installation fails on Alpine Linux

[bastistician]

In my Alpine Linux system, compilation of 'rxode2ll' fails with the dubious error

/usr/include/fortify/stdlib.h:23:15: fatal error: stdlib.h: No such file or directory

(The complete error message is attached below.)

The error seems to be related to the use of -isystem rather than -I to specify header locations, probably resulting in a problematic include order, at least on this system. I see that 'rxode2ll' already has a "workaround" for Windows, where it will use -I rather than -isystem and I can confirm that this would also fix installation on Alpine Linux:

diff --git a/inst/tools/workaround.R b/inst/tools/workaround.R
index ed779f8..e1d35b8 100644
--- a/inst/tools/workaround.R
+++ b/inst/tools/workaround.R
@@ -21,7 +21,7 @@ if (.Platform$OS.type == "windows" && !file.exists("src/Makevars.win")) {
   close(file.out)
 } else {
   file.out <- file("src/Makevars", "wb")
-  writeLines(gsub("@ISYSTEM@", "isystem", .in),
+  writeLines(gsub("@ISYSTEM@", if (R.version$os == "linux-musl") "I" else "isystem", .in),
              file.out)
   close(file.out)
 }

error log

g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG  -I'/home/runner/R-patched/lib/Rcpp/include' -I'/home/runner/R-patched/lib/RcppEigen/include' -I'/home/runner/R-patched/lib/StanHeaders/include' -I'/home/runner/R-patched/lib/BH/include' -I'/home/runner/R-patched/lib/RcppParallel/include' -I/usr/local/include   -fopenmp -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/home/runner/R-patched/lib/BH/include" -isystem"/home/runner/R-patched/lib/RcppEigen/include" -isystem'/home/runner/R-patched/lib/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW   -isystem/usr/include -DTBB_INTERFACE_NEW -isystem'/home/runner/R-patched/lib/StanHeaders/include/src'  -isystem"/home/runner/R-patched/lib/Rcpp/include" -fpic  -O2 -mtune=native -D__MUSL__ -Wno-ignored-attributes   -c RcppExports.cpp -o RcppExports.o
In file included from /usr/include/c++/13.2.1/cstdlib:79,
                 from /usr/include/c++/13.2.1/ext/string_conversions.h:43,
                 from /usr/include/c++/13.2.1/bits/basic_string.h:4109,
                 from /usr/include/c++/13.2.1/string:54,
                 from /usr/include/c++/13.2.1/bits/locale_classes.h:40,
                 from /usr/include/c++/13.2.1/bits/ios_base.h:41,
                 from /usr/include/c++/13.2.1/streambuf:43,
                 from /usr/include/c++/13.2.1/bits/streambuf_iterator.h:35,
                 from /usr/include/c++/13.2.1/iterator:66,
                 from /home/runner/R-patched/lib/RcppEigen/include/RcppEigenForward.h:25,
                 from /home/runner/R-patched/lib/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/usr/include/fortify/stdlib.h:23:15: fatal error: stdlib.h: No such file or directory
   23 | #include_next <stdlib.h>
      |               ^~~~~~~~~~
compilation terminated.

[bastistician]

Fixed via #8.

[mattfidler]

Thanks @bastistician

[mattfidler]

Updated on CRAN