Re: CNEr does not build

[Martin Morgan <martin.morgan@roswellpark.org>]

On 05/30/2018 08:57 AM, Andreas Tille wrote:
> 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].

src/alignment.c isn't mentioned in Makevars / Makevars.common and so is 
not compiled (I agree, it couldn't be!) -- another file that should be 
removed.

> 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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