On Sat, 8 Feb 2020 at 23:50, Dirk Eddelbuettel <e...@debian.org> wrote:
>
>
> On 8 February 2020 at 22:36, Iñaki Ucar wrote:
> | lme4 fails to compile with this misterious message in Fedora Rawhide
> | with gcc10 (see the build log and more details in [1]). There is no
> | "fun" in lme4, but there are several local definitions of "fun" in
> | RcppEigen, used by lme4, under inst/include/RcppEigenStubs.h. These
>
> Shouldn't what is in RcppEigen be protected by namespaces?
>
> Also, the ever-vigilant Prof Ripley emailed dozens of people last year about
> gcc10 changes (for C, though). If this were systemic I cam sure we'd hear
> from him.
Prof. Ripley was probably looking for issues listed in the gcc 10
porting guide (omissions of "extern" in C, and argument mismatches in
Fortran). This is about C linkage in a C++ package, and a quite
strange error: lme4 is the only package on CRAN showing this issue
with RcppEigen, so maybe it went unnoticed.
> | are the relevant lines from the assembler output:
> |
> | fun:
> | .zero 8
> | .section .rodata
> | .LC5:
> | .string "cholmod_free_factor"
> |
> | ...
> |
> | fun:
> | .zero 8
> | .section .rodata
> | .LC8:
> | .string "cholmod_start"
> |
> | So it seems that, unless lme4 is doing something improper in
> | src/lme4CholmodDecomposition.h, this is a bug in RcppEigen due to the
> | use of inline and static (or in gcc 10?). Thoughts? Should I open an
> | issue in RcppEigen?
>
> Better yet, provide a fix?
I'd be more than happy to provide a fix, but I have no clue about
what's happening here, why gcc 10 generates duplicated symbols for
these functions (where previous versions did not), and where is the
issue to fix (lme4, RcppEigen or even gcc 10). And that's why I'm
posting here.
> You're the one with a reproducible system :)
How so, gcc 10 is all it's needed. And Fedora Rawhide can be used
through docker to avoid the burden of installing a new toolchain:
$ docker run -it --rm fedora:rawhide
$ dnf install R
$ Rscript -e 'install.packages("lme4", repos="https://cloud.r-project.org";)'
Iñaki
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