Re: r-base215. r-base-30 and r-base31

Okay, I now see that disables the use of pcre. Guess someone should open a
PR upstream, no? Do we really gain anything of use by having R-base build
against pcre?

On Tuesday, April 29, 2014, Jack Howarth <[email protected]> wrote:

> Well, empirically it fixed the r-base214 build on 10.8 for me by just
> changing --with-system-pcre to --with-pcre=%p. It would be highly irregular
> for the --with-system-pcre option not to be pushing the headers in
> /usr/include to be used.
>
> On Tuesday, April 29, 2014, Daniel Macks <[email protected]> wrote:
>
> (sorry if this email goes out twice!)
>
> I don't think that's the meaning of "system". R appears to have optional
> onboard/internal sources of various dependencies as an alternative to using
> ones existing "on the system". *Where* on the system is a different issue.
> You can probably check the .d files to see exactly which headers are being
> loaded to see if it's matched.
> dan
>
> On Tue, 29 Apr 2014 13:21:08 -0400, Jack Howarth <
> [email protected]> wrote:
> Isn't this just a header mismatch? We have both a build depends on
> libpcre1 and --with-system-pcre which is illogical. I am testing with
> --with-system-pcre changed to --with-pcre=%p. FYI, macports doesn't pass
> either flag and incorrectly ignores pcre.
>
>
> On Tuesday, April 29, 2014, Daniel Macks <[email protected]> wrote:
>
>        Using (apparently-)undocumented, internal implementation details
> that are known to change in different versions is *always* a problem. Any
> solution that doesn't involve actually not-doing-that is merely deferring
> the same failure from occurring again in the future when those details
> change again. dan
>
> On Tue, 29 Apr 2014 13:12:14 -0400, Jack Howarth <
> [email protected]> wrote:
> Daniel,      Isn't the real problem that r-base in fink is being built
> with --with-system-pcre but the fink lib pcre.1.dylib ends up linked into
> libR. I assume we need a BuildConflicts on libpcre1 in order to have the
> system pcre used.                                Jack
>
> On Tuesday, April 29, 2014, Daniel Macks <[email protected]> wrote:
>
>        On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks <
> [email protected]> wrote:
> On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
>
>        <[email protected]> wrote:
> > The r-base214 packaging seems to have test suite issues when built >
> against Xcode 5.1 on darwin12…
> >
> > Testing examples for package ‘utils’
> > /sw/src/fink.build/r-base214-2.14.2-9/R-2.14.2/bin/BATCH: line 60: >
> 34097 Trace/BPT trap: 5       ${R_HOME}/bin/R -f ${in} ${opts} >
> ${R_BATCH_OPTIONS} > ${out} 2>&1
> >  Error: testing 'utils' failed
> > Execution halted
>
> The failure appears to be due to an unresolved __pcre_valid_utf (or
> similarly  named) symbol in libR.dylib. The R library is trying to use a
> private  symbol in libpcre by guessing what it's called (and what its
> parameters  are) in various different libpcre versions, but our most recent
> libpcre dropped  that symbol altogether. Obviously a fragile situation to
> rely on  undocumented non-public content. One useful change we can make is
> to patch out the "-undefined  dynamic_lookup" from the configure script.
> That flag causes undefined  symbols to be ignored by the linker, leaving
> them to cause problems at  runtime. By removing the flag, the linking
> itself fails right away  rather than leaving a possibly mis-built library.
> ..which reveals that util.dylib is missing -llzma in even in r-base30 and
> r-base31 (ones that do not have the pcre problem). dan
>
>  --
> Daniel Macks
> [email protected]
>
> -------------------------
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> Daniel Macks
> [email protected]
>
> -------------------------
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