Github actions error on Ubuntu installing a dependency

Package development
1

Github actions (both pkgdown and R CMD check) are failing on ubuntu for my "weird" package:

I'm using the latest workflow files from r-lib/actions.

I've isolated the problem as arising due to the installation of the R package interpolation which is a dependency. But the error message is unhelpful (at least to me):

2024-12-15T03:42:36.8920900Z make: *** [/opt/R/4.4.2/lib/R/etc/Makeconf:204: RcppExports.o] Error 1
2024-12-15T03:42:36.8921150Z ERROR: compilation failed for package ‘interpolation’

The system requirements for this package are "C++ 17, gmp". Could that be the issue? How to fix it?

2

I see a lot more output in the logs:

2024-12-15T06:07:36.2808005Z ℹ Building interpolation 0.1.1
2024-12-15T06:07:42.7306096Z ✖ Failed to build interpolation 0.1.1 (6.2s)
2024-12-15T06:07:44.9025898Z Error: 
2024-12-15T06:07:44.9026906Z ! error in pak subprocess
2024-12-15T06:07:44.9027492Z Caused by error in `stop_task_build(state, worker)`:
2024-12-15T06:07:44.9028137Z ! Failed to build source package interpolation.
2024-12-15T06:07:44.9028656Z Full installation output:
2024-12-15T06:07:44.9029529Z * installing *source* package ‘interpolation’ ...
2024-12-15T06:07:44.9030497Z ** package ‘interpolation’ successfully unpacked and MD5 sums checked
2024-12-15T06:07:44.9031776Z staged installation is only possible with locking
2024-12-15T06:07:44.9032348Z ** using non-staged installation
2024-12-15T06:07:44.9032715Z ** libs
2024-12-15T06:07:44.9033342Z using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
2024-12-15T06:07:44.9033872Z using C++17
2024-12-15T06:07:44.9036391Z g++ -std=gnu++17 -I"/opt/R/4.4.2/lib/R/include" -DNDEBUG  -I'/home/runner/work/_temp/Library/Rcpp/include' -I'/home/runner/work/_temp/Library/RcppCGAL/include' -I'/home/runner/work/_temp/Library/BH/include' -I/usr/local/include   -DCGAL_HEADER_ONLY=1  -fpic  -g -O2  -Wall -pedantic  -c RcppExports.cpp -o RcppExports.o
2024-12-15T06:07:44.9038826Z In file included from /home/runner/work/_temp/Library/BH/include/boost/cstdfloat.hpp:27,
2024-12-15T06:07:44.9040166Z                  from /home/runner/work/_temp/Library/BH/include/boost/multiprecision/detail/float128_functions.hpp:15,
2024-12-15T06:07:44.9041823Z                  from /home/runner/work/_temp/Library/BH/include/boost/multiprecision/detail/fpclassify.hpp:13,
2024-12-15T06:07:44.9043243Z                  from /home/runner/work/_temp/Library/BH/include/boost/multiprecision/detail/default_ops.hpp:15,
2024-12-15T06:07:44.9044719Z                  from /home/runner/work/_temp/Library/BH/include/boost/multiprecision/detail/generic_interconvert.hpp:12,
2024-12-15T06:07:44.9046089Z                  from /home/runner/work/_temp/Library/BH/include/boost/multiprecision/number.hpp:12,
2024-12-15T06:07:44.9047274Z                  from /home/runner/work/_temp/Library/BH/include/boost/multiprecision/cpp_int.hpp:19,
2024-12-15T06:07:44.9048380Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Quotient.h:37,
2024-12-15T06:07:44.9049625Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Kernel_d/Cartesian_const_iterator_d.h:20,
2024-12-15T06:07:44.9050889Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Homogeneous/VectorH2.h:23,
2024-12-15T06:07:44.9052298Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Homogeneous/predicates_on_directionsH2.h:22,
2024-12-15T06:07:44.9053675Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Homogeneous/DirectionH2.h:100,
2024-12-15T06:07:44.9054990Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Homogeneous/Homogeneous_base.h:29,
2024-12-15T06:07:44.9056243Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Simple_homogeneous.h:20,
2024-12-15T06:07:44.9057470Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Exact_kernel_selector.h:24,
2024-12-15T06:07:44.9058657Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Filtered_kernel.h:22,
2024-12-15T06:07:44.9060033Z                  from /home/runner/work/_temp/Library/RcppCGAL/include/CGAL/Exact_predicates_inexact_constructions_kernel.h:21,
2024-12-15T06:07:44.9061035Z                  from interpolation_types.h:7,
2024-12-15T06:07:44.9061913Z                  from RcppExports.cpp:4:
2024-12-15T06:07:44.9063448Z /home/runner/work/_temp/Library/BH/include/boost/math/cstdfloat/cstdfloat_cmath.hpp:714:16: warning: non-standard suffix on floating constant [-Wpedantic]
2024-12-15T06:07:44.9064753Z   714 |                else if (x == BOOST_FLOAT128_C(0.0))
2024-12-15T06:07:44.9065260Z       |                ^~~~
2024-12-15T06:07:44.9066965Z /home/runner/work/_temp/Library/BH/include/boost/math/cstdfloat/cstdfloat_cmath.hpp:717:16: warning: non-standard suffix on floating constant [-Wpedantic]
2024-12-15T06:07:44.9068488Z   717 |                if (::BOOST_CSTDFLOAT_FLOAT128_FABS(x) < BOOST_CSTDFLOAT_FLOAT128_MIN)
2024-12-15T06:07:44.9069121Z       |                ^~
...

and the RcppCGAL package was updated a couple of days ago, so probably that update broke interpolation. It also fails for me the same way on macOS, so this will be probably fixed by a new CRAN release of RcppCGAL.

Until then, you can use the older version of RcppCGAL on GitHub Actions, add RcppCGAL@5.6.4 to extra-packages in the setup-r-dependencies step.

Or, you can do nothing and wait until interpolation builds start failing on CRAN as well, and CRAN forces either interpolation or RcppCGAL to update. This will probably takes weeks, though.

1 Like