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dear list,
i changed my os from win xp to mac os x (10.3) and upgraded R to Version R-2.0.0. now i would like to install a source package which contains fortran code. unfortunately it seems to that the way to compile it is not the same as under windows. under windows i used the special folder "src" and the command R CMD INSTALL ...
but no it doesn't work under mac. first: if i am not wrong there is no src folder and if i try to use R CMD INSTALL then i get this message:
(andqua@g4an:Scource)R CMD INSTALL Test -l /Users/andqua/Documents/Rlibrary/
* Installing *binary* package 'rsmooth' ...
* DONE (Test)
which is wrong because it is no binary. furthernore the package manager tells me there is no package called Test. if i try to install this package with the package installer then i get following error message:
gzip: /Users/andqua/Documents/Rlibrary/Scource/Test.zip has more than one entry--rest ignored
ERROR: cannot extract package from '/Users/andqua/Documents/Rlibrary/Scource/Test.zip'
npackage installation failed
i will be very happy if somebody can tell me what i am doing wrong or give me some sources to read in the internet because i do not found any hints in the R FAQ for mac os x and the faq for building packages in R.
thanks in advance
andreas
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installation of source library with fortran code
10 messages · Byron Ellis, Don MacQueen, Andreas Quandt +5 more
Could you post a transcript of what you're trying to do? In general OS X's behavior is much closer to UNIX/Linux than WinXP (especially when it comes to the command-line utilities). In general, assuming you have an R package downloaded called "package_1_0_0.tar.gz" on your desktop you would execute the following from a Terminal window: # cd ~/Desktop # R CMD INSTALL package_1_0_0.tar.gz The caps are very important (there is actually a system utility called 'install') and you shouldn't actually have to unpack anything. If you're attempting to install a FORTRAN-based package you will need to install g77 from hpc.sourceforge.net as it is not included in Apple's Developer's Tools (for some unfathomable reason. Dear Apple, please ship g77 with Tiger). The appropriate version number is in the FAQ and the installation instructions for g77 are available on its website.
On Nov 15, 2004, at 2:47 AM, Andreas Quandt wrote:
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version=3.0.0
dear list,
i changed my os from win xp to mac os x (10.3) and upgraded R to
Version R-2.0.0. now i would like to install a source package which
contains fortran code. unfortunately it seems to that the way to
compile it is not the same as under windows. under windows i used the
special folder "src" and the command R CMD INSTALL ...
but no it doesn't work under mac. first: if i am not wrong there is no
src folder and if i try to use R CMD INSTALL then i get this message:
(andqua@g4an:Scource)R CMD INSTALL Test -l
/Users/andqua/Documents/Rlibrary/
* Installing *binary* package 'rsmooth' ...
* DONE (Test)
which is wrong because it is no binary. furthernore the package
manager tells me there is no package called Test. if i try to install
this package with the package installer then i get following error
message:
gzip: /Users/andqua/Documents/Rlibrary/Scource/Test.zip has more than
one entry--rest ignored
ERROR: cannot extract package from
'/Users/andqua/Documents/Rlibrary/Scource/Test.zip'
npackage installation failed
i will be very happy if somebody can tell me what i am doing wrong or
give me some sources to read in the internet because i do not found
any hints in the R FAQ for mac os x and the faq for building packages
in R.
thanks in advance
andreas
________________________________________________________________ Verschicken Sie romantische, coole und witzige Bilder per SMS! _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--- Byron Ellis (ellis@stat.harvard.edu) "Oook" -- The Librarian
dear bryon,
Could you post a transcript of what you're trying to do?
i try to make a package from existing r functions. that means i load the functions with "source()" in R and use "package.skeleton()". After it i add the fortran code (written under win) in the src-folder and try "R CMD check" which tells me the package is not a source package: * checking for working latex ... OK * using log directory '/Users/andqua/Documents/TMP/Test.Rcheck' * checking for file 'Rsmooth/DESCRIPTION' ... OK * checking if this is a source package ... ERROR Only *source* packages can be checked. If i try to build a tar.gz file with "R CMD build" than i get following message: (andqua@g4an:Rlibrary)R CMD INSTALL Test/ -l /Users/andqua/Documents/Rlibrary/ * Installing *binary* package 'Test' ... * DONE (Test) for my understanding this should be wrong because the package is no binary and if i try to load this package with "library(test)" i get the error message that the packagae is unknown. So i guss the problem is the fortran code (devweloped under win xp) but i have no idea to solve this problem because should can compile the code because g77 is installed and gcc also. Furthermore i have no administrative rights at this pc but that should be not a problem if i change add my own folder "Rlibrary" with ".libPaths()" to the known libraries. hope the descripion of my problem was more detailed now and helps to find a answer for my problem. best regards andreas
At 12:52 PM +0100 11/15/04, Andreas Quandt wrote:
dear bryon, Could you post a transcript of what you're trying to do? i try to make a package from existing r functions. that means i load the functions with "source()" in R and use "package.skeleton()". After it i add the fortran code (written under win) in the src-folder and try "R CMD check" which tells me the package is not a source package: * checking for working latex ... OK * using log directory '/Users/andqua/Documents/TMP/Test.Rcheck' * checking for file 'Rsmooth/DESCRIPTION' ... OK * checking if this is a source package ... ERROR Only *source* packages can be checked. If i try to build a tar.gz file with "R CMD build" than i get following message:
But the message below is from INSTALL, not from BUILD. ??
(andqua@g4an:Rlibrary)R CMD INSTALL Test/ -l /Users/andqua/Documents/Rlibrary/ * Installing *binary* package 'Test' ... * DONE (Test) for my understanding this should be wrong because the package is no binary and if i try to load this package with "library(test)" i get the error message that the packagae is unknown. So i guss the problem is the fortran code (devweloped under win xp) but i have no idea to solve this problem because should can compile the code because g77 is installed and gcc also.
If you try to compile your fortran outside of R does it succeed? This will help us to find out if the problem is the fortran code.
Furthermore i have no administrative rights at this pc but that should be not a problem if i change add my own folder "Rlibrary" with ".libPaths()" to the known libraries. hope the descripion of my problem was more detailed now and helps to find a answer for my problem. best regards andreas
-Don
-------------------------------------- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA
dear bryon, thank you for your fast answer. i figured with some other help the error out (path of g77 and i made the mistake to copy + paste the DESCRIPTION file made under windows with 1.9.0) and so now it is working. thanks again! cheers andreas
6 days later
My version of R has taken to stopping every now and again with the following error 2004-11-22 09:21:45.928 R[1428] *** NSTimer discarding exception 'NSInternalInconsistencyException' (reason 'dataRepresentationOfType: is a subclass responsibility but has not been overridden.') that raised during firing of timer with target 3b0ff0 and selector 'runRELP:' I'm running OS X 10.3.6 and am at a loss as to where to start tracking this. Any suggestions? G.J.
Umh, we are trying to see what the problem is. To overcome this problem press "esc", then R should continue to work. stefano
On Nov 22, 2004, at 2:56 AM, Gareth Janacek wrote:
My version of R has taken to stopping every now and again with the following error 2004-11-22 09:21:45.928 R[1428] *** NSTimer discarding exception 'NSInternalInconsistencyException' (reason 'dataRepresentationOfType: is a subclass responsibility but has not been overridden.') that raised during firing of timer with target 3b0ff0 and selector 'runRELP:' I'm running OS X 10.3.6 and am at a loss as to where to start tracking this. Any suggestions? G.J.
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On Nov 22, 2004, at 5:59 PM, stefano iacus wrote:
Umh, we are trying to see what the problem is. To overcome this problem press "esc", then R should continue to work.
I think this one is not the same as the long-paste-problem. I suspect that this one was introduced by the external editor support. Rob, can you, please, check it? Please correct me if I'm wrong. Unfortunately I'm overly busy the next week [and w/o my desktop computer], so I won't be able to check it :(. Gareth, can you, please, try to find a reproducible example? That would help localizing it more precisely .. Thanks. Cheers, Simon
On Nov 22, 2004, at 2:56 AM, Gareth Janacek wrote:
My version of R has taken to stopping every now and again with the following error 2004-11-22 09:21:45.928 R[1428] *** NSTimer discarding exception 'NSInternalInconsistencyException' (reason 'dataRepresentationOfType: is a subclass responsibility but has not been overridden.') that raised during firing of timer with target 3b0ff0 and selector 'runRELP:' I'm running OS X 10.3.6 and am at a loss as to where to start tracking this. Any suggestions? G.J.
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Hi, I am in the process of testing the R.framework I built using darwinports. For some reason I can't seem to install packages into the framework using the GUI (compiled from source available yesterday). Everything works fine from the R.app command line though. Anyone have an idea what might be going wrong? I swear this worked yesterday. Thanks, Kjell Output from GUI installer: trying URL `http://cran.r-project.org/bin/macosx/2.0/BradleyTerry_0.7-2.tgz' Content type `application/x-tar' length 128711 bytes opened URL ================================================== downloaded 125Kb Error in unpackPkg(foundpkgs[okp, 2], pkgnames[okp], lib, installWithVers) : Unable to create temp directory /Library/Frameworks/R.framework/Resources/library/file4431b782 Output from command line installer: > install.packages("BradleyTerry") trying URL `http://cran.r-project.org/src/contrib/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 215684 bytes opened URL ================================================== downloaded 210Kb trying URL `http://cran.r-project.org/src/contrib/BradleyTerry_0.7-2.tar.gz' Content type `application/x-tar' length 120342 bytes opened URL ================================================== downloaded 117Kb Delete downloaded files (y/N)? The packages are in /tmp/Rtmp22570/Rinstdir1c06dac8 * Installing *source* package 'BradleyTerry' ... ** R ** inst ** help >>> Building/Updating help pages for package 'BradleyTerry' Formats: text html latex example BradleyTerry text html latex example * DONE (BradleyTerry)
1 day later
Simon and Gareth,
I think this path is taken if Save As is chosen with Quartz as the key
window. By adding
below method into the file RQuartz.m (I did it just above the
saveDocument method) the
problem is resolved.
- (IBAction)saveDocumentAs:(id)sender
{
[self saveDocument:nil];
}
Gareth, please let me know if you occasionally build R yourself, use
the nightly
version from Simon or the general distribution from Stefano. If
possible I would
like to get you a version to verify if this indeed solves the problem.
Thanks,
Rob
On Nov 22, 2004, at 9:34 AM, Simon Urbanek wrote:
On Nov 22, 2004, at 5:59 PM, stefano iacus wrote:
Umh, we are trying to see what the problem is. To overcome this problem press "esc", then R should continue to work.
I think this one is not the same as the long-paste-problem. I suspect that this one was introduced by the external editor support. Rob, can you, please, check it? Please correct me if I'm wrong. Unfortunately I'm overly busy the next week [and w/o my desktop computer], so I won't be able to check it :(. Gareth, can you, please, try to find a reproducible example? That would help localizing it more precisely .. Thanks. Cheers, Simon
On Nov 22, 2004, at 2:56 AM, Gareth Janacek wrote:
My version of R has taken to stopping every now and again with the following error 2004-11-22 09:21:45.928 R[1428] *** NSTimer discarding exception 'NSInternalInconsistencyException' (reason 'dataRepresentationOfType: is a subclass responsibility but has not been overridden.') that raised during firing of timer with target 3b0ff0 and selector 'runRELP:' I'm running OS X 10.3.6 and am at a loss as to where to start tracking this. Any suggestions? G.J.
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