r-spatial / r-spatial/s2

Unable to Compile using R CMD INSTALL on Openbsd 7.5

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C++
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Description

Hello,

I am trying to compile on Openbsd 7.5 arm64 and am not able to. I cannot find the specific error to try and fix it. I received 5 warnings, which generally don't stop compilation, and one error. The error is not helpful for me to try and correct. Any help or suggestions would be greatly appreciated. My output is pasted below. Thank you in advance.

Running R CMD build...

  • checking for file '/tmp/Rtmp6MJRxP/remotesf69769fecab/r-spatial-s2-3ac03ff/DESCRIPTION' ... OK
  • preparing 's2':
  • checking DESCRIPTION meta-information ... OK
  • cleaning src
  • running 'cleanup'
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
    Removed empty directory 's2/vignettes'
  • building 's2_1.1.7.tar.gz'
  • installing source package 's2' ...
    ** using staged installation
    Found pkg-config cflags and libs!
    Testing compiler using PKG_CFLAGS=
    rm: src/main.exe: No such file or directory
    Using PKG_LIBS=-lssl -lcrypto
    Using PKG_CFLAGS= -DIS_LITTLE_ENDIAN
    ** libs
    c++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/wk/include' -I/usr/local/include -DIS_LITTLE_ENDIAN -pthread -fpic -O2 -pipe -c absl/base/internal/cycleclock.cc -o absl/base/internal/cycleclock.o
    c++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/wk/include' -I/usr/local/include -DIS_LITTLE_ENDIAN -pthread -fpic -O2 -pipe -c absl/base/internal/low_level_alloc.cc -o absl/base/internal/low_level_alloc.o
    In file included from absl/base/internal/low_level_alloc.cc:24:
    In file included from ../src/absl/base/call_once.h:34:
    In file included from ../src/absl/base/internal/invoke.h:64:
    ../src/absl/meta/type_traits.h:301:36: warning: builtin __has_trivial_destructor is deprecated; use
    __is_trivially_destructible instead [-Wdeprecated-builtins]
    : std::integral_constant<bool, __has_trivial_destructor(T) &&
    ^
    ../src/absl/meta/type_traits.h:350:36: warning: builtin __has_trivial_constructor is deprecated; use
    __is_trivially_constructible instead [-Wdeprecated-builtins]
    : std::integral_constant<bool, __has_trivial_constructor(T) &&
    ^
    ../src/absl/meta/type_traits.h:494:17: warning: builtin __has_trivial_assign is deprecated; use
    __is_trivially_assignable instead [-Wdeprecated-builtins]
    bool, __has_trivial_assign(typename std::remove_reference::type) &&
    ^
    ../src/absl/meta/type_traits.h:559:8: warning: builtin __has_trivial_copy is deprecated; use
    __is_trivially_copyable instead [-Wdeprecated-builtins]
    (__has_trivial_copy(ExtentsRemoved) || !kIsCopyOrMoveConstructible) &&
    ^
    ../src/absl/meta/type_traits.h:560:8: warning: builtin __has_trivial_assign is deprecated; use
    __is_trivially_assignable instead [-Wdeprecated-builtins]
    (__has_trivial_assign(ExtentsRemoved) || !kIsCopyOrMoveAssignable) &&
    ^
    5 warnings generated.
    c++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/wk/include' -I/usr/local/include -DIS_LITTLE_ENDIAN -pthread -fpic -O2 -pipe -c absl/base/internal/raw_logging.cc -o absl/base/internal/raw_logging.o
    absl/base/internal/raw_logging.cc:205:3: error: use of undeclared identifier 'syscall'
    syscall(SYS_write, STDERR_FILENO, s, len);
    ^
    1 error generated.
    gmake: *** [/usr/local/lib/R/etc/Makeconf:174: absl/base/internal/raw_logging.o] Error 1
    ERROR: compilation failed for package 's2'
  • removing '/usr/local/lib/R/library/s2'
    Warning message:
    In i.p(...) :
    installation of package '/tmp/Rtmp6MJRxP/filef69753cdc09f/s2_1.1.7.tar.gz' had non-zero exit status

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with absl/base/internal/raw_logging.cc at the syscall(SYS_write, ...) call and compare the OpenBSD 7.5 arm64 build context shown in the log. Trace the package's bundled absl sources and R CMD INSTALL build configuration; done means s2 installs successfully on that platform without the compilation error.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, r
Domain
build-system, operating-systems
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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