[R-SIG-Mac] third party installer

David Winsemius dwinsemius at comcast.net
Mon May 9 23:08:26 CEST 2016 

> On May 9, 2016, at 1:19 PM, David Winsemius <dwinsemius at comcast.net> wrote:
> 
> 
>> On May 9, 2016, at 1:04 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
>> 
>> 
>> On May 9, 2016, at 2:50 PM, Mick Jordan <mick.jordan at oracle.com> wrote:
>> 
>>> What third party installer is used for the standard Mac OS X build? Looking at the following I can't figure out where lzma is coming from. I am using MacPorts (on El Cap) which puts lzma in /opt/local/include.
>>> 
>> 
>> 
>> No 3rd party, only static libs used on CRAN, i.e., what is in
>> http://r.research.att.com/libs/
> 
> It wasn't obvious where lzma was being derived in any of those sources, so I made my best efforts and decided it was probably from xz-5.2.1.tar.bz2
> 
> Was my searching correct?
> 

As a followup can anyone suggest how I should  address (or whether I should even worry about) the error reported when I follow the installation advice for that package on that page:

$ curl -O http://r.research.att.com/libs/xz-5.2.1-darwin.13-x86_64.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  617k  100  617k    0     0   352k      0  0:00:01  0:00:01 --:--:--  352k
david-winsemiuss-mac-pro:~ davidwinsemius$ sudo tar fvxz xz-5.2.1-darwin.13-x86_64.tar.gz -C /
Password:
x usr/: Can't set user=0/group=0 for usrCan't update time for usr
x usr/local/
x usr/local/bin/
x usr/local/include/
x usr/local/lib/
x usr/local/share/
x usr/local/share/doc/
x usr/local/share/man/
x usr/local/share/man/man1/
x usr/local/share/man/man1/lzcat.1
x usr/local/share/man/man1/lzcmp.1
x usr/local/share/man/man1/lzdiff.1
x usr/local/share/man/man1/lzegrep.1
x usr/local/share/man/man1/lzfgrep.1
x usr/local/share/man/man1/lzgrep.1
x usr/local/share/man/man1/lzless.1
x usr/local/share/man/man1/lzma.1
x usr/local/share/man/man1/lzmadec.1
x usr/local/share/man/man1/lzmainfo.1
x usr/local/share/man/man1/lzmore.1
x usr/local/share/man/man1/unlzma.1
x usr/local/share/man/man1/unxz.1
x usr/local/share/man/man1/xz.1
x usr/local/share/man/man1/xzcat.1
x usr/local/share/man/man1/xzcmp.1
x usr/local/share/man/man1/xzdec.1
x usr/local/share/man/man1/xzdiff.1
x usr/local/share/man/man1/xzegrep.1
x usr/local/share/man/man1/xzfgrep.1
x usr/local/share/man/man1/xzgrep.1
x usr/local/share/man/man1/xzless.1
x usr/local/share/man/man1/xzmore.1
x usr/local/share/doc/xz/
x usr/local/share/doc/xz/AUTHORS
x usr/local/share/doc/xz/COPYING
x usr/local/share/doc/xz/COPYING.GPLv2
x usr/local/share/doc/xz/examples/
x usr/local/share/doc/xz/examples_old/
x usr/local/share/doc/xz/faq.txt
x usr/local/share/doc/xz/history.txt
x usr/local/share/doc/xz/lzma-file-format.txt
x usr/local/share/doc/xz/NEWS
x usr/local/share/doc/xz/README
x usr/local/share/doc/xz/THANKS
x usr/local/share/doc/xz/TODO
x usr/local/share/doc/xz/xz-file-format.txt
x usr/local/share/doc/xz/examples_old/xz_pipe_comp.c
x usr/local/share/doc/xz/examples_old/xz_pipe_decomp.c
x usr/local/share/doc/xz/examples/00_README.txt
x usr/local/share/doc/xz/examples/01_compress_easy.c
x usr/local/share/doc/xz/examples/02_decompress.c
x usr/local/share/doc/xz/examples/03_compress_custom.c
x usr/local/share/doc/xz/examples/04_compress_easy_mt.c
x usr/local/share/doc/xz/examples/Makefile
x usr/local/lib/liblzma.a
x usr/local/lib/liblzma.la
x usr/local/lib/pkgconfig/
x usr/local/lib/pkgconfig/liblzma.pc
x usr/local/include/lzma/
x usr/local/include/lzma.h
x usr/local/include/lzma/base.h
x usr/local/include/lzma/bcj.h
x usr/local/include/lzma/block.h
x usr/local/include/lzma/check.h
x usr/local/include/lzma/container.h
x usr/local/include/lzma/delta.h
x usr/local/include/lzma/filter.h
x usr/local/include/lzma/hardware.h
x usr/local/include/lzma/index.h
x usr/local/include/lzma/index_hash.h
x usr/local/include/lzma/lzma12.h
x usr/local/include/lzma/stream_flags.h
x usr/local/include/lzma/version.h
x usr/local/include/lzma/vli.h
x usr/local/bin/lzcat
x usr/local/bin/lzcmp
x usr/local/bin/lzdiff
x usr/local/bin/lzegrep
x usr/local/bin/lzfgrep
x usr/local/bin/lzgrep
x usr/local/bin/lzless
x usr/local/bin/lzma
x usr/local/bin/lzmadec
x usr/local/bin/lzmainfo
x usr/local/bin/lzmore
x usr/local/bin/unlzma
x usr/local/bin/unxz
x usr/local/bin/xz
x usr/local/bin/xzcat
x usr/local/bin/xzcmp
x usr/local/bin/xzdec
x usr/local/bin/xzdiff
x usr/local/bin/xzegrep
x usr/local/bin/xzfgrep
x usr/local/bin/xzgrep
x usr/local/bin/xzless
x usr/local/bin/xzmore
tar: Error exit delayed from previous errors.

System Version:	OS X 10.11.4 (15E65)
  Kernel Version:	Darwin 15.4.0

Model Name:	Mac Pro
  Model Identifier:	MacPro3,1
  Processor Name:	Quad-Core Intel Xeon
  Processor Speed:	2.8 GHz
  Number of Processors:	2
  Total Number of Cores:	8
  L2 Cache (per Processor):	12 MB
  Memory:	32 GB

(This is probably not really necessary from a current R session;)
R version 3.3.0 RC (2016-05-01 r70572) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

--snipped a bunch of pkg loading information

[R.app GUI 1.68 (7201) x86_64-apple-darwin13.4.0]

-- 
David.

> -- 
> David.
> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> Mick Jordan
>>> 
>>> $ head /Library/Frameworks/R.framework/Resources/etc/Makeconf
>>> # etc/Makeconf.  Generated from Makeconf.in by configure.
>>> #
>>> # ${R_HOME}/etc/Makeconf
>>> #
>>> # R was configured using the following call
>>> # (not including env. vars and site configuration)
>>> # configure  'CC=clang' 'CXX=clang++' 'OBJC=clang' 'F77=gfortran-4.8' 'FC=gfortran-4.8' 'CFLAGS=-Wall -mtune=core2 -g -O2' 'CXXFLAGS=-Wall -mtune=core2 -g -O2' 'OBJCFLAGS=-Wall -mtune=core2 -g -O2' 'FCFLAGS=-Wall -g -O2' 'F77FLAGS=-Wall -g -O2' '--with-system-zlib' '--enable-memory-profiling' 'CPPFLAGS=-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include' '--x-libraries=/opt/X11/lib' '--x-includes=/usr/local/include' '--enable-R-framework'
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
>> _______________________________________________
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>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius
> Alameda, CA, USA
> 
> _______________________________________________
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David Winsemius
Alameda, CA, USA

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