Re: CNEr does not build
Hi Martin,
On Tue, May 29, 2018 at 12:50:35PM -0400, Martin Morgan wrote:
> For what it's worth, R will not create a configure file from configure.ac on
> package install, so the presence of configure.ac seems to be a red herring
> -- there is no point in patching configure.ac or to search for
> src/Makevars.in, since neither of these are used.
Thanks for the hint.
> For me
>
> R CMD build CNEr && R CMD INSTALL CNEr*gz
>
> compiles and installs 'as expected'.
>
> Of course one wonders why configure.ac is present if not used, or vv for
> configure, src/Makevars.in
After I removed configure.ac it builds for me. Thanks a lot for the hint.
However, I insist that this
$ grep -Ri cpEndTarget src/*
src/alignment.c: int nrGapsTarget, nrGapsQuery, cpStartTarget, cpEndTarget, cpStartQuery, cpEndQuery;
src/alignment.c: cpEndTarget = 0;
src/alignment.c: cpENdTarget = j;
looks highly suspicious and this
$ grep -R "INTEGER(newqStart)" src/*
src/alignment.c: INTEGER(newqStart) = j + INTEGER(axtqStart)
as well. I have no idea how this can be build by any C compiler and
would strongly recommend to consider (or enhance) this patch[1].
Kind regards and thanks again for your help
Andreas.
[1] https://salsa.debian.org/r-pkg-team/r-bioc-cner/blob/master/debian/patches/fix_syntax.patch
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