Build failure on M2 Mac with conda-forge r-base

[wakelin-g]

Hi there,

In a fresh conda environment with conda-forge r-base 4.3.2, RProtoBufLib fails to build. First, this is raised:

checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized

followed ultimately by:

In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:10:10: fatal error: 'google/protobuf/port_def.inc' file not found
   10 | #include <google/protobuf/port_def.inc>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [Makevars:15: libGatingSet.pb] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’

I think the root of the error is similar to that reported in grimbough/Rhdf5lib#54, as running

unset host_alias
unset build_alias

prior to building prevents the error from being raised.

Full trace

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'BiocVersion', 'RProtoBufLib'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocVersion_3.18.1.tar.gz'
Content type 'application/x-gzip' length 973 bytes
==================================================
downloaded 973 bytes

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/RProtoBufLib_2.14.0.tar.gz'
Content type 'application/x-gzip' length 2976515 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package ‘BiocVersion’ ...
** using staged installation
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocVersion)
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for arm64-apple-darwin20.0.0-gcc... arm64-apple-darwin20.0.0-clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether arm64-apple-darwin20.0.0-clang accepts -g... yes
checking for arm64-apple-darwin20.0.0-clang option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether arm64-apple-darwin20.0.0-clang++ -std=gnu++17 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... Invalid configuration `arm64-apple-darwin20.0.0': machine `arm64-apple' not recognized
configure: error: /bin/sh ./config.sub arm64-apple-darwin20.0.0 failed
make: *** No rule to make target 'install'.  Stop.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘clang version 17.0.6’
using C++11
using SDK: ‘MacOSX14.2.sdk’
arm64-apple-darwin20.0.0-clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -fPIC -I../inst/include/ -I/private/var/folders/zj/tndd8h_93y37yt6k7p1zwkg00000gn/T/RtmpqxSL3k/R.INSTALLeb02701f885c/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.dylib GatingSet_pb_lib/GatingSet.pb.cc
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:10:10: fatal error: 'google/protobuf/port_def.inc' file not found
   10 | #include <google/protobuf/port_def.inc>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [Makevars:15: libGatingSet.pb] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/Users/griffen/mambaforge/envs/temp/lib/R/library/RProtoBufLib’