[R-SIG-Mac] Fab editor, enhance?

Wed Jan 16 10:49:03 CET 2008

Dear all -

while we are commenting on features that could go into the currently  
amazing editor, what about batch indenting?  Or have I missed that?

andrew

---------------------------------------------------------------------------------
Dr. Andrew Beckerman
Department of Animal and Plant Sciences, University of Sheffield,
Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
ph +44 (0)114 222 0026; fx +44 (0)114 222 0002
http://www.beckslab.staff.shef.ac.uk/
----------------------------------------------------------------------------------

On 15 Jan 2008, at 19:36, Ken Nussear wrote:

> Hi
>
> Just wondering if there is a way to "batch comment" in the R editor? I
> like to paste model outputs in with my scripts and comment them out so
> I can follow things later. I thought it would be useful to be able to
> insert a comment symbol to a batch of lines all at once.
>
> Any thoughts?
>
> Ken
>
> --
> Kenneth E. Nussear
> Research Herpetologist, USGS
> (702) 564-4515  Fax  (702) 564-4600
> knussear at usgs.gov
>
>
> On Jan 15, 2008, at 3:00 AM, r-sig-mac-request at stat.math.ethz.ch  
> wrote:
>
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>> Today's Topics:
>>
>>  1. Re:  [R] Install RSPerl in Leopard (Prof Brian Ripley)
>>  2.  building R package (Guillaume Blanchet)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 14 Jan 2008 19:08:26 +0000 (GMT)
>> From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
>> Subject: Re: [R-SIG-Mac] [R] Install RSPerl in Leopard
>> To: David Ochoa <dogcaesar at gmail.com>
>> Cc: r-sig-mac at r-project.org
>> Message-ID: <Pine.LNX.4.64.0801141812190.12548 at gannet.stats.ox.ac.uk>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> On Mon, 14 Jan 2008, Prof Brian Ripley wrote:
>>
>>> This is not the most appropriate list.  But the first answer is
>>> that the
>>> package is not aware of sub-architectures, introduced a while back
>>> in R.
>>>
>>> The best thing is to follow the posting guide and contact the
>>> author: if that
>>> fails, people on R-sig-mac might be able to walk you through the
>>> changes
>>> needed.  It perhaps is as simple as editing
>>> RSPerl/src/RinPerlMakefile.in to say
>>>
>>> include $(R_HOME)/etc$(R_ARCH)/Makeconf
>>>
>>> That should fix the first problem.  But
>>>
>>>> cc1: error: invalid option ?arch=nocona?
>>>
>>> suggests there might be a further problem (for which use R-sig-mac).
>>
>> On my system at least that seems a compiler options mismatch (it
>> works on
>> my self-built version of R-devel with the above change).  Removing
>> -march=nocona in entries in
>>
>> /Library/Frameworks/R.framework/Resources/etc/i386/Makeconf
>>
>> on the CRAN build made this go to completion.  (My build does not
>> have those.)  You can override in CFLAGS in personal Makevars (see
>> 'Writing R Extensions').
>>
>> But I'll let those more expert than I on R-sig-mac comment on that
>> issue.
>>
>>>
>>>
>>>
>>> On Mon, 14 Jan 2008, David Ochoa wrote:
>>>
>>>> Hi,
>>>>
>>>> I am having problems installing RSPerl 0.92-1 in my Mac OSX 10.5.1.
>>>> I?ve installed correctly R-2.6.1 with the .mpkg.
>>>> I run the next command: <R CMD INSTALL --configure-args='  --with-
>>>> in-
>>>> perl ' RSPerl>
>>>> And the next error message appears:
>>>>
>>>>
>>>>
>>>> RSPerl
>>>> * Installing to library '/Library/Frameworks/R.framework/Resources/
>>>> library'
>>>> * Installing *source* package 'RSPerl' ...
>>>> checking for perl... /usr/bin/perl
>>>> No support for any of the Perl modules from calling Perl from R.
>>>> *****************************************************
>>>>
>>>>      Set PERL5LIB to /Library/Frameworks/R.framework/Resources/
>>>> library/RSPerl/perl
>>>>
>>>> *****************************************************
>>>> Testing: -F/Library/Frameworks/R.framework/.. -framework R
>>>> Using '/usr/bin/perl' as the perl executable
>>>> Perl modules (no):
>>>> Adding R package to list of Perl modules to enable callbacks to R
>>>> from
>>>> Perl
>>>> Creating the C code for dynamically loading modules with native  
>>>> code
>>>> for Perl:  R
>>>> modules:   R; linking:
>>>> checking for gcc... gcc
>>>> checking for C compiler default output file name... a.out
>>>> checking whether the C compiler works... yes
>>>> checking whether we are cross compiling... no
>>>> checking for suffix of executables...
>>>> checking for suffix of object files... o
>>>> checking whether we are using the GNU C compiler... yes
>>>> checking whether gcc accepts -g... yes
>>>> checking for gcc option to accept ISO C89... none needed
>>>> Support R in Perl: yes
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> config.status: creating inst/scripts/RSPerl.csh
>>>> config.status: creating inst/scripts/RSPerl.bsh
>>>> config.status: creating src/RinPerlMakefile
>>>> config.status: creating src/Makefile.PL
>>>> config.status: creating cleanup
>>>> config.status: creating src/R.pm
>>>> config.status: creating R/perl5lib.R
>>>> making target all in RinPerlMakefile
>>>> RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/
>>>> Makeconf: No such file or directory
>>>> make: *** No rule to make target `/Library/Frameworks/R.framework/
>>>> Resources/etc/Makeconf'.  Stop.
>>>> calling make -f Makefile.perl install
>>>> make: Makefile.perl: No such file or directory
>>>> make: *** No rule to make target `Makefile.perl'.  Stop.
>>>> chmod: blib/lib/R.pm: No such file or directory
>>>> Finished configuration
>>>> ** libs
>>>> ** arch - i386
>>>> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-
>>>> version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/
>>>> R.framework/Resources/include -I/Library/Frameworks/R.framework/
>>>> Resources/include/i386 -I.  -arch i386 -arch ppc -g -pipe -fno-
>>>> common -
>>>> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration-
>>>> after-
>>>> statement -I/usr/local/include  -I/System/Library/Perl/5.8.8/ 
>>>> darwin-
>>>> thread-multi-2level/CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -
>>>> DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2 -
>>>> march=nocona -c Converters.c -o Converters.o
>>>> cc1: error: invalid option ?arch=nocona?
>>>> lipo: can't open input file: /var/folders/qc/qcR--kvAHYGoOkmr3ZNtvk
>>>> ++
>>>> +TM/-Tmp-//cclHWEBN.out (No such file or directory)
>>>> make: *** [Converters.o] Error 1
>>>> chmod: /Library/Frameworks/R.framework/Resources/library/RSPerl/
>>>> libs/
>>>> i386/*: No such file or directory
>>>> ERROR: compilation failed for package 'RSPerl'
>>>> ** Removing '/Library/Frameworks/R.framework/Resources/library/
>>>> RSPerl'
>>>>
>>>>
>>>>
>>>>
>>>> Have I will changed any enviroment variable?
>>>> Can anybody help me?
>>>> Thanks
>>>>
>>>>
>>>>
>>>> David
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>>
>>
>> -- 
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 14 Jan 2008 14:42:07 -0700
>> From: "Guillaume Blanchet" <gblanchet.list at gmail.com>
>> Subject: [R-SIG-Mac] building R package
>> To: r-sig-mac at stat.math.ethz.ch
>> Message-ID:
>> 	<2f2c96cb0801141342u111cecf4m4ca4e5da68228dbd at mail.gmail.com>
>> Content-Type: text/plain
>>
>> Hi all !
>>
>> I just installed Mac OS X 10.5.1 on my Intel MacBook Pro. Since I
>> have my
>> personal packages that I build and modify every so often I also
>> installed
>> Xcode 3. My packages contain either some C code, some Fortran code
>> or both.
>>
>> However, I can not build a binary of my package, which I know to be
>> error-free since they were running without any bugs when I was
>> running Tiger
>> (Mac OS 10.4.11).
>>
>> The message that is sent to me when I launch the command "R CMD build
>> --binary AEM" (AEM being the name of my package) in the terminal is:
>>
>>
>> macintosh:AEM Package ti-guiblanc$ R CMD build --binary AEM
>> * checking for file 'AEM/DESCRIPTION' ... OK
>> * preparing 'AEM':
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * removing junk files
>> * checking for LF line-endings in source and make files
>> * checking for empty or unneeded directories
>> * building binary distribution
>> /var/folders/+5/+5Ch2A6BEb4+iULWkg5XEU+++TI/-Tmp-/Rinst965351719
>> * Installing *source* package 'AEM' ...
>> ** libs
>> ** arch - i386
>> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
>> -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
>> -I/Library/Frameworks/R.framework/Resources/include
>> -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -
>> fPIC
>> -g -O2 -march=nocona -c buildbinary.c -o buildbinary.o
>> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
>> -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib
>> -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -
>> undefined
>> dynamic_lookup -single_module -multiply_defined suppress -L/usr/
>> local/lib -o
>> AEM.so buildbinary.o   -F/Library/Frameworks/R.framework/.. -
>> framework R
>> ld: warning, duplicate dylib
>> /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.1.dylib
>> ** arch - ppc
>> gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk
>> -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
>> -I/Library/Frameworks/R.framework/Resources/include
>> -I/Library/Frameworks/R.framework/Resources/include/ppc
>> -I/usr/local/include    -fPIC  -g -O2 -c buildbinary.c -o
>> buildbinary.o
>> gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk
>> -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib
>> -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -
>> undefined
>> dynamic_lookup -single_module -multiply_defined suppress -L/usr/
>> local/lib -o
>> AEM.so buildbinary.o   -F/Library/Frameworks/R.framework/.. -
>> framework R
>> ld: warning, duplicate dylib
>> /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.1.dylib
>> ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libstdc++.
>> 6.dylib, file
>> is not of required architecture
>> collect2: ld returned 1 exit status
>> make: *** [AEM.so] Error 1
>> chmod:
>> /var/folders/+5/+5Ch2A6BEb4+iULWkg5XEU+++TI/-Tmp-/Rinst965351719/AEM/
>> libs/ppc/*:
>> No such file or directory
>> ERROR: compilation failed for package 'AEM'
>> ** Removing
>> '/var/folders/+5/+5Ch2A6BEb4+iULWkg5XEU+++TI/-Tmp-/Rinst965351719/ 
>> AEM'
>> ERROR
>> * installation failed
>>
>>
>> My knowledge of the UNIX code and the terminal is limited, so please
>> be
>> gentle !
>>
>> Thanks in advance for any help.
>>
>> Have a nice day !
>>
>> Guillaume Blanchet
>> PhD. candidate
>> University of Alberta
>>
>> 	[[alternative HTML version deleted]]
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>> End of R-SIG-Mac Digest, Vol 59, Issue 8
>> ****************************************
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