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

(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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