Re: [Fink-devel] r-base215. r-base-30 and r-base31
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
--
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dma...@netspace.org
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks dma...@netspace.org
wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
dma...@netspace.org
--
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
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
howarth.at.f...@gmail.com 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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks
dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
dma...@netspace.org
-
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks
dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
--
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dma...@netspace.org
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Re: [Fink-devel] 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
howarth.at.f...@gmail.com 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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks
dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
dma...@netspace.org
-
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks
dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
--
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dma...@netspace.org
-
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Re: [Fink-devel] 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 howarth.at.f...@gmail.com 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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks
dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
dma...@netspace.org
-
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
Why would they want a bug report against such an old version? Are newer
versions not-broken? I'm pretty sure I already mentioned exactly what
change they made in newer versions to avoid trying to access the
internals of the external libpcre.
dan
On Tue, 29 Apr 2014 13:44:34 -0400, Jack Howarth
howarth.at.f...@gmail.com wrote:
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 howarth.at.f...@gmail.com 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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks
dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
--
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
My mistake. I thought you had said the problem existed in the newer
versions but was latent rather than fixed.
On Tuesday, April 29, 2014, Daniel Macks dma...@netspace.org wrote:
Why would they want a bug report against such an old version? Are newer
versions not-broken? I'm pretty sure I already mentioned exactly what
change they made in newer versions to avoid trying to access the internals
of the external libpcre.
dan
On Tue, 29 Apr 2014 13:44:34 -0400, Jack Howarth
howarth.at.f...@gmail.com wrote:
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 howarth.at.f...@gmail.com
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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org 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
howarth.at.f...@gmail.com 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 dma...@netspace.org wrote:
On Mon, 28 Apr 2014 22:38:02 -0400, Daniel Macks
dma...@netspace.org wrote:
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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
dma...@netspace.org
-
--
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[Fink-devel] r-base215. r-base-30 and r-base31
Baba,
I have added r-base31 packaging to the 10.7 tree and updated the
r-base215 and r-base30 packaging to build with gcc49-compiler like r-base31
and to be aware of the new package. 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} 21
Error: testing 'utils' failed
Execution halted
There are quite a few differences between the r-base214 and r-base215 info
files so I am not sure what is the exact cause of the build issue. However,
since upstream no longer lists the 2.14.x series as supported on their home
page, we should just drop that package like we did with r-base213.
Jack
ps I also modified the rnmr-r.info file to be aware of the new r-base31
release and it builds fine against it.
--
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
Jack,
2014/04/29 9:55、Jack Howarth howarth.at.f...@gmail.com のメール：
I have added r-base31 packaging to the 10.7 tree and updated the
r-base215 and r-base30 packaging to build with gcc49-compiler like r-base31
and to be aware of the new package. 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} 21
Error: testing 'utils' failed
Execution halted
There are quite a few differences between the r-base214 and r-base215 info
files so I am not sure what is the exact cause of the build issue. However,
since upstream no longer lists the 2.14.x series as supported on their home
page, we should just drop that package like we did with r-base213.
Jack
ps I also modified the rnmr-r.info file to be aware of the new r-base31
release and it builds fine against it.
Thanks. I’ve have been too busy to commit r-base31.
We can drop 2.14, though some people may still be interested in 2.15.
FYI, there are several reports to R-SIG-Mac mailing list that some CRAN
packages do not work on R 3.1+Marvericks combination. Maybe because Marvericks
uses libc++ instead of libstdc++, but I haven’t looked yet.
https://stat.ethz.ch/pipermail/r-sig-mac/2014-April/thread.html
—
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Re: [Fink-devel] r-base215. r-base-30 and r-base31
On Mon, 28 Apr 2014 20:55:18 -0400, Jack Howarth
howarth.at.f...@gmail.com 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} 21
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.
There are quite a few differences between the r-base214 and r-base215
info files so I am not sure what is the exact cause of the build
issue. However, since upstream no longer lists the 2.14.x series as
supported on their home page, we should just drop that package like
we did with r-base213.
Looks like R now (as of 215) contains the actual internal pcre code it
wants (copied from pcre's sources), so it becomes insensitive to
changes in libpcre's internals. compare src/main/util.c around line
2159, and see the new valid_utf.h file added to support it.
dan
--
Daniel Macks
dma...@netspace.org
--
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