Re: [Fink-devel] R-3.3 packages
On 5/28/16 5:20 PM, 美彦 馬場 wrote: > Dear all, > > May I update R related packages that are in libs/rmods to be used with the > latest r-base33? > > Most of them have no maintainer, but some maitained by David Fang and myself. > > I will also update to the latest versions. There's no problem with updating any unmaintained package with a R-3.3 variant (assuming it builds). Hanspeter -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] R-3.3 packages
Dear all, May I update R related packages that are in libs/rmods to be used with the latest r-base33? Most of them have no maintainer, but some maitained by David Fang and myself. I will also update to the latest versions. -- BABA Yoshihiko -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] r-base hardcodes full path to sed that's used at buildtime
Hanspeter, 2014/06/14 11:43、Hanspeter Niederstrasser f...@snaggledworks.com のメール： When building another pkg that uses r-base30, I get this error: -- Using R at /sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R /sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R: line 191: /sw/bin/sed: No such file or directory ERROR: option '-e' requires a non-empty argument -- R architecture is -- Looking for R_HOME /sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R: line 191: /sw/bin/sed: No such file or directory ERROR: option '-e' requires a non-empty argument CMake Error at rkward/rbackend/FindR.cmake:32 (MESSAGE): Could NOT determine R_HOME (probably you misspecified the location of R) Call Stack (most recent call first): rkward/rbackend/CMakeLists.txt:1 (INCLUDE) I’ve fixed R script to use /usr/bin/sed for r-base31, r-base30 and r-base215 on 10.7 tree. Please update and try again. — BABA Yoshihiko -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] r-base hardcodes full path to sed that's used at buildtime
When building another pkg that uses r-base30, I get this error: -- Using R at /sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R /sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R: line 191: /sw/bin/sed: No such file or directory ERROR: option '-e' requires a non-empty argument -- R architecture is -- Looking for R_HOME /sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R: line 191: /sw/bin/sed: No such file or directory ERROR: option '-e' requires a non-empty argument CMake Error at rkward/rbackend/FindR.cmake:32 (MESSAGE): Could NOT determine R_HOME (probably you misspecified the location of R) Call Stack (most recent call first): rkward/rbackend/CMakeLists.txt:1 (INCLUDE) Package manager version: 0.37.0 Distribution version: selfupdate-cvs Thu Jun 12 19:48:20 2014, 10.7, x86_64 Trees: local/main local/nieder/10.4/main stable/main local/nieder/3rdparty/main local/nieder/10.7/main local/injected Xcode.app: 4.6.3 Xcode command-line tools: 4.6.0.0.1.1365549073 Max. Fink build jobs: 8 Hanspeter -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
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
--
Daniel Macks
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
--
Daniel Macks
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
--
Daniel Macks
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
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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
--
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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
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[Fink-devel] r-base215-2.15.2-1
Baba,
Is it okay if I update the r-base215 packaging with the change...
--- r-base215.info 2012-10-09 09:20:22.0 -0400
+++ /sw/fink/10.7/local/main/finkinfo/r-base215.info2012-12-07
20:20:54.0 -0500
@@ -1,14 +1,14 @@
Info2:
Package: r-base215
-Version: 2.15.0
-Revision: 5
+Version: 2.15.2
+Revision: 1
Description: R Framework
Maintainer: BABA Yoshihiko babayoshih...@mac.com
Depends: %N-shlibs (=%v-%r)
-BuildDepends: bzip2-dev, cairo, glib2-dev, gcc47-compiler, libgettext8-dev,
libiconv-dev, libncurses5, libjpeg8, libpng15, pango1-xft2-ft219-dev, pcre,
pkgconfig, readline5, tcltk-dev, x11-dev, fink (= 0.28.1),
fink-package-precedence, flag-sort, glitz
+BuildDepends: bzip2-dev, cairo, glib2-dev, gcc47-compiler, libgettext8-dev,
libiconv-dev, libncurses5, libjpeg8, libpng15, pango1-xft2-ft219-dev, pcre,
pkgconfig, readline5, tcltk-dev, x11-dev, fink (= 0.28.1),
fink-package-precedence, flag-sort (= 0.5), glitz
Source: http://cran.r-project.org/src/base/R-2/R-%v.tar.gz
-Source-MD5: 905f638990492618559202cc1e48a867
+Source-MD5: 346d16bab26fcae15e53755be8a69b00
PatchFile: %n.patch
PatchFile-MD5: 81f9fc3bc5834d89b1472b71ce799f9f
# PatchScript: sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
...to update it to the latest upstream release. Also all of the r-base21x info
files need the (= 0.5) dependency added
for flag-sort BuildDepends to insure that /opt/X11 isn't used instead of /sw
for X11 components on 10.8 (as discussed in
the x11 graphics from r-base on 10.8? thread on the fink-users mailing list).
Jack
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[Fink-devel] r-base213 -m failures on Lion
Baba, The current r-base213 package fails -m during its InfoTest on Mac OS X 10.7 against Xcode 4.3.2 in 10.7 fink (whereas r-base213 in 10.6 x86_64 fink passes -m fine against Xcode 4.2). i can't test this until later tonight but there is a bugzilla... https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14685 which suggests that the 2.13.x series has problems on Lion with VecLib. While the bugzilla indicates this doesn't exist in the 2.14 series, it is unclear if the fix was identified and backported to the 2.13 branch. If not, perhaps removing... --with-blas=-framework vecLib -dylib_file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib:/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib on 10.7 and replacing it with the bundled R-blas would fix the Lion regressions for r-base312. I notice that MacPorts older 2.13.1 packaging wasn't using VecLib... https://trac.macports.org/browser/trunk/dports/math/R/Portfile?rev=85597 Jack ps We also need to update the r-base214 packaging in both 10.4 and 10.7 stable so that the perl change... perl -pi -e s,Resources,Versions/$FW_VER/Resources,g Library/Frameworks/R.framework/Resources/bin/R is in place. The current r-base214-2.14.0-6 packaging has R from the r-base214 split-off hard-coded to use the files obtained from the symlinks in the r-base package. This means that 1) r-base must be installed for the R in r-base214 to work (which is not the desired behavior) and 2) if an r-base from a different r-base21x release is installed, the R from r-base214 will be broken because it uses files from the wrong r-base release. This is fixed in... http://sourceforge.net/tracker/?func=detailaid=3517612group_id=17203atid=414256 -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] R and its packages
Hi all, I installed r-base, then tried to install its packages inside R environment, with the error below. The binary version of R didn't have such error. Would it be Fink's problem? R version 2.11.0 (2010-04-22) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. install.packages(sp) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://essrc.hyogo-u.ac.jp/cran/src/contrib/sp_0.9-69.tar.gz' Content type 'application/x-gzip' length 536637 bytes (524 Kb) opened URL == downloaded 524 Kb * installing *source* package ‘sp’ ... ** libs gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c Rcentroid.c -o Rcentroid.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c gcdist.c -o gcdist.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c pip.c -o pip.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c pip2.c -o pip2.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c sp_xports.c -o sp_xports.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c surfaceArea.c -o surfaceArea.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c zerodist.c -o zerodist.o gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -F/sw/Library/Frameworks/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation ld: warning: in /sw/Library/Frameworks/R.framework/R, file was built for i386 which is not the architecture being linked (x86_64) ld: warning: in /sw/lib/libintl.dylib, file was built for i386 which is not the architecture being linked (x86_64) installing to /sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs ** R ** data ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so': dlopen(/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so, 6): no suitable image found. Did find: /sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so: mach-o, but wrong architecture ERROR: loading failed * removing ‘/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp’ The downloaded packages are in ‘/private/var/folders/FF/FFUvwZUMHNy0Shp4TusaJk+++TI/-Tmp-/RtmpRd78TR/downloaded_packages’ Updating HTML index of packages in '.Library' Warning message: In install.packages(sp) : installation of package 'sp' had non-zero exit status -- BABA Yoshihiko http://homepage.mac.com/babayoshihiko -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] R and its packages
Are you using the i386 or x86_64 architecture of fink? On Sep 27, 2010, at 9:35 PM, BABA Yoshihiko wrote: Hi all, I installed r-base, then tried to install its packages inside R environment, with the error below. The binary version of R didn't have such error. Would it be Fink's problem? R version 2.11.0 (2010-04-22) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. install.packages(sp) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://essrc.hyogo-u.ac.jp/cran/src/contrib/sp_0.9-69.tar.gz' Content type 'application/x-gzip' length 536637 bytes (524 Kb) opened URL == downloaded 524 Kb * installing *source* package ‘sp’ ... ** libs gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c Rcentroid.c -o Rcentroid.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c gcdist.c -o gcdist.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c pip.c -o pip.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c pip2.c -o pip2.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c sp_xports.c -o sp_xports.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c surfaceArea.c -o surfaceArea.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c zerodist.c -o zerodist.o gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -F/sw/Library/Frameworks/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation ld: warning: in /sw/Library/Frameworks/R.framework/R, file was built for i386 which is not the architecture being linked (x86_64) ld: warning: in /sw/lib/libintl.dylib, file was built for i386 which is not the architecture being linked (x86_64) installing to /sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs ** R ** data ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so': dlopen(/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so, 6): no suitable image found. Did find: /sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so: mach-o, but wrong architecture ERROR: loading failed * removing ‘/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp’ The downloaded packages are in ‘/private/var/folders/FF/FFUvwZUMHNy0Shp4TusaJk+++TI/-Tmp-/RtmpRd78TR/downloaded_packages’ Updating HTML index of packages in '.Library' Warning message: In install.packages(sp) : installation of package 'sp' had non-zero exit status -- BABA Yoshihiko http://homepage.mac.com/babayoshihiko -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing.
Re: [Fink-devel] R and its packages
Anyway, I suspect from your error message that you are using 10.6-i386. The R environment, on the other hand, is making calls to gcc with no arch flag so it defaults to x86_64, and your libraries are not compatible with that... -- Dave On Sep 27, 2010, at 9:43 PM, David R. Morrison wrote: Are you using the i386 or x86_64 architecture of fink? On Sep 27, 2010, at 9:35 PM, BABA Yoshihiko wrote: Hi all, I installed r-base, then tried to install its packages inside R environment, with the error below. The binary version of R didn't have such error. Would it be Fink's problem? R version 2.11.0 (2010-04-22) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. install.packages(sp) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://essrc.hyogo-u.ac.jp/cran/src/contrib/sp_0.9-69.tar.gz' Content type 'application/x-gzip' length 536637 bytes (524 Kb) opened URL == downloaded 524 Kb * installing *source* package ‘sp’ ... ** libs gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c Rcentroid.c -o Rcentroid.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c gcdist.c -o gcdist.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c pip.c -o pip.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c pip2.c -o pip2.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c sp_xports.c -o sp_xports.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c surfaceArea.c -o surfaceArea.o gcc -std=gnu99 -I/sw/Library/Frameworks/R.framework/Resources/include -I/sw/include-fPIC -g -O2 -c zerodist.c -o zerodist.o gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -F/sw/Library/Frameworks/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation ld: warning: in /sw/Library/Frameworks/R.framework/R, file was built for i386 which is not the architecture being linked (x86_64) ld: warning: in /sw/lib/libintl.dylib, file was built for i386 which is not the architecture being linked (x86_64) installing to /sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs ** R ** data ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so': dlopen(/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so, 6): no suitable image found. Did find: /sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp/libs/sp.so: mach-o, but wrong architecture ERROR: loading failed * removing ‘/sw/Library/Frameworks/R.framework/Versions/2.11/Resources/library/sp’ The downloaded packages are in ‘/private/var/folders/FF/FFUvwZUMHNy0Shp4TusaJk+++TI/-Tmp-/RtmpRd78TR/downloaded_packages’ Updating HTML index of packages in '.Library' Warning message: In install.packages(sp) : installation of package 'sp' had non-zero exit status -- BABA Yoshihiko http://homepage.mac.com/babayoshihiko -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] r-base, OSX's ld, 10.5.2, and a conversation from March
Hello, Searching the internet, I came across this discussion: -- From: Martin Costabel Date: 2008-03-10 00:00:45 Dominique Dhumieres wrote: Do you have atlas-shlibs installed? If yes, could you try if removing it allows you to build r-base? The answer is yes to both questions. r-base is now installed on intel OSX 10.5.2 with gcc43. OK, so it's again Leopard's braindead /usr/bin/ld that is to blame here. I'll fix it in CVS, using the same dylib_file hack as in the octave package. -- Martin -- ...I'm personally currently messing around with my own install of ATLAS, LAPACK, and R (I love Fink and use it, but I'm interested in running the less stable version of ATLAS which isn't out in Fink yet), and am having the same problem Dhumieres references above: Warning in solve.default(rgb) : unable to load shared library \ '/Volumes/MacBook/sw/src/fink.build/r-base-2.6.0-1/R-2.6.0/modules//lapack.so': \ dlopen(/Volumes/MacBook/sw/src/fink.build/r-base-2.6.0-1/R-2.6.0/modules//lapack.so, \ 6): Symbol not found: _cblas_cdotc_sub Referenced from: \ ...while I know this list is dedicated to Fink installs, it would be fantastic if Martin or someone with similar knowledge could explain in a touch more detail what the fix was in the current fink distro so that those not using fink for R could benefit...specifically, what the fix is or how it was accomplished. I have verified in a number of ways that the _cblas_cdotc_sub is present in the lapack/atlas commands I have sent to R...so I'm nearly certain I'm having the same problem referenced by Dominique above. Many thanks! Adam Kramer -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] r-base, OSX's ld, 10.5.2, and a conversation from March
On Sun, Jan 18, 2009 at 06:09:31PM -0800, Adam D. I. Kramer wrote: Hello, Searching the internet, I came across this discussion: -- From: Martin Costabel Date: 2008-03-10 00:00:45 Dominique Dhumieres wrote: Do you have atlas-shlibs installed? If yes, could you try if removing it allows you to build r-base? The answer is yes to both questions. r-base is now installed on intel OSX 10.5.2 with gcc43. OK, so it's again Leopard's braindead /usr/bin/ld that is to blame here. I'll fix it in CVS, using the same dylib_file hack as in the octave package. -- Martin -- ...I'm personally currently messing around with my own install of ATLAS, LAPACK, and R (I love Fink and use it, but I'm interested in running the less stable version of ATLAS which isn't out in Fink yet), and am having the same problem Dhumieres references above: Warning in solve.default(rgb) : unable to load shared library \ '/Volumes/MacBook/sw/src/fink.build/r-base-2.6.0-1/R-2.6.0/modules//lapack.so': \ dlopen(/Volumes/MacBook/sw/src/fink.build/r-base-2.6.0-1/R-2.6.0/modules//lapack.so, \ 6): Symbol not found: _cblas_cdotc_sub Referenced from: \ ...while I know this list is dedicated to Fink installs, it would be fantastic if Martin or someone with similar knowledge could explain in a touch more detail what the fix was in the current fink distro so that those not using fink for R could benefit...specifically, what the fix is or how it was accomplished. I have verified in a number of ways that the _cblas_cdotc_sub is present in the lapack/atlas commands I have sent to R...so I'm nearly certain I'm having the same problem referenced by Dominique above. All fink packages are described by text files in our CVS repository. Take a look at: http://fink.cvs.sourceforge.net/fink/dists/10.4/unstable/main/finkinfo/sci/r-base.info to see what ./configure flags, env vars, or other patching is being done. As usual for CVS, HEAD is the present package in unstable, and you can look back through the dated history to see who changed what when why. dan -- Daniel Macks dma...@netspace.org http://www.netspace.org/~dmacks -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] R
Alexander Hansen wrote: [] So let's say we updated r-base to 2.8.0. It would install stuff in %p/Library/Frameworks/R.framework/Versions/2.8 , and then anything that linked to the older version of libR.dylib wouldn't be able to find it. Currently only labplot and rpy-py* depend on r-base, so forcing rebuilds isn't terribly hard (thought labplot takes a while to rebuild). It would be better to come up with a scheme in which we can leave the library around for a particular R version (like our standard -shlibs). Why not have a -shlibs splitoff and then choose new package names for every update, just as for any other package where the dylibs are clearly versioned? Whether the version is marked in the basename or in some other path componenent of the dylib shouldn't logically matter. -- Martin - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
[Fink-devel] R
We've had a long-standing issue with the r-base package that complicates updates. Basically the problem is that each new major version of r-base stashes its files in a versioned directory within its framework, and anything that links the R library therefore requires that versioning. For example: $ otool -L /sw2/lib/python2.5/site-packages/_rpy2070.so /sw2/lib/python2.5/site-packages/_rpy2070.so: /sw2/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libR.dylib (compatibility version 2.7.0, current version 2.7.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.1) (which was built against the r-base version from the tracker https://sourceforge.net/tracker/?func=detailatid=414256aid=1955281group_id=17203 , since I had that installed but not the release version (2.6.0) ) So let's say we updated r-base to 2.8.0. It would install stuff in %p/Library/Frameworks/R.framework/Versions/2.8 , and then anything that linked to the older version of libR.dylib wouldn't be able to find it. Currently only labplot and rpy-py* depend on r-base, so forcing rebuilds isn't terribly hard (thought labplot takes a while to rebuild). It would be better to come up with a scheme in which we can leave the library around for a particular R version (like our standard -shlibs). - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
