolimbot]

@edzer I think this is ready...what do you think?

[edzer]

Wow, that looks like a massive overhaul, great!

We now get the NOTE

* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential

did you try without specifying C++14, or shall I try to do so?

[paleolimbot]

This should be using C++17...which platform is giving the C++14 note?

(I think the newest version of S2 requires C++17 anyway, but one constraint of using "system" abseil is that we have to build with the same C++ standard that Abseil was built against, which we should maybe have a test compile to check for).

[edzer]

This should be using C++17...which platform is giving the C++14 note?

Sorry, I hadn't checked out the branch correctly.

[paleolimbot]

If you're generally on board, I'll clean this up and merge, then work on updating s2. After all that, we'll probably need some configure script modifications to make sure this works everywhere (and update the install/development instructions to ensure that isn't too painful).

[edzer]

I now see:

* checking C++ specification ... OK
  Not all R platforms support C++17

which is not a NOTE but only a message (but may bite use nevertheless on some CRAN platform), but also

* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.

which you tried to address in DESCRIPTION, so let's leave it like it is. I'm running it through win-builder / r-devel now.

[edzer]

Fantastic, good to go!!

[edzer]

FYI - on Ubuntu 22.04, after apt-get installing libabsl-dev, I see at the end:

   g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o s2.so 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 wk-impl.o -Ls2 -ls2static -Wl -labsl_cord -labsl_raw_hash_set -labsl_hashtablez_sampler -labsl_exponential_biased -labsl_synchronization -labsl_graphcycles_internal -labsl_stacktrace -Wl -labsl_symbolize -labsl_malloc_internal -labsl_time -labsl_civil_time -labsl_time_zone -labsl_hash -labsl_city -labsl_bad_optional_access -labsl_bad_variant_access -labsl_wyhash -labsl_str_format_internal -labsl_strings -labsl_strings_internal -labsl_int128 -labsl_throw_delegate -labsl_demangle_internal -Wl -labsl_base -labsl_spinlock_wait -labsl_debugging_internal -labsl_raw_logging_internal -labsl_log_severity -l:libssl.so.3 -l:libcrypto.so.3 -L/usr/lib/R/lib -lR
   g++: error: unrecognized command-line option ‘-Wl’; did you mean ‘-W’?
   g++: error: unrecognized command-line option ‘-Wl’; did you mean ‘-W’?
   g++: error: unrecognized command-line option ‘-Wl’; did you mean ‘-W’?
   make[1]: *** [/usr/share/R/share/make/shlib.mk:10: s2.so] Error 1
   make[1]: Leaving directory '/home/edzer/git/s2/src'
   ERROR: compilation failed for package ‘s2’

and earlier:

ℹ Re-compiling s2 (debug build)
── R CMD INSTALL ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  installing *source* package ‘s2’ ...
   ** using staged installation
   Found pkg-config cflags and libs!
   Testing compiler using PKG_CFLAGS=
   -Wl -labsl_base -labsl_raw_logging_internal -labsl_log_severity -labsl_spinlock_wait
   ** Using abseil-cpp from pkg-config
   :/home/edzer/git/s2/tools/pkgconfig
   Using PKG_LIBS=-Wl -labsl_cord -labsl_raw_hash_set -labsl_hashtablez_sampler -labsl_exponential_biased -labsl_synchronization -labsl_graphcycles_internal -labsl_stacktrace -Wl -labsl_symbolize -labsl_malloc_internal -labsl_time -labsl_civil_time -labsl_time_zone -labsl_hash -labsl_city -labsl_bad_optional_access -labsl_bad_variant_access -labsl_wyhash -labsl_str_format_internal -labsl_strings -labsl_strings_internal -labsl_int128 -labsl_throw_delegate -labsl_demangle_internal -Wl -labsl_base -labsl_spinlock_wait -labsl_debugging_internal -labsl_raw_logging_internal -labsl_log_severity -l:libssl.so.3 -l:libcrypto.so.3
   Using PKG_CFLAGS=  -DOPENSSL_SUPPRESS_DEPRECATED -DIS_LITTLE_ENDIAN

this is

Get:1 http://de.archive.ubuntu.com/ubuntu jammy/main amd64 libabsl-dev amd64 0~20210324.2-2 [918 kB]

maybe a too old version of absl?

[paleolimbot]

Not all R platforms support C++17

We can try a few things here if this is a problem...the main thing is that the Abseil dependency and the s2 R package need to use the same C++ standard, and it's easier if we just say it's C++17 everywhere. When we update s2 that might add a constraint as well so I think that issue should be punted until those files are also swapped out.

GNU make is a SystemRequirements.

That's a great point...I think we can fix that by deleting the cmake build directory (which is the tool that generates the offending makefiles). Keeping the build directory was sort of nice for development if you didn't have a system abseil (most stable-track linux distros), but I think I've rigged it so that you can do tools/build_absl.sh path/to/somwhere + R_S2_ABSL_HOME=path/to/somewhere as a workaround.

[paleolimbot]

maybe a too old version of absl?

Probably...I should add a version check. What does pkg-config absl_base --libs get you? (It seems like it's getting you something invalid)

[edzer]

What does pkg-config absl_base --libs get you?

$ pkg-config absl_base --libs
-Wl -labsl_base -labsl_raw_logging_internal -labsl_log_severity -labsl_spinlock_wait

[paleolimbot]

I've added a minimum version to the .pc file such that it will at least reject the version present on 22.04...it seems strange that pkg-config gives invalid flags but I also don't think that "system" abseil has been around for very long and maybe just nobody uses it (or always uses it via cmake).

Before a release we will need to add some docker-compose checks to ensure this will actually work with the system-provided abseil when it's detected.

[paleolimbot]

Here goes nothing!