[Fink-devel] work-in-progress branch to install all compiler wrappers in the .deb

2014-04-28 Thread Alexander Hansen
The current Fink release (0.36.4.1) dynamically generates the compiler 
wrappers for clang/clang++ (via functions in Fink::PkgVersion).  We 
currently remove the wrappers when updating fink, and new ones are 
generated for the next build operation.  This isn't 100% reliable, though.

I've generated a work-in-progress branch in the fink github repository 
(i.e. I don't think it's quite ready to be a pull request) called 
compiler_wrapper_in_deb.  As the name suggests, in this branch all of 
the compiler wrappers get installed in the .deb.

Fink::PkgVersion hasn't been altered, because I haven't had time to 
explore the full ramifications of altering the wrapper generation there 
(not well commented or documented).  For example, are temporary wrappers 
generated to build dpkg-bootstrap?  Also, in the event of user error, in 
principle the various ensure* functions will attempt to regenerate the 
compiler wrappers, which is useful.  Though I'd argue that it's poor 
from a maintenance standpoint to have separate copies of the wrapper 
scripts stored as heredocs within PkgVersion.pm and as normal files, 
which is what we've been doing for a while now.

Anyway, feedback is appreciated.
-- 
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/

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[Fink-devel] Time to close 10.6 down officially?

2014-04-28 Thread Alexander Hansen
Pros:

1) We're back to one architecture (albeit with two C++ ABI standards).
2) We're back to one package tree.
3) Fewer platforms to have to test base packages on.
4) No feelings of guilt for people who have been only updating for 10.7+ 
(OK, there probably aren't many of those).
5) Minimal effort to do it.  We just ensure that the next fink release 
won't bootstrap on 10.6 and don't put a .info file there, rather than 
doing a 10.6-EOL directory (though that will also work).
6) Sorry, we don't support that OS any more  has a nice ring to it.

Cons:

1) People will complain.  Though it's not like we said 10.6 is 
unsupported, so make sure to 'rm -rf /sw'.

It'd be nice to get this done in a couple of weeks.
-- 
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/

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[Fink-devel] r-base215. r-base-30 and r-base31

2014-04-28 Thread Jack Howarth
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

2014-04-28 Thread 美彦 馬場
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

2014-04-28 Thread Daniel Macks
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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Daniel Macks
dma...@netspace.org



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