[R-pkg-devel] R package build- C compilation issue related to math.h

[Andrew Simmons]

You could install VirtualBox if you wanted to test it yourself, or if you
have the tarball available online somewhere, I can try building it.

On Wed., Oct. 19, 2022, 19:57 Vincent Plagnol, <vincent.plagnol using gmail.com>
wrote:

> Dear all at R-package-devel,
>
> I am struggling with a R package build.
> It builds fine on my mac, which is my usual work environment. But when I
> submit to CRAN, while the windows version is fine, the debian version fails
> with a cryptic message:
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> ** installing *source* package ‘ExomeDepth’ ...** using staged
> installation** libsg++-12  -std=gnu++14 -I"/home/hornik/tmp/R/include"
> -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT
> -D_FORTIFY_SOURCE=2   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c
> CNV_estimate.cpp -o CNV_estimate.ogcc-12  -I"/home/hornik/tmp/R/include"
> -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT
> -D_FORTIFY_SOURCE=2   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic
> -mtune=native  -c ExomeDepth_init.c -o ExomeDepth_init.ogcc-12
>  -I"/home/hornik/tmp/R/include" -DNDEBUG   -I/usr/local/include
> -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=2   -fpic  -g -O2 -Wall
> -Wstrict-prototypes -pedantic -mtune=native  -c VP_gamma.c -o VP_gamma.oIn
> file included from gsl_math.h:22,                 from
> VP_gamma.c:23:/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error:
> expected ‘;’ before ‘extern’   85 | __MATHCALL_VEC (acosh,, (_Mdouble_
> __x));      |
> ^~~~~~~~~~~~~~/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error:
> expected ‘;’ before ‘extern’   87 | __MATHCALL_VEC (asinh,, (_Mdouble_
> __x));      | ^~~~~~~~~~~~~~*
>
>
> It is painful to debug because I don't have a debian machine. Furthermore
> the issue seems to be in the file called at line 22 of gsl_math.sh which is
> #include <math.h>
> These are rather arcane (to me) building blocks of C and I don't get why it
> would suddenly create some issue on Debian (but not on mac or windows).
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> My issue is perhaps that I copied substantial amount of the GSL library (as
> opposed to using it as dependency) but it would be painful to do otherwise
> now (this is an old package that has started to complain only recently).
>
> Any and all advice is welcome to help me interpret what I see here.
>
> Thanks,
>
> Vincent
>
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