subject:"\[R\-SIG\-Mac\] HELP"

Re: [R-SIG-Mac] Help on reducing size of shared libraries on MacOS on CRAN

2023-03-18 Thread Ken Beath

A random sample of packages linking to Rcpp shows that many have NOTEs for 
installed package size.

I would avoid using special compiler flags, as this is something that may cause 
problems in the future.

Ken

> On 19 Mar 2023, at 8:27 am, Gilberto Camara  
> wrote:
> 
> Hi Simon
> 
> Many thanks for your quick response.  
> 
> My concern has to do with the CRAN Repository Policies, which state: 
> "Maintainers will be asked to update packages which show any warnings or 
> significant notes”. Since the concept of what are “significant notes" is not 
> clearly defined, it is natural that maintainers would like their packages to 
> be free of any NOTE.
> 
> That said, your explanation is quite helpful and informative.
> 
> Best regards
> Gilberto
> 
> 
> Prof Dr Gilberto Camara
> Senior Researcher
> National Institute for Space Research (INPE), Brazil
> https://gilbertocamara.org/
> =
> 
> 
> 
> 
>> On 18 Mar 2023, at 18:19, Simon Urbanek  wrote:
>> 
>> Gilberto,
>> 
>> Please note that size checks are not really relevant for binary packages - 
>> it is normal for binaries to be large as they may include static libraries 
>> (e.g., rgdal has 273Mb). Also note that 4.8Mb is rather small for a library 
>> since it also includes debugging symbols (CRAN packages are built with 
>> --dsym to make debugging easier) - so is there a particular reason you are 
>> concerned about the size? You can always remove the debugging symbols 
>> (libs/*.dsym) on your machine if you have issues with size.
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On 19/03/2023, at 07:02, Gilberto Camara  
>>> wrote:
>>> 
>>> Dear R-SIG-MAC members
>>> 
>>> We are the developers of R package sits and would like to ask for your help 
>>> in solving a problem with library size on R macOS binaries. 
>>> 
>>> Before submission to CRAN, version 1.3.0 of sits 
>>> (https://cran.r-project.org/web/packages/sits/index.html) has been tested 
>>> in various environments, including Ubuntu, Fedora, CRAN winbuilder (all 
>>> flavors). We have tested sits-1.3.0 on r-release-mac-x86_64 and 
>>> r-release-macos-arm64 with the following configurations:
>>> 
>>> - r-release-macos-x86_64: R 4.2.2, MacMini 3.2GHz, 6 cores, 32 MB RAM, 
>>> macOS Ventura 3.2.1, Apple clang version 14.0.3 (clang-1403.0.22.14.1).
>>> 
>>> - r-release-macos-arm64: R 4.2.2, MacBookAir, chip ARM M1, 8 cores, 16 MB 
>>> RAM, macOS Monterrey 12.6,  Apple clang version 14.0.0 
>>> (clang-1400.0.29.201). 
>>> 
>>> In our configuration of r-release-macos-x86_64, the installed size is 3.8 
>>> MB, and the libs directory size is 436 KB. On r-release-macos-arm64, the 
>>> installed size is 5.4 MB and the libs directory size is 1.6 MB. 
>>> 
>>> The current CRAN check on sits version 1.3.0 reports a NOTE on 
>>> r-release-macos-arm64 and r-oldrel-macos-arm64, with an installation size 
>>> of 7.3Mb with the libs directory size reported as 4.8Mb. CRAN is using 
>>> Apple clang version 13.0.0 ((clang-1300.0.29.30) on r-release-macos-arm64 
>>> and Apple clang version 12.0.0 (clang-1200.0.32.29) on 
>>> r-oldrel-macos-arm64. 
>>> 
>>> There is a 3.2 MB difference in size between what CRAN reports and what we 
>>> obtain in our tests for r-release-macos-arm64. We would appreciate your 
>>> guidance on how to address this problem and, if possible, point to a 
>>> reliable way to reduce package size in macOS. 
>>> 
>>> Note that our package links to RCpp and RCppArmadillo.
>>> 
>>> Our current Makevars configuration is given below
>>> ==
>>> # suggestion by Dirk Eddelbuettel
>>> SHLIB_CXXLDFLAGS = -Wlto,-S -shared
>>> SHLIB_CXX11LDFLAGS = -Wlto,-S -shared
>>> SHLIB_CXX14LDFLAGS = -Wlto,-S -shared
>>> SHLIB_FCLDFLAGS = -Wlto,-S -shared
>>> SHLIB_LDFLAGS = -Wlto,-S -shared
>>> 
>>> ## suggestion by Dirk Eddelbuettel
>>> PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
>>> PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
>>> 
>>> strippedLib: $(SHLIB)
>>> if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" 
>>> ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
>>> 
>>> clean:
>>> rm -f $(OBJECTS)
>>> 
>>> .phony: strippedLib clean
>>> ===
>>> 
>>> Any help would be much appreciated. 
>>> 
>>> Best regards
>>> Gilberto
>>> 
>>> Prof Dr Gilberto Camara
>>> Senior Researcher
>>> National Institute for Space Research (INPE), Brazil
>>> https://gilbertocamara.org/
>>> =
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> [email protected]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
> 
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htt

Re: [R-SIG-Mac] Help on reducing size of shared libraries on MacOS on CRAN

2023-03-18 Thread Gilberto Camara

Hi Simon

Many thanks for your quick response.  

My concern has to do with the CRAN Repository Policies, which state: 
"Maintainers will be asked to update packages which show any warnings or 
significant notes”. Since the concept of what are “significant notes" is not 
clearly defined, it is natural that maintainers would like their packages to be 
free of any NOTE.

That said, your explanation is quite helpful and informative.

Best regards
Gilberto


Prof Dr Gilberto Camara
Senior Researcher
National Institute for Space Research (INPE), Brazil
https://gilbertocamara.org/
=




> On 18 Mar 2023, at 18:19, Simon Urbanek  wrote:
> 
> Gilberto,
> 
> Please note that size checks are not really relevant for binary packages - it 
> is normal for binaries to be large as they may include static libraries 
> (e.g., rgdal has 273Mb). Also note that 4.8Mb is rather small for a library 
> since it also includes debugging symbols (CRAN packages are built with --dsym 
> to make debugging easier) - so is there a particular reason you are concerned 
> about the size? You can always remove the debugging symbols (libs/*.dsym) on 
> your machine if you have issues with size.
> 
> Cheers,
> Simon
> 
> 
>> On 19/03/2023, at 07:02, Gilberto Camara  
>> wrote:
>> 
>> Dear R-SIG-MAC members
>> 
>> We are the developers of R package sits and would like to ask for your help 
>> in solving a problem with library size on R macOS binaries. 
>> 
>> Before submission to CRAN, version 1.3.0 of sits 
>> (https://cran.r-project.org/web/packages/sits/index.html) has been tested in 
>> various environments, including Ubuntu, Fedora, CRAN winbuilder (all 
>> flavors). We have tested sits-1.3.0 on r-release-mac-x86_64 and 
>> r-release-macos-arm64 with the following configurations:
>> 
>> - r-release-macos-x86_64: R 4.2.2, MacMini 3.2GHz, 6 cores, 32 MB RAM, macOS 
>> Ventura 3.2.1, Apple clang version 14.0.3 (clang-1403.0.22.14.1).
>> 
>> - r-release-macos-arm64: R 4.2.2, MacBookAir, chip ARM M1, 8 cores, 16 MB 
>> RAM, macOS Monterrey 12.6,  Apple clang version 14.0.0 
>> (clang-1400.0.29.201). 
>> 
>> In our configuration of r-release-macos-x86_64, the installed size is 3.8 
>> MB, and the libs directory size is 436 KB. On r-release-macos-arm64, the 
>> installed size is 5.4 MB and the libs directory size is 1.6 MB. 
>> 
>> The current CRAN check on sits version 1.3.0 reports a NOTE on 
>> r-release-macos-arm64 and r-oldrel-macos-arm64, with an installation size of 
>> 7.3Mb with the libs directory size reported as 4.8Mb. CRAN is using Apple 
>> clang version 13.0.0 ((clang-1300.0.29.30) on r-release-macos-arm64 and 
>> Apple clang version 12.0.0 (clang-1200.0.32.29) on r-oldrel-macos-arm64. 
>> 
>> There is a 3.2 MB difference in size between what CRAN reports and what we 
>> obtain in our tests for r-release-macos-arm64. We would appreciate your 
>> guidance on how to address this problem and, if possible, point to a 
>> reliable way to reduce package size in macOS. 
>> 
>> Note that our package links to RCpp and RCppArmadillo.
>> 
>> Our current Makevars configuration is given below
>> ==
>> # suggestion by Dirk Eddelbuettel
>> SHLIB_CXXLDFLAGS = -Wlto,-S -shared
>> SHLIB_CXX11LDFLAGS = -Wlto,-S -shared
>> SHLIB_CXX14LDFLAGS = -Wlto,-S -shared
>> SHLIB_FCLDFLAGS = -Wlto,-S -shared
>> SHLIB_LDFLAGS = -Wlto,-S -shared
>> 
>> ## suggestion by Dirk Eddelbuettel
>> PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
>> PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
>> 
>> strippedLib: $(SHLIB)
>> if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" 
>> ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
>> 
>> clean:
>> rm -f $(OBJECTS)
>> 
>> .phony: strippedLib clean
>> ===
>> 
>> Any help would be much appreciated. 
>> 
>> Best regards
>> Gilberto
>> 
>> Prof Dr Gilberto Camara
>> Senior Researcher
>> National Institute for Space Research (INPE), Brazil
>> https://gilbertocamara.org/
>> =
>> 
>> ___
>> R-SIG-Mac mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 

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Re: [R-SIG-Mac] Help on reducing size of shared libraries on MacOS on CRAN

2023-03-18 Thread Simon Urbanek

Gilberto,

Please note that size checks are not really relevant for binary packages - it 
is normal for binaries to be large as they may include static libraries (e.g., 
rgdal has 273Mb). Also note that 4.8Mb is rather small for a library since it 
also includes debugging symbols (CRAN packages are built with --dsym to make 
debugging easier) - so is there a particular reason you are concerned about the 
size? You can always remove the debugging symbols (libs/*.dsym) on your machine 
if you have issues with size.

Cheers,
Simon


> On 19/03/2023, at 07:02, Gilberto Camara  
> wrote:
> 
> Dear R-SIG-MAC members
> 
> We are the developers of R package sits and would like to ask for your help 
> in solving a problem with library size on R macOS binaries. 
> 
> Before submission to CRAN, version 1.3.0 of sits 
> (https://cran.r-project.org/web/packages/sits/index.html) has been tested in 
> various environments, including Ubuntu, Fedora, CRAN winbuilder (all 
> flavors). We have tested sits-1.3.0 on r-release-mac-x86_64 and 
> r-release-macos-arm64 with the following configurations:
> 
> - r-release-macos-x86_64: R 4.2.2, MacMini 3.2GHz, 6 cores, 32 MB RAM, macOS 
> Ventura 3.2.1, Apple clang version 14.0.3 (clang-1403.0.22.14.1).
> 
> - r-release-macos-arm64: R 4.2.2, MacBookAir, chip ARM M1, 8 cores, 16 MB 
> RAM, macOS Monterrey 12.6,  Apple clang version 14.0.0 (clang-1400.0.29.201). 
> 
> In our configuration of r-release-macos-x86_64, the installed size is 3.8 MB, 
> and the libs directory size is 436 KB. On r-release-macos-arm64, the 
> installed size is 5.4 MB and the libs directory size is 1.6 MB. 
> 
> The current CRAN check on sits version 1.3.0 reports a NOTE on 
> r-release-macos-arm64 and r-oldrel-macos-arm64, with an installation size of 
> 7.3Mb with the libs directory size reported as 4.8Mb. CRAN is using Apple 
> clang version 13.0.0 ((clang-1300.0.29.30) on r-release-macos-arm64 and Apple 
> clang version 12.0.0 (clang-1200.0.32.29) on r-oldrel-macos-arm64. 
> 
> There is a 3.2 MB difference in size between what CRAN reports and what we 
> obtain in our tests for r-release-macos-arm64. We would appreciate your 
> guidance on how to address this problem and, if possible, point to a reliable 
> way to reduce package size in macOS. 
> 
> Note that our package links to RCpp and RCppArmadillo.
> 
> Our current Makevars configuration is given below
> ==
> # suggestion by Dirk Eddelbuettel
> SHLIB_CXXLDFLAGS = -Wlto,-S -shared
> SHLIB_CXX11LDFLAGS = -Wlto,-S -shared
> SHLIB_CXX14LDFLAGS = -Wlto,-S -shared
> SHLIB_FCLDFLAGS = -Wlto,-S -shared
> SHLIB_LDFLAGS = -Wlto,-S -shared
> 
> ## suggestion by Dirk Eddelbuettel
> PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
> PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
> 
> strippedLib: $(SHLIB)
>   if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` 
> == "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
> 
> clean:
>   rm -f $(OBJECTS)
> 
> .phony: strippedLib clean
> ===
> 
> Any help would be much appreciated. 
> 
> Best regards
> Gilberto
> 
> Prof Dr Gilberto Camara
> Senior Researcher
> National Institute for Space Research (INPE), Brazil
> https://gilbertocamara.org/
> =
> 
> ___
> R-SIG-Mac mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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[R-SIG-Mac] Help on reducing size of shared libraries on MacOS on CRAN

2023-03-18 Thread Gilberto Camara

Dear R-SIG-MAC members

We are the developers of R package sits and would like to ask for your help in 
solving a problem with library size on R macOS binaries. 

Before submission to CRAN, version 1.3.0 of sits 
(https://cran.r-project.org/web/packages/sits/index.html) has been tested in 
various environments, including Ubuntu, Fedora, CRAN winbuilder (all flavors). 
We have tested sits-1.3.0 on r-release-mac-x86_64 and r-release-macos-arm64 
with the following configurations:

- r-release-macos-x86_64: R 4.2.2, MacMini 3.2GHz, 6 cores, 32 MB RAM, macOS 
Ventura 3.2.1, Apple clang version 14.0.3 (clang-1403.0.22.14.1).

- r-release-macos-arm64: R 4.2.2, MacBookAir, chip ARM M1, 8 cores, 16 MB RAM, 
macOS Monterrey 12.6,  Apple clang version 14.0.0 (clang-1400.0.29.201). 

In our configuration of r-release-macos-x86_64, the installed size is 3.8 MB, 
and the libs directory size is 436 KB. On r-release-macos-arm64, the installed 
size is 5.4 MB and the libs directory size is 1.6 MB. 

The current CRAN check on sits version 1.3.0 reports a NOTE on 
r-release-macos-arm64 and r-oldrel-macos-arm64, with an installation size of 
7.3Mb with the libs directory size reported as 4.8Mb. CRAN is using Apple clang 
version 13.0.0 ((clang-1300.0.29.30) on r-release-macos-arm64 and Apple clang 
version 12.0.0 (clang-1200.0.32.29) on r-oldrel-macos-arm64. 

There is a 3.2 MB difference in size between what CRAN reports and what we 
obtain in our tests for r-release-macos-arm64. We would appreciate your 
guidance on how to address this problem and, if possible, point to a reliable 
way to reduce package size in macOS. 

Note that our package links to RCpp and RCppArmadillo.

Our current Makevars configuration is given below
==
# suggestion by Dirk Eddelbuettel
SHLIB_CXXLDFLAGS = -Wlto,-S -shared
SHLIB_CXX11LDFLAGS = -Wlto,-S -shared
SHLIB_CXX14LDFLAGS = -Wlto,-S -shared
SHLIB_FCLDFLAGS = -Wlto,-S -shared
SHLIB_LDFLAGS = -Wlto,-S -shared

## suggestion by Dirk Eddelbuettel
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

strippedLib: $(SHLIB)
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` 
== "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi

clean:
rm -f $(OBJECTS)

.phony: strippedLib clean
===

Any help would be much appreciated. 

Best regards
Gilberto

Prof Dr Gilberto Camara
Senior Researcher
National Institute for Space Research (INPE), Brazil
https://gilbertocamara.org/
=

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Re: [R-SIG-Mac] help with GUI for R.4.0.0 for Mac Catalina

2019-12-05 Thread Bryan Hanson

Not exactly helpful, but I have had the exact same experience for over a month. 
 I don’t think that GUI is in the package.   Bryan

> On Dec 5, 2019, at 6:32 PM, William Revelle  wrote:
> 
> Dear friends,
> 
> I am trying to do the final tests on the next version of psych.  I am testing 
> it on r 4.0.0 which I can do using X-Quartz and R CMD  … etc.
> 
> However, it would be nice to run R.4.0.0  with Simon’s GUI for my normal 
> work.  I have tried to load 4.0,0 several times from the R.developers page 
> (for Macs) which says that the GUI is included.  However, the GUI fails to 
> appear any where.
> 
> I can run 4.0.0 with R-Studio or X-Quartz so I clearly have R installed.  But 
> the GUI does not open. (the 3.6.1 GUI breaks).
> 
> I assume that I am missing something.  Hints would be appreciated.
> 
> Bill
> 
> William Revelle  personality-project.org/revelle.html
> Professor   personality-project.org
> Department of Psychology www.wcas.northwestern.edu/psych/
> Northwestern University  www.northwestern.edu/
> Use R for psychology personality-project.org/r
> It is 2   minutes to midnight   www.thebulletin.org
> 
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[R-SIG-Mac] help with GUI for R.4.0.0 for Mac Catalina

2019-12-05 Thread William Revelle

Dear friends,

I am trying to do the final tests on the next version of psych.  I am testing 
it on r 4.0.0 which I can do using X-Quartz and R CMD  … etc.

However, it would be nice to run R.4.0.0  with Simon’s GUI for my normal work.  
I have tried to load 4.0,0 several times from the R.developers page (for Macs) 
which says that the GUI is included.  However, the GUI fails to appear any 
where.

I can run 4.0.0 with R-Studio or X-Quartz so I clearly have R installed.  But 
the GUI does not open. (the 3.6.1 GUI breaks).

I assume that I am missing something.  Hints would be appreciated.

Bill

William Revellepersonality-project.org/revelle.html
Professor personality-project.org
Department of Psychology www.wcas.northwestern.edu/psych/
Northwestern Universitywww.northwestern.edu/
Use R for psychology personality-project.org/r
It is 2   minutes to midnight   www.thebulletin.org

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Re: [R-SIG-Mac] Help Topic Search banner will not close

2019-05-03 Thread BATES Timothy

Just to say can replicate this problem: the button text is erased and the 
expand search window can’t be closed and neither button responds to user input 
once yes is chosen.

Happens every time. was present for a couple of versions ago.

R version: R version 3.6.0 (2019-04-26)

On 2 May 2019, at 07:54, Kirk Steyer via R-SIG-Mac 
mailto:[email protected]>> wrote:

In R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
[R.app GUI 1.70 (7632) x86_64-apple-darwin15.6.0]

when doing a search query in R help and after selecting “Yes”, once returning 
from http://127.0.0.1:15299/doc/html/Search?results=1 to R.app the Help window 
will not close when selecting “No”


The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336.

[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] HELP

2018-03-20 Thread BATES Timothy

Just FYI, I've had a lot of students in the last 2-weeks reporting errors like 
this about other packages with dependencies that have their own dependencies.

The full chain doesn't appear to be being followed.

For some, on Macs I think, they also have the problem of install.packages() 
trying to install a source version which is newer than the current CRAN binary, 
and then failing because the required compiler isn't present.

Also, sometimes a package will get listed as being installed one or more times 
(this happened for "crayon" last week) , then not ending up installed at all.

There was a strange issue with the "stringi" package being missing despite 
multiple install.packages() calls by students to the top level package that 
ultimately wanted it.

Most solved by reading the error, manually installing (forcing binary if 
necessary) the missing package, and repeating until done.

Of course this leads to lots of "it's broken"  and "no... it didn't work" 
hassles :-)

Best, tim (currently happy the mac TZ warning has gone away in 3.4.4 :-) )

> On 20 Mar 2018, at 4:01 pm, Keith O'Hara  wrote:
> 
> The dependence seems to come from rms -> multcomp -> mvtnorm. 
> 
> Keith
> 
>> On Mar 20, 2018, at 11:44 AM, David Winsemius  wrote:
>> 
>> 
>>> On Mar 20, 2018, at 8:35 AM, Keith O'Hara  wrote:
>>> 
>>> Did you try reinstalling the mvtnorm package?
>>> 
>>> Keith
>>> 
 On Mar 19, 2018, at 10:56 PM, Yonabeth Nava de Escalante 
  wrote:

 I am trying to install the ‘rms’ package in my Mac OS X Yosemite 10.10.5. 
 When I try to load the library I get this error:

> library(rms)
 Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 
 : 
 there is no package called ‘mvtnorm’
 Error: package or namespace load failed for ‘rms’

 I tried installing the dependencies with 

 install.packages("rms",dependencies = TRUE)

 I also tried

 install.packages("rms", repos=c("http://rstudio.org/_packages";, 
 "http://cran.rstudio.com”))

 However, I keep getting the same error. 
[[alternative HTML version deleted]]
>> 
>> I can confirm this behavior. I load rms from startup in my .Rprofile file 
>> and if mvtrnorm is missing I also get:
>> 
>> Error: package or namespace load failed for ‘rms’ in loadNamespace(i, 
>> c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
>> there is no package called ‘mvtnorm’
>> 
>> To me it signals a needt to let the package maintainer know about the issue.
>> 
>>> maintainer("rms")
>> [1] "Frank E Harrell Jr "
>> 

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>>> 
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>> 
>> David Winsemius
>> Alameda, CA, USA
>> 
>> 'Any technology distinguishable from magic is insufficiently advanced.'   
>> -Gehm's Corollary to Clarke's Third Law
>> 
>> 
>> 
>> 
>> 
> 
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-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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Re: [R-SIG-Mac] HELP

2018-03-20 Thread Keith O'Hara

The dependence seems to come from rms -> multcomp -> mvtnorm. 

Keith

> On Mar 20, 2018, at 11:44 AM, David Winsemius  wrote:
> 
> 
>> On Mar 20, 2018, at 8:35 AM, Keith O'Hara  wrote:
>> 
>> Did you try reinstalling the mvtnorm package?
>> 
>> Keith
>> 
>>> On Mar 19, 2018, at 10:56 PM, Yonabeth Nava de Escalante 
>>>  wrote:
>>> 
>>> I am trying to install the ‘rms’ package in my Mac OS X Yosemite 10.10.5. 
>>> When I try to load the library I get this error:
>>> 
 library(rms)
>>> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 
>>> : 
>>> there is no package called ‘mvtnorm’
>>> Error: package or namespace load failed for ‘rms’
>>> 
>>> I tried installing the dependencies with 
>>> 
>>> install.packages("rms",dependencies = TRUE)
>>> 
>>> I also tried
>>> 
>>> install.packages("rms", repos=c("http://rstudio.org/_packages";, 
>>> "http://cran.rstudio.com”))
>>> 
>>> However, I keep getting the same error. 
>>> [[alternative HTML version deleted]]
> 
> I can confirm this behavior. I load rms from startup in my .Rprofile file and 
> if mvtrnorm is missing I also get:
> 
> Error: package or namespace load failed for ‘rms’ in loadNamespace(i, 
> c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
> there is no package called ‘mvtnorm’
> 
> To me it signals a needt to let the package maintainer know about the issue.
> 
>> maintainer("rms")
> [1] "Frank E Harrell Jr "
> 
>>> 
>>> ___
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>> 
>> ___
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> 
> David Winsemius
> Alameda, CA, USA
> 
> 'Any technology distinguishable from magic is insufficiently advanced.'   
> -Gehm's Corollary to Clarke's Third Law
> 
> 
> 
> 
> 

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Re: [R-SIG-Mac] HELP

2018-03-20 Thread David Winsemius


> On Mar 20, 2018, at 8:35 AM, Keith O'Hara  wrote:
> 
> Did you try reinstalling the mvtnorm package?
> 
> Keith
> 
>> On Mar 19, 2018, at 10:56 PM, Yonabeth Nava de Escalante 
>>  wrote:
>> 
>> I am trying to install the ‘rms’ package in my Mac OS X Yosemite 10.10.5. 
>> When I try to load the library I get this error:
>> 
>>> library(rms)
>> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
>> there is no package called ‘mvtnorm’
>> Error: package or namespace load failed for ‘rms’
>> 
>> I tried installing the dependencies with 
>> 
>> install.packages("rms",dependencies = TRUE)
>> 
>> I also tried
>> 
>> install.packages("rms", repos=c("http://rstudio.org/_packages";, 
>> "http://cran.rstudio.com”))
>> 
>> However, I keep getting the same error. 
>>  [[alternative HTML version deleted]]

I can confirm this behavior. I load rms from startup in my .Rprofile file and 
if mvtrnorm is missing I also get:

Error: package or namespace load failed for ‘rms’ in loadNamespace(i, 
c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘mvtnorm’

To me it signals a needt to let the package maintainer know about the issue.

> maintainer("rms")
[1] "Frank E Harrell Jr "

>> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] HELP

2018-03-20 Thread Keith O'Hara

Did you try reinstalling the mvtnorm package?

Keith

> On Mar 19, 2018, at 10:56 PM, Yonabeth Nava de Escalante 
>  wrote:
> 
> I am trying to install the ‘rms’ package in my Mac OS X Yosemite 10.10.5. 
> When I try to load the library I get this error:
> 
>> library(rms)
> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
>  there is no package called ‘mvtnorm’
> Error: package or namespace load failed for ‘rms’
> 
> I tried installing the dependencies with 
> 
> install.packages("rms",dependencies = TRUE)
> 
> I also tried
> 
> install.packages("rms", repos=c("http://rstudio.org/_packages";, 
> "http://cran.rstudio.com”))
> 
> However, I keep getting the same error. 
>   [[alternative HTML version deleted]]
> 
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[R-SIG-Mac] HELP

2018-03-20 Thread Yonabeth Nava de Escalante

I am trying to install the ‘rms’ package in my Mac OS X Yosemite 10.10.5. When 
I try to load the library I get this error:

> library(rms)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘mvtnorm’
Error: package or namespace load failed for ‘rms’

I tried installing the dependencies with 

install.packages("rms",dependencies = TRUE)

I also tried

install.packages("rms", repos=c("http://rstudio.org/_packages";, 
"http://cran.rstudio.com”))

However, I keep getting the same error. 
[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] help: change of e-mail address

2018-02-01 Thread peter dalgaard

Um, no we can't! 

You are writing to all subscribers of the list and we cannot mess with 
eachother's subscriptions. 

In case of administrative trouble, you need 

>  [email protected]

However, are you _sure_ that it didn't work to follow the instructions at 
https://stat.ethz.ch/mailman/listinfo/r-sig-mac ?

Notice in particular that the system cannot retroactively change recipients on 
things that have already been sent, and that mails can sit in mailer queues for 
some time. I.e., you may recieve mails to the old address for a while until the 
new address takes effect.

-pd

> On 1 Feb 2018, at 08:39 , Hagens, M. (Mathilde)  wrote:
> 
> To whom it may concern,
> 
> I've been trying to change my e-mail address unsuccessfully via the World 
> Wide Web. Could you please change my e-mail address to 
> [email protected]? 
> 
> Thank you,
> Mathilde
> 
> Dr. M. (Mathilde) Hagens | Assistant Professor | Department of Soil Quality | 
> Wageningen University & Research | Droevendaalsesteeg 4, 6708 PB Wageningen, 
> the Netherlands | tel. +31 317 487 775 | 
> www.wur.nl/en/Persons/Mathilde-dr.-M-Mathilde-Hagens.htm | Please note new 
> e-mail address: [email protected]
> 
> 
> 
> From: R-SIG-Mac [[email protected]] on behalf of 
> [email protected] [[email protected]]
> Sent: Thursday, February 01, 2018 06:22
> To: [email protected]
> Subject: R-SIG-Mac Digest, Vol 180, Issue 1
> 
> Send R-SIG-Mac mailing list submissions to
>[email protected]
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> or, via email, send a message with subject or body 'help' to
>[email protected]
> 
> You can reach the person managing the list at
>[email protected]
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-SIG-Mac digest..."
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-- 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [email protected]  Priv: [email protected]

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[R-SIG-Mac] help: change of e-mail address

2018-01-31 Thread Hagens, M. (Mathilde)

To whom it may concern,

I've been trying to change my e-mail address unsuccessfully via the World Wide 
Web. Could you please change my e-mail address to [email protected]? 

Thank you,
Mathilde

Dr. M. (Mathilde) Hagens | Assistant Professor | Department of Soil Quality | 
Wageningen University & Research | Droevendaalsesteeg 4, 6708 PB Wageningen, 
the Netherlands | tel. +31 317 487 775 | 
www.wur.nl/en/Persons/Mathilde-dr.-M-Mathilde-Hagens.htm | Please note new 
e-mail address: [email protected]



From: R-SIG-Mac [[email protected]] on behalf of 
[email protected] [[email protected]]
Sent: Thursday, February 01, 2018 06:22
To: [email protected]
Subject: R-SIG-Mac Digest, Vol 180, Issue 1

Send R-SIG-Mac mailing list submissions to
[email protected]

To subscribe or unsubscribe via the World Wide Web, visit
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
or, via email, send a message with subject or body 'help' to
[email protected]

You can reach the person managing the list at
[email protected]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-SIG-Mac digest..."
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Re: [R-SIG-Mac] Help! R Freezes When Clicking on the Icons

2016-07-07 Thread David Winsemius


> On Jul 5, 2016, at 6:25 AM, Scott Novogoratz  wrote:
> 
> While it started as an occasional freeze, I now can no longer get the R.app 
> Source Script icon to perform.  Each time I click it, I get the spinning 
> pinwheel and need to Force Quit R.
> 
> Here’s my sessionInfo():
> > sessionInfo()
> R version 3.3.1 Patched (2016-06-28 r70858)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X El Capitan (10.11.5)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> loaded via a namespace (and not attached):
> [1] zoo_1.7-13  xts_0.9-7   grid_3.3.1  IBrokers_0.9-12
> [5] lattice_0.20-33

The presence of `zoo`, `xts`, and `IBrokers` in that list of non-attached 
namespaces seems unexplained. It's surely not a part of the standard base 
installation. `lattice` and `grid` are also not loaded by default so this 
suggests you have not completely removed all traces from the prior 
installation. Check to see that there isn't an .Rprofile or .Rdata still in the 
startup directory. (And delete them if there.)


> 
> Here’s my About R info:
> 
> 
> With help from David Winsemius, here’s what I tried so far:
>   1. Deleting the .Rdata and the .Rapp.history files from my working 
> directory
>   2. Reinstalling R

I actually suggested reinstalling the R.app GUI using the binary installer at:
http://r.research.att.com/mavericks/R-3.3-branch/R-GUI-7238-3.3-mavericks-Release.dmg

I'm now wondering if it would be of value to instead install the Debug version:
http://r.research.att.com/mavericks/R-devel/R-GUI-7238-3.4-mavericks-Debug.dmg 
but that is a decision above my pay grade.

>   3. Setting my working directory on startup
> 
> Additionally, I have 3 Macs and all of them are having the same problem.
> 
> Does anyone have any ideas on fixing this problem?
> 
> Thank you for your suggestions.
> 
> Scott Novogoratz
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David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] Help! Freezes Consistently When Trying to Execute R Source Script

2016-07-03 Thread David Winsemius

I’m not at the level where I could effectively debug this issue and normally I 
wouldn’t jump in, but this is a long holiday weekend in the US and it wouldn’t 
surprise me if Simon didn’t see this for a couple of days.  I would first try 
deleting R.app from the Applications folder and re-installing it with a clean 
copy:

http://r.research.att.com/mavericks/R-3.3-branch/R-GUI-7238-3.3-mavericks-Release.dmg

I do see  “debug” versions but I have never seen it suggested that ordinary 
users deploy those versions as a first step.

I would also delete the .Rdata and the .Rapp.history files from your working 
directory. They have a record of getting corrupted an causing instabilities of 
obscure causes. They are “hidden files” so you either need to “show them” in 
the Finder or you need to sue Terminal.app to run a bash session and use mv. 
This is the first method:

Open Terminal found in Finder > Applications > Utilities
In Terminal, paste the following:  defaults write com.apple.finder 
AppleShowAllFiles YES
Press return
Hold the ‘Option/alt’ key, then right click on the Finder icon in the dock and 
click Relaunch.
Tor reverse that after deleting those files you would use the same steps with 
NO substituted for YES. (My preference is for leaving the hidden files shown.)

Best;
David Winsemius 

> On Jul 3, 2016, at 9:41 AM, Scott Novogoratz  wrote:
> 
> While it started as an occasional freeze, I now can no longer get the R.app 
> Source Script icon to perform.  Each time I click it, I get the spinning 
> pinwheel and need to Force Quit R.
> 
> Here’s my sessionInfo():
> > sessionInfo()
> R version 3.3.1 Patched (2016-06-28 r70858)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X El Capitan (10.11.5)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> loaded via a namespace (and not attached):
> [1] zoo_1.7-13  xts_0.9-7   grid_3.3.1  IBrokers_0.9-12
> [5] lattice_0.20-33
> 
> Here’s my About R info:
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] Help files not available

2016-03-08 Thread peter dalgaard


> On 08 Mar 2016, at 15:26 , Marc Schwartz  wrote:
> 
> Hi,
> 
> Did you folks re-install R (and XQuartz) after upgrading to El Capitan?

Apropos: Notice that the latest broad-ranging security issue for OSX involves 
the Sparkle upgrade architecture used by XQuartz. For now, be careful no to 
update XQuartz over insecure connections (open WiFi, etc.) 

-pd


> 
> As per the R Installation and Administration manual:
> 
> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Installing-R-under-OS-X
> 
> "If you update your OS X version, you should re-install R (and perhaps 
> XQuartz): the installer tailors the installation to the current version of 
> the OS."
> 
> 
> I am running El Capitan with R 3.2.3 and although I don't use the default GUI 
> (I use ESS), I can run the GUI and get help files without issue.
> 
> Regards,
> 
> Marc Schwartz
> 
> 
>> On Feb 25, 2016, at 5:42 PM, Josh Izzard  wrote:
>> 
>> I also have this problem, I do not know what it is from
>> 
>> On Wednesday, February 10, 2016 at 11:44:24 PM UTC-5, Gray, Joshua wrote:
>> I am having trouble with my R installation after upgrading to El Capitan 
>> (although the timing could be entirely coincidental). The help files are not 
>> available, for instance: 
>> 
>>> help("lm") 
>> 
>> Opens the help window in the R GUI, but the message there is: Error in 
>> file(out, "wt") : cannot open the connection 
>> 
>> Similarly: 
>> 
>>> ?lm 
>> Warning message: 
>> In file(out, "wt") : 
>>  cannot open file 
>> '/var/folders/68/x1590pm56yvbbhrkcshd1_ywgn/T//RtmpJfjb7P/Rhttpd3bb208bacf':
>>  No such file or directory 
>>> 
>> 
>> The problem persists after a restart of R and the computer. 
>> 
>> Installation details: R 3.2.1 GUI 1.66 Mavericks build 
>> System details: OS X 10.11.1 
>> 
>> Thanks in advance for your help 
> 
> ___
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [email protected]  Priv: [email protected]

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Re: [R-SIG-Mac] Help files not available

2016-03-08 Thread Marc Schwartz

Hi,

Did you folks re-install R (and XQuartz) after upgrading to El Capitan?

As per the R Installation and Administration manual:

https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Installing-R-under-OS-X

"If you update your OS X version, you should re-install R (and perhaps 
XQuartz): the installer tailors the installation to the current version of the 
OS."


I am running El Capitan with R 3.2.3 and although I don't use the default GUI 
(I use ESS), I can run the GUI and get help files without issue.

Regards,

Marc Schwartz


> On Feb 25, 2016, at 5:42 PM, Josh Izzard  wrote:
> 
> I also have this problem, I do not know what it is from
> 
> On Wednesday, February 10, 2016 at 11:44:24 PM UTC-5, Gray, Joshua wrote:
> I am having trouble with my R installation after upgrading to El Capitan 
> (although the timing could be entirely coincidental). The help files are not 
> available, for instance: 
> 
> > help("lm") 
> 
> Opens the help window in the R GUI, but the message there is: Error in 
> file(out, "wt") : cannot open the connection 
> 
> Similarly: 
> 
> > ?lm 
> Warning message: 
> In file(out, "wt") : 
>   cannot open file 
> '/var/folders/68/x1590pm56yvbbhrkcshd1_ywgn/T//RtmpJfjb7P/Rhttpd3bb208bacf':
>  No such file or directory 
> > 
> 
> The problem persists after a restart of R and the computer. 
> 
> Installation details: R 3.2.1 GUI 1.66 Mavericks build 
> System details: OS X 10.11.1 
> 
> Thanks in advance for your help 

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Re: [R-SIG-Mac] Help files not available

2016-03-08 Thread Josh Izzard

I also have this problem, I do not know what it is from

On Wednesday, February 10, 2016 at 11:44:24 PM UTC-5, Gray, Joshua wrote:
>
> I am having trouble with my R installation after upgrading to El Capitan 
> (although the timing could be entirely coincidental). The help files are 
> not available, for instance: 
>
> > help("lm") 
>
> Opens the help window in the R GUI, but the message there is: Error in 
> file(out, "wt") : cannot open the connection 
>
> Similarly: 
>
> > ?lm 
> Warning message: 
> In file(out, "wt") : 
>   cannot open file 
> '/var/folders/68/x1590pm56yvbbhrkcshd1_ywgn/T//RtmpJfjb7P/Rhttpd3bb208bacf':
>  
> No such file or directory 
> > 
>
> The problem persists after a restart of R and the computer. 
>
> Installation details: R 3.2.1 GUI 1.66 Mavericks build 
> System details: OS X 10.11.1 
>
> Thanks in advance for your help 
>
>
> [[alternative HTML version deleted]] 
>
> ___ 
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> [email protected]  
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac 
>
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[R-SIG-Mac] Help files not available

2016-02-10 Thread Gray, Joshua

I am having trouble with my R installation after upgrading to El Capitan 
(although the timing could be entirely coincidental). The help files are not 
available, for instance:

> help("lm")

Opens the help window in the R GUI, but the message there is: Error in 
file(out, "wt") : cannot open the connection

Similarly:

> ?lm
Warning message:
In file(out, "wt") :
  cannot open file 
'/var/folders/68/x1590pm56yvbbhrkcshd1_ywgn/T//RtmpJfjb7P/Rhttpd3bb208bacf':
 No such file or directory
>

The problem persists after a restart of R and the computer.

Installation details: R 3.2.1 GUI 1.66 Mavericks build
System details: OS X 10.11.1

Thanks in advance for your help


[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] Help page key bindings

2015-08-16 Thread Carl Witthoft



May I suggest an alternative?   Since MacOS allows you to bind the 
keystroke of your choice to any menu item (on an app-specific basis), 
if the "help/forwards" and "help/backwards" were added to a menu, then 
everyone could set whatever bindings they prefer.



--
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[email protected]
http://witthoft.com/resume

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Re: [R-SIG-Mac] Help with windowWillClose notification

2014-09-04 Thread Duncan Murdoch

I believe I have finally fixed this.  Thanks to Simon who gave the right
solution:  use the windowWillClose notification rather than the dealloc
message.  Thanks also to Neil Tiffin who told me something about how to
implement this, and to Michail Vidiassov who did some nice debugging.

For future reference, here's a summary:

The dealloc method of my object was not called immediately when the
window was closed, so there was a period when rgl thought it had a
window but didn't.  Switching the cleanup code to the windowWillClose
notification fixed this, as I already mentioned.

To add my GLView object as a delegate to receive that notification, I
needed to declare that it supported the NSWindowDelegate protocol when
it was declared, and needed to tell the window to use it as a delegate
via [osxWindow setDelegate:view].

Duncan Murdoch

On 21/08/2014, 8:03 AM, Duncan Murdoch wrote:
> I'm hoping someone here who understands Cocoa programming can help me
> with my rgl problems (previously mentioned in the "rgl for R-devel"
> thread in July).
> 
> To recap:  I had a bug report that this sequence crashes R.app:
> 
> library(rgl)
> demo(subdivision)
> 
> #  Close the window by clicking on the X
> 
> rgl.demo.subdivision() # This fn was created by the demo
> 
> I can track down the problem to see that the cleanup code that was
> supposed to be called when the window was closed wasn't called yet,
> so rgl tries to put the new plotting results into a window that isn't
> there, and dies.
> 
> The cleanup code was tied to a -dealloc method on the NSOpenGLView
> object; Simon's guess was that the deallocation is asynchronous, and
> just hasn't been called yet.  Simon suggested it should be on a
> "windowWillClose:" notification.
> 
> Okay, so I've tried to do it on the windowWillClose notification, but I
> really don't know what I'm doing, so the current version still dies.
> Sometimes it gives an R.app error about an "unrecognized selector sent"
>  and sometimes it just crashes.  Generally it makes it a little further
> than the previous version, letting the second window open and only dying
> when I close it.
> 
> Does anyone know of any other examples of R packages that open Cocoa
> windows, so I could see how they do their cleanup?  Or would anyone like
> to volunteer to look at the code and tell me what I'm doing wrong?
> 
> Duncan Murdoch
>

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[R-SIG-Mac] Help with windowWillClose notification

2014-08-21 Thread Duncan Murdoch

I'm hoping someone here who understands Cocoa programming can help me
with my rgl problems (previously mentioned in the "rgl for R-devel"
thread in July).

To recap:  I had a bug report that this sequence crashes R.app:

library(rgl)
demo(subdivision)

#  Close the window by clicking on the X

rgl.demo.subdivision() # This fn was created by the demo

I can track down the problem to see that the cleanup code that was
supposed to be called when the window was closed wasn't called yet,
so rgl tries to put the new plotting results into a window that isn't
there, and dies.

The cleanup code was tied to a -dealloc method on the NSOpenGLView
object; Simon's guess was that the deallocation is asynchronous, and
just hasn't been called yet.  Simon suggested it should be on a
"windowWillClose:" notification.

Okay, so I've tried to do it on the windowWillClose notification, but I
really don't know what I'm doing, so the current version still dies.
Sometimes it gives an R.app error about an "unrecognized selector sent"
 and sometimes it just crashes.  Generally it makes it a little further
than the previous version, letting the second window open and only dying
when I close it.

Does anyone know of any other examples of R packages that open Cocoa
windows, so I could see how they do their cleanup?  Or would anyone like
to volunteer to look at the code and tell me what I'm doing wrong?

Duncan Murdoch

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Re: [R-SIG-Mac] HELP: R for Mac OS 10.9 Mavericks Malfunction

2014-07-07 Thread Prof Brian Ripley


On 07/07/2014 15:12, Senyo Norgbey, MD wrote:

On opening terminal.app, here is my equivalent below..

Last login: Mon Jul  7 08:04:16 on console

Senyo-Norgbeys-MacBook-Pro:~ sennorg$ locale

LANG=

LC_COLLATE="C"

LC_CTYPE="UTF-8"

LC_MESSAGES="C"

LC_MONETARY="C"

LC_NUMERIC="C"

LC_TIME="C"

LC_ALL=


Can you please provide me further instructions on how to
proceed with my problem..??


Correct

LC_CTYPE="UTF-8"

That is simply not a locale name.  Given where you are, most likely you want

export LC_CTYPE=en_US.UTF-8

(assuming a bash shell).  But you might also want to find out what you 
did to your poor Mac to get these settings.




Kind regards...



*Senyo Norgbey, MD**MS Candidate '14*

*Johns Hopkins University School of Medicine, *
*Division of Health Sciences Informatics,*

*2024 East Monument Street/Suite 1-200*

*Baltimore, MD 21205*


*(+1) 443-529-3519(+233) 24-335-5561*



*[email protected] [email protected] *


On Thu, Jul 3, 2014 at 11:26 AM, peter dalgaard  wrote:


Follow instructions in the MacOSX FAQ, section 7(!).

(The "9" in the warning is a relic from an older FAQ document.)

If you  need further guidance open up Terminal.app and tell us what is
your equivalent of

Peters-iMac:R pd$ locale
LANG=
LC_COLLATE="en_US.UTF-8"
LC_CTYPE="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_ALL="en_US.UTF-8"

(i.e. just enter "locale" at the prompt)

-pd


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1 South Parks Road, +44 1865 272866 (PA)
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Re: [R-SIG-Mac] HELP: R for Mac OS 10.9 Mavericks Malfunction

2014-07-07 Thread Senyo Norgbey, MD

On opening terminal.app, here is my equivalent below..

Last login: Mon Jul  7 08:04:16 on console

Senyo-Norgbeys-MacBook-Pro:~ sennorg$ locale

LANG=

LC_COLLATE="C"

LC_CTYPE="UTF-8"

LC_MESSAGES="C"

LC_MONETARY="C"

LC_NUMERIC="C"

LC_TIME="C"

LC_ALL=


Can you please provide me further instructions on how to
proceed with my problem..??

Kind regards...



*Senyo Norgbey, MD**MS Candidate '14*

*Johns Hopkins University School of Medicine, *
*Division of Health Sciences Informatics,*

*2024 East Monument Street/Suite 1-200*

*Baltimore, MD 21205*


*(+1) 443-529-3519(+233) 24-335-5561*



*[email protected] [email protected] *


On Thu, Jul 3, 2014 at 11:26 AM, peter dalgaard  wrote:

> Follow instructions in the MacOSX FAQ, section 7(!).
>
> (The "9" in the warning is a relic from an older FAQ document.)
>
> If you  need further guidance open up Terminal.app and tell us what is
> your equivalent of
>
> Peters-iMac:R pd$ locale
> LANG=
> LC_COLLATE="en_US.UTF-8"
> LC_CTYPE="en_US.UTF-8"
> LC_MESSAGES="en_US.UTF-8"
> LC_MONETARY="en_US.UTF-8"
> LC_NUMERIC="en_US.UTF-8"
> LC_TIME="en_US.UTF-8"
> LC_ALL="en_US.UTF-8"
>
> (i.e. just enter "locale" at the prompt)
>
> -pd

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Re: [R-SIG-Mac] HELP: R for Mac OS 10.9 Mavericks Malfunction

2014-07-03 Thread Adrian Dușa

On Thu, Jul 3, 2014 at 6:09 PM, Senyo Norgbey, MD  wrote:
> Hello..
>
> After installing the above named version of R on my Macbook Pro and
> starting it, the message below appears in the R window...
> [...]

Try opening a Terminal, and type this:

  defaults write org.R-project.R force.LANG en_US.UTF-8

(adjust language options as needed, for me this solved it)

Hope this helps,
Adrian

PS: please note you only need this address "[email protected]"
to ask for help

-- 
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
1, Schitu Magureanu Bd.
050025 Bucharest sector 5
Romania
Tel.:+40 21 3126618 \
+40 21 3120210 / int.101
Fax: +40 21 3158391

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Re: [R-SIG-Mac] HELP: R for Mac OS 10.9 Mavericks Malfunction

2014-07-03 Thread peter dalgaard

Follow instructions in the MacOSX FAQ, section 7(!).

(The "9" in the warning is a relic from an older FAQ document.)

If you  need further guidance open up Terminal.app and tell us what is your 
equivalent of

Peters-iMac:R pd$ locale
LANG=
LC_COLLATE="en_US.UTF-8"
LC_CTYPE="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_ALL="en_US.UTF-8"

(i.e. just enter "locale" at the prompt)

-pd

On 03 Jul 2014, at 17:09 , Senyo Norgbey, MD  wrote:

> Hello..
> 
> After installing the above named version of R on my Macbook Pro and
> starting it, the message below appears in the R window...
> 
> *R version 3.1.0 (2014-04-10) -- "Spring Dance"*
> *Copyright (C) 2014 The R Foundation for Statistical Computing*
> *Platform: x86_64-apple-darwin13.1.0 (64-bit)*
> 
> *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.*
> 
> *During startup - Warning messages:*
> *1: Setting LC_CTYPE failed, using "C" *
> *2: Setting LC_COLLATE failed, using "C" *
> *3: Setting LC_TIME failed, using "C" *
> *4: Setting LC_MESSAGES failed, using "C" *
> *5: Setting LC_MONETARY failed, using "C" *
> *[R.app GUI 1.63 (6734) x86_64-apple-darwin13.1.0]*
> 
> *WARNING: You're using a non-UTF8 locale, therefore only ASCII characters
> will work.*
> *Please read R for Mac OS X FAQ (see Help) section 9 and adjust your system
> preferences accordingly.*
> *[History restored from /Users/sennorg/.Rapp.history]*
> 
> *starting httpd help server ... done*
> *> *
> *> *
> 
> How can i fix this..?? Need your help ASAP..
> 
> Kind regards..
> 
> 
> 
> *Senyo Norgbey, MD**MS Candidate '14*
> 
> *Johns Hopkins University School of Medicine, *
> *Division of Health Sciences Informatics,*
> 
> *2024 East Monument Street/Suite 1-200*
> 
> *Baltimore, MD 21205*
> 
> 
> *(+1) 443-529-3519(+233) 24-335-5561*
> 
> 
> 
> *[email protected] [email protected] *
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: [email protected]  Priv: [email protected]

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Re: [R-SIG-Mac] HELP: R for Mac OS 10.9 Mavericks Malfunction

2014-07-03 Thread Senyo Norgbey, MD

Ok Adrian..

Will try that and give you feedback..

Thanks a lot..

Kind regards..



*Senyo Norgbey, MD**MS Candidate '14*

*Johns Hopkins University School of Medicine, *
*Division of Health Sciences Informatics,*

*2024 East Monument Street/Suite 1-200*

*Baltimore, MD 21205*


*(+1) 443-529-3519(+233) 24-335-5561*



*[email protected] [email protected] *

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[R-SIG-Mac] HELP: R for Mac OS 10.9 Mavericks Malfunction

2014-07-03 Thread Senyo Norgbey, MD

Hello..

After installing the above named version of R on my Macbook Pro and
starting it, the message below appears in the R window...

*R version 3.1.0 (2014-04-10) -- "Spring Dance"*
*Copyright (C) 2014 The R Foundation for Statistical Computing*
*Platform: x86_64-apple-darwin13.1.0 (64-bit)*

*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.*

*During startup - Warning messages:*
*1: Setting LC_CTYPE failed, using "C" *
*2: Setting LC_COLLATE failed, using "C" *
*3: Setting LC_TIME failed, using "C" *
*4: Setting LC_MESSAGES failed, using "C" *
*5: Setting LC_MONETARY failed, using "C" *
*[R.app GUI 1.63 (6734) x86_64-apple-darwin13.1.0]*

*WARNING: You're using a non-UTF8 locale, therefore only ASCII characters
will work.*
*Please read R for Mac OS X FAQ (see Help) section 9 and adjust your system
preferences accordingly.*
*[History restored from /Users/sennorg/.Rapp.history]*

*starting httpd help server ... done*
*> *
*> *

How can i fix this..?? Need your help ASAP..

Kind regards..



*Senyo Norgbey, MD**MS Candidate '14*

*Johns Hopkins University School of Medicine, *
*Division of Health Sciences Informatics,*

*2024 East Monument Street/Suite 1-200*

*Baltimore, MD 21205*


*(+1) 443-529-3519(+233) 24-335-5561*



*[email protected] [email protected] *

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Re: [R-SIG-Mac] Help on the quartz font problem

2013-07-12 Thread Yanyuan Zhu

Dear David

I tried to hide all my personal fonts in the directory 
/Users/(home)/Library/Fonts, and use the system fonts only, then it works fine. 
You are right, thanks !


On Jul 13, 2013, at 1:54 AM, David Winsemius  wrote:

> 
> On Jul 12, 2013, at 3:45 AM, Yanyuan Zhu wrote:
> 
>> Dear All, I got some problems in displaying my font when I plot by R.
>> 
>> Here's the environment I use
>> x86_64-apple-darwin10.8.0
>> R version 3.0.1 (2013-05-16) -- "Good Sport"
>> 
>> When I try to plot a figure in either Rstudio or Emacs(with ESS), for 
>> example, the following command
>> 
>> plot(Dep.real.ln~AggGRP.real.ln,
>> ylab="Depreciation (ln)", 
>> xlab=expression(paste(Sigma, " GRP (ln)"))
>> )
>> abline(DepAggGRP.lm)
>> b0 <- round(DepAggGRP.lm.sum$coefficients[1,1], 2)
>> b1 <- round(DepAggGRP.lm.sum$coefficients[2,1],2)
>> r2 <- round(DepAggGRP.lm.sum$r.squared,2)
>> eqn <- bquote(italic(y)==.(b0)+.(b1)*italic(x)*"," ~~r^2==.(r2))
>> #italic(y) == .(b0) + .(b1) * italic(x) ","~~R^2 == .(r2))
>> text(9.5, 7.0, eqn, pos=4)
>> 
>> I got the output pdf like attached. Obviously the font fails to display 
>> greek words in xlab, and some basic operation symbols in text(). I try to 
>> open the pdf in PDF viewer, say, acrobat reader, it works fine, as attached.
>> 
>> After googling a while, I see it might be due to the quartz settings. But I 
>> really dont know how to do that: can I change my settings, to let my quartz 
>> display plot font correctly, just like the acrobat reader does, plz?
>> 
> 
> I suspect you have two copies of the Symbol font on you machine, one of which 
> is corrupt,  and that AcrobatReader is smarter than RStudio in deciding which 
> one to access. Use Fontbook.app (possibily in /Applications/Utilities/ if not 
> in /Applications/ ) to see if my guess is correct ...  and if it is, then 
> delete the one that displays a blank page.
> 
> -- 
> David.
> 
> 
>> thanks in advance.
>> 
>> here are some of my  R output that might be needed.
>> 
>>> quartzFont()
>> Error in checkQuartzFont(family) : 
>>  argument "family" is missing, with no default
>>> quartzFonts()
>> $serif
>> [1] "Times-Roman"  "Times-Bold"   "Times-Italic"
>> [4] "Times-BoldItalic"
>> 
>> $sans
>> [1] "Helvetica" "Helvetica-Bold"   
>> [3] "Helvetica-Oblique" "Helvetica-BoldOblique"
>> 
>> $mono
>> [1] "Courier" "Courier-Bold""Courier-Oblique"
>> [4] "Courier-BoldOblique"
>> 
>> 
>> -- 
>> > PM.png>___
>> R-SIG-Mac mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius
> Alameda, CA, USA
> 
> 

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Re: [R-SIG-Mac] Help on the quartz font problem

2013-07-12 Thread David Winsemius


On Jul 12, 2013, at 3:45 AM, Yanyuan Zhu wrote:

> Dear All, I got some problems in displaying my font when I plot by R.
> 
> Here's the environment I use
> x86_64-apple-darwin10.8.0
> R version 3.0.1 (2013-05-16) -- "Good Sport"
> 
> When I try to plot a figure in either Rstudio or Emacs(with ESS), for 
> example, the following command
> 
> plot(Dep.real.ln~AggGRP.real.ln,
>  ylab="Depreciation (ln)", 
>  xlab=expression(paste(Sigma, " GRP (ln)"))
>  )
> abline(DepAggGRP.lm)
> b0 <- round(DepAggGRP.lm.sum$coefficients[1,1], 2)
> b1 <- round(DepAggGRP.lm.sum$coefficients[2,1],2)
> r2 <- round(DepAggGRP.lm.sum$r.squared,2)
> eqn <- bquote(italic(y)==.(b0)+.(b1)*italic(x)*"," ~~r^2==.(r2))
> #italic(y) == .(b0) + .(b1) * italic(x) ","~~R^2 == .(r2))
> text(9.5, 7.0, eqn, pos=4)
> 
> I got the output pdf like attached. Obviously the font fails to display greek 
> words in xlab, and some basic operation symbols in text(). I try to open the 
> pdf in PDF viewer, say, acrobat reader, it works fine, as attached.
> 
> After googling a while, I see it might be due to the quartz settings. But I 
> really dont know how to do that: can I change my settings, to let my quartz 
> display plot font correctly, just like the acrobat reader does, plz?
> 

I suspect you have two copies of the Symbol font on you machine, one of which 
is corrupt,  and that AcrobatReader is smarter than RStudio in deciding which 
one to access. Use Fontbook.app (possibily in /Applications/Utilities/ if not 
in /Applications/ ) to see if my guess is correct ...  and if it is, then 
delete the one that displays a blank page.

-- 
David.


> thanks in advance.
> 
> here are some of my  R output that might be needed.
> 
> > quartzFont()
> Error in checkQuartzFont(family) : 
>   argument "family" is missing, with no default
> > quartzFonts()
> $serif
> [1] "Times-Roman"  "Times-Bold"   "Times-Italic"
> [4] "Times-BoldItalic"
> 
> $sans
> [1] "Helvetica" "Helvetica-Bold"   
> [3] "Helvetica-Oblique" "Helvetica-BoldOblique"
> 
> $mono
> [1] "Courier" "Courier-Bold""Courier-Oblique"
> [4] "Courier-BoldOblique"
> 
> 
> -- 
>  PM.png>___
> R-SIG-Mac mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] help(foo, help_type = "text")

2013-03-15 Thread David Winsemius


On Mar 14, 2013, at 2:58 PM, ian m s white wrote:

> When I use the R.app GUI, underlined text produced by help(…, help_type = 
> "text") appears as
> 
> _^Ht_^He_^Hx_^Ht
> 
> (for example). Any cure for this?

If you choose an external editor (in the Editor Preferences panel), you get 
whatever display style that editor executes for highlighted/underlined text. 
Textwrangler.app will display it with interspersed underline characters.

-- 
David.

> 
>> sessionInfo()
> R version 2.15.3 (2013-03-01)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base 
> 
> loaded via a namespace (and not attached):
> [1] tools_2.15.3
>> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> ___
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David Winsemius
Alameda, CA, USA

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[R-SIG-Mac] help(foo, help_type = "text")

2013-03-14 Thread ian m s white

When I use the R.app GUI, underlined text produced by help(…, help_type = 
"text") appears as

_^Ht_^He_^Hx_^Ht

(for example). Any cure for this?

> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

loaded via a namespace (and not attached):
[1] tools_2.15.3
> 
-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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Re: [R-SIG-Mac] help with Tcl/Tk

2012-12-05 Thread Ivan Calandra


Hi Ray!

That was it!! I didn't know about this, but now it works perfectly; 
thanks a lot!


Ivan

--
Ivan CALANDRA
Université de Bourgogne
UMR CNRS/uB 6282 Biogéosciences
6 Boulevard Gabriel
21000 Dijon, FRANCE
+33(0)3.80.39.63.06
[email protected]
http://biogeosciences.u-bourgogne.fr/calandra

Le 04/12/12 17:53, Ray DiGiacomo, Jr. a écrit :

Bonjour Ivan,

Did you have a chance to install the "tcltk-8.5.5-x11.dmg" file at:

http://cran.r-project.org/bin/macosx/tools/

Best Regards,

Ray DiGiacomo, Jr.
Healthcare Predictive Analytics Specialist
Master R Trainer
President, Lion Data Systems LLC
President, The Orange County R User Group
Board Member, TDWI
[email protected] 
(m) 408-425-7851
San Juan Capistrano, California USA
twitter.com/liondatasystems 
linkedin.com/in/raydigiacomojr 
youtube.com/user/liondatasystems/videos 



Check out my one-on-one web-based R Training Courses at 
liondatasystems.com/courses 








On Tue, Dec 4, 2012 at 1:51 AM, Ivan Calandra 
mailto:[email protected]>> 
wrote:


Dear users,

In trying to use tcltk, svDialogs and gsubfn I have encountered an
error that seems to stem from package Tcl/Tk.


I can load tcltk, everything looks fine, but if I try
?tk_choose.dir or whatever, then R hangs and I have to force exit.

I have tried with svDialogs as well and here is what happens:

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

> library(svDialogs)
Le chargement a nécessité le package : svGUI
Le chargement a nécessité le package : svMisc
Le chargement a nécessité le package : tcltk
Chargement de Tcl/Tk...
 *** caught bus error ***
address 0x1, cause 'non-existent physical address'

Traceback:
 1: sys.parent()
 2: sys.function(sys.parent())
 3: formals(sys.function(sys.parent()))
 4: match.arg(encoding)
 5: match(match.arg(encoding), c("", "bytes", "UTF-8"))
 6: textConnection("rval", "w", local = TRUE)
 7: capture.output(print(args(dlgDir)))
 8: paste(capture.output(print(args(dlgDir))), collapse = "")
 9: gsub("\\s+", " ", paste(capture.output(print(args(dlgDir))),
collapse = ""))
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(expr, error = function(e) {call <-
conditionCall(e)if (!is.null(call)) {if
(identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)  
 dcall <- deparse(call)[1L]prefix <- paste("Error in",
dcall, ": ")LONG <- 75L msg <- conditionMessage(e)  
 sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type =

"w") + nchar(sm[1L], type = "w")if (is.na
(w)) w <- 14L + nchar(dcall, type = "b")
+ nchar(sm[1L], type = "b")if (w > LONG)
prefix <- paste0(prefix, "\n  ")} else prefix <- "Error : "  
 msg <- paste0(prefix, conditionMessage(e), "\n")

.Internal(seterrmessage(msg[1L]))if (!silent &&
identical(getOption("show.error.messages"), TRUE)) { cat(msg,
file = stderr()) .Internal(printDeferredWarnings())}
invisible(structure(msg, class = "try-error", condition = e))})
14: try(gsub("\\s+", " ",
paste(capture.output(print(args(dlgDir))), collapse = "")),
silent = TRUE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

> mydir <- dlgDir()

Everything from ***caught bus error*** appears only when I type
the last line (mydir <- dlgDir()).

I have the same problem with any function from gsubfn, i.e. any
function that uses tcltk...


Can anyone help me?

Ivan

-- 
Ivan CALANDRA

Université de Bourgogne
UMR CNRS/uB 6282 Biogéosciences
6 Boulevard Gabriel
21000 Dijon, FRANCE
+33(0)3.80.39.63.06 
[email protected] 
http://biogeosciences.u-bourgogne.fr/calandra

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Re: [R-SIG-Mac] help with Tcl/Tk

2012-12-04 Thread Ray DiGiacomo, Jr.

Bonjour Ivan,

Did you have a chance to install the "tcltk-8.5.5-x11.dmg" file at:

http://cran.r-project.org/bin/macosx/tools/

Best Regards,

Ray DiGiacomo, Jr.
Healthcare Predictive Analytics Specialist
Master R Trainer
President, Lion Data Systems LLC
President, The Orange County R User Group
Board Member, TDWI
[email protected]
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On Tue, Dec 4, 2012 at 1:51 AM, Ivan Calandra
wrote:

> Dear users,
>
> In trying to use tcltk, svDialogs and gsubfn I have encountered an error
> that seems to stem from package Tcl/Tk.
>
>
> I can load tcltk, everything looks fine, but if I try ?tk_choose.dir or
> whatever, then R hangs and I have to force exit.
>
> I have tried with svDialogs as well and here is what happens:
>
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> locale:
> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.**UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-**8
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> > library(svDialogs)
> Le chargement a nécessité le package : svGUI
> Le chargement a nécessité le package : svMisc
> Le chargement a nécessité le package : tcltk
> Chargement de Tcl/Tk...
>  *** caught bus error ***
> address 0x1, cause 'non-existent physical address'
>
> Traceback:
>  1: sys.parent()
>  2: sys.function(sys.parent())
>  3: formals(sys.function(sys.**parent()))
>  4: match.arg(encoding)
>  5: match(match.arg(encoding), c("", "bytes", "UTF-8"))
>  6: textConnection("rval", "w", local = TRUE)
>  7: capture.output(print(args(**dlgDir)))
>  8: paste(capture.output(print(**args(dlgDir))), collapse = "")
>  9: gsub("\\s+", " ", paste(capture.output(print(**args(dlgDir))),
> collapse = ""))
> 10: doTryCatch(return(expr), name, parentenv, handler)
> 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 12: tryCatchList(expr, classes, parentenv, handlers)
> 13: tryCatch(expr, error = function(e) {call <- conditionCall(e)if
> (!is.null(call)) {if (identical(call[[1L]], quote(doTryCatch)))
> call <- sys.call(-4L)dcall <- deparse(call)[1L]
>  prefix <- paste("Error in", dcall, ": ")LONG <- 75L msg <-
> conditionMessage(e)sm <- strsplit(msg, "\n")[[1L]] w <- 14L +
> nchar(dcall, type = "w") + nchar(sm[1L], type = "w")if (is.na(w))
> w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
> type = "b")if (w > LONG) prefix <- paste0(prefix,
> "\n  ")} else prefix <- "Error : "msg <- paste0(prefix,
> conditionMessage(e), "\n") .Internal(seterrmessage(msg[**1L]))if
> (!silent && identical(getOption("show.**error.messages"), TRUE))
> { cat(msg, file = stderr()) .Internal(**printDeferredWarnings())}
> invisible(structure(msg, class = "try-error", condition = e))})
> 14: try(gsub("\\s+", " ", paste(capture.output(print(**args(dlgDir))),
>   collapse = "")), silent = TRUE)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> > mydir <- dlgDir()
>
> Everything from ***caught bus error*** appears only when I type the last
> line (mydir <- dlgDir()).
>
> I have the same problem with any function from gsubfn, i.e. any function
> that uses tcltk...
>
>
> Can anyone help me?
>
> Ivan
>
> --
> Ivan CALANDRA
> Université de Bourgogne
> UMR CNRS/uB 6282 Biogéosciences
> 6 Boulevard Gabriel
> 21000 Dijon, FRANCE
> +33(0)3.80.39.63.06
> [email protected]
> http://biogeosciences.u-**bourgogne.fr/calandra
>
> __**_
> R-SIG-Mac mailing list
> [email protected]
> https://stat.ethz.ch/mailman/**listinfo/r-sig-mac
>

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[R-SIG-Mac] help with Tcl/Tk

2012-12-04 Thread Ivan Calandra


Dear users,

In trying to use tcltk, svDialogs and gsubfn I have encountered an error 
that seems to stem from package Tcl/Tk.


I can load tcltk, everything looks fine, but if I try ?tk_choose.dir or 
whatever, then R hangs and I have to force exit.


I have tried with svDialogs as well and here is what happens:

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

> library(svDialogs)
Le chargement a nécessité le package : svGUI
Le chargement a nécessité le package : svMisc
Le chargement a nécessité le package : tcltk
Chargement de Tcl/Tk...
 *** caught bus error ***
address 0x1, cause 'non-existent physical address'

Traceback:
 1: sys.parent()
 2: sys.function(sys.parent())
 3: formals(sys.function(sys.parent()))
 4: match.arg(encoding)
 5: match(match.arg(encoding), c("", "bytes", "UTF-8"))
 6: textConnection("rval", "w", local = TRUE)
 7: capture.output(print(args(dlgDir)))
 8: paste(capture.output(print(args(dlgDir))), collapse = "")
 9: gsub("\\s+", " ", paste(capture.output(print(args(dlgDir))), 
collapse = ""))

10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(expr, error = function(e) {call <- conditionCall(e)
if (!is.null(call)) {if (identical(call[[1L]], 
quote(doTryCatch))) call <- sys.call(-4L)dcall <- 
deparse(call)[1L]prefix <- paste("Error in", dcall, ": ")
LONG <- 75L msg <- conditionMessage(e)sm <- strsplit(msg, 
"\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = 
"w")if (is.na(w)) w <- 14L + nchar(dcall, type = 
"b") + nchar(sm[1L], type = "b")if (w > 
LONG) prefix <- paste0(prefix, "\n  ")} else prefix <- 
"Error : "msg <- paste0(prefix, conditionMessage(e), "\n") 
.Internal(seterrmessage(msg[1L]))if (!silent && 
identical(getOption("show.error.messages"), TRUE)) { cat(msg, 
file = stderr()) .Internal(printDeferredWarnings())} 
invisible(structure(msg, class = "try-error", condition = e))})
14: try(gsub("\\s+", " ", paste(capture.output(print(args(dlgDir))), 
collapse = "")), silent = TRUE)


Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

> mydir <- dlgDir()

Everything from ***caught bus error*** appears only when I type the last 
line (mydir <- dlgDir()).


I have the same problem with any function from gsubfn, i.e. any function 
that uses tcltk...


Can anyone help me?

Ivan

--
Ivan CALANDRA
Université de Bourgogne
UMR CNRS/uB 6282 Biogéosciences
6 Boulevard Gabriel
21000 Dijon, FRANCE
+33(0)3.80.39.63.06
[email protected]
http://biogeosciences.u-bourgogne.fr/calandra

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[R-SIG-Mac] help with Tcl/Tk

2012-11-29 Thread Ivan Calandra


Dear users,

In trying to use tcltk::tk_choose.dir() and svDialogs::dlgDir() I have 
encountered an error that seems to stem from package Tcl/Tk.


I can load tcltk, everything looks fine, but if I try ?tk_choose.dir or 
whatever, then R hangs and I have to force exit.


I have tried with svDialogs as well and here is what happens:

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

> library(svDialogs)
Le chargement a nécessité le package : svGUI
Le chargement a nécessité le package : svMisc
Le chargement a nécessité le package : tcltk
Chargement de Tcl/Tk...
 *** caught bus error ***
address 0x1, cause 'non-existent physical address'

Traceback:
 1: sys.parent()
 2: sys.function(sys.parent())
 3: formals(sys.function(sys.parent()))
 4: match.arg(encoding)
 5: match(match.arg(encoding), c("", "bytes", "UTF-8"))
 6: textConnection("rval", "w", local = TRUE)
 7: capture.output(print(args(dlgDir)))
 8: paste(capture.output(print(args(dlgDir))), collapse = "")
 9: gsub("\\s+", " ", paste(capture.output(print(args(dlgDir))), 
collapse = ""))

10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(expr, error = function(e) {call <- conditionCall(e)
if (!is.null(call)) {if (identical(call[[1L]], 
quote(doTryCatch))) call <- sys.call(-4L)dcall <- 
deparse(call)[1L]prefix <- paste("Error in", dcall, ": ")
LONG <- 75L msg <- conditionMessage(e)sm <- strsplit(msg, 
"\n")[[1L]]w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], 
type = "w")if (is.na(w)) w <- 14L + nchar(dcall, 
type = "b") + nchar(sm[1L], type = "b")if (w > 
LONG) prefix <- paste0(prefix, "\n  ")}else prefix 
<- "Error : "msg <- paste0(prefix, conditionMessage(e), "\n") 
.Internal(seterrmessage(msg[1L]))if (!silent && 
identical(getOption("show.error.messages"), TRUE)) { cat(msg, 
file = stderr()) .Internal(printDeferredWarnings())}
invisible(structure(msg, class = "try-error", condition = e))})
14: try(gsub("\\s+", " ", paste(capture.output(print(args(dlgDir))), 
collapse = "")), silent = TRUE)


Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

> mydir <- dlgDir()

Everything from ***caught bus error*** appears only when I type the last 
line (mydir <- dlgDir()).


Can anyone help me?

Ivan

--
Ivan CALANDRA
Université de Bourgogne
UMR CNRS/uB 6282 Biogéosciences
6 Boulevard Gabriel
21000 Dijon, FRANCE
+33(0)3.80.39.63.06
[email protected]
http://biogeosciences.u-bourgogne.fr/calandra

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Re: [R-SIG-Mac] HELP : problem "failed" during installation R for Mac OS X

2012-10-17 Thread Simon Urbanek

Agnesia,

On Oct 16, 2012, at 7:03 PM, agnesia adhissa wrote:

> Dear All,
> 
> I am so sorry, i would like to ask about my problem during installation of R 
> in my mac. I already installed the R 2.15.1 package. But there are some error 
> appears in the windows, which are :
> 
> 
> During startup - Warning messages:
> 1: Setting LC_CTYPE failed, using "C" 
> 2: Setting LC_COLLATE failed, using "C" 
> 3: Setting LC_TIME failed, using "C" 
> 4: Setting LC_MESSAGES failed, using "C" 
> 5: Setting LC_PAPER failed, using "C" 
> [R.app GUI 1.52 (6188) i386-apple-darwin9.8.0]
> 
> WARNING: You're using a non-UTF8 locale, therefore only ASCII characters will 
> work.
> Please read R for Mac OS X FAQ (see Help) section 9 and adjust your system 
> preferences accordingly.
> 
> Besides that, i can not work on the "New Document" or "New Rd Document". I 
> can only work on the R console. I need to work in other new documents so that 
> i will be able to save the file and commands includes in it. 
> 
> What should i do to make the R works on my Mac? Do i need to download another 
> source? I already read the FAQ but i did not find anything that suits my 
> problems. I am looking forward for your help.
> 

The Mac FAQ 9:
http://r.research.att.com/man/RMacOSX-FAQ.html#Internationalization-of-the-R_002eapp
suits your problem exactly as the message says - please follow the advice it 
gives.

Cheers,
Simon


> Thank you very much in advance for your help.
> 
> Sincerely,
> 
> agnesia
>   [[alternative HTML version deleted]]
> 
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[R-SIG-Mac] HELP : problem "failed" during installation R for Mac OS X

2012-10-17 Thread agnesia adhissa

Dear All,

I am so sorry, i would like to ask about my problem during installation of R in 
my mac. I already installed the R 2.15.1 package. But there are some error 
appears in the windows, which are :


During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_PAPER failed, using "C" 
[R.app GUI 1.52 (6188) i386-apple-darwin9.8.0]

WARNING: You're using a non-UTF8 locale, therefore only ASCII characters will 
work.
Please read R for Mac OS X FAQ (see Help) section 9 and adjust your system 
preferences accordingly.

Besides that, i can not work on the "New Document" or "New Rd Document". I can 
only work on the R console. I need to work in other new documents so that i 
will be able to save the file and commands includes in it. 

What should i do to make the R works on my Mac? Do i need to download another 
source? I already read the FAQ but i did not find anything that suits my 
problems. I am looking forward for your help.

Thank you very much in advance for your help.

Sincerely,

agnesia
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Re: [R-SIG-Mac] Help on using R CMD SHLIB for compiling shared libraries calling Fortran?

2011-12-14 Thread Jooil Kim

Hi Simon, 

Thanks, I'll try that!

Cheers,

Jooil 

-- 
Jooil Kim
Postdoc Fellow
Scripps Institution of Oceanography, UC San Diego
Mailing address:
9500 Gilman Drive # 0244
La Jolla, CA 92093-0244, USA
For FedEx/UPS:
8675 Discovery Way, Vaughan Hall Rm. 447
La Jolla, CA 92037, USA



On Tuesday, December 13, 2011 at 5:51 PM, Simon Urbanek wrote:

> Jooil,
> 
> most recent Xcode in Lion removes gcc-4.2, so you may want to install it from 
> either from Xcode 4.0/4.1 or from
> http://r.research.att.com/tools/
> 
> The direct link is
> http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg
> 
> Also you can remove the Fortran you installed before (using 
> gfortran-uninstall) since more recent Fortran is part of the above package.
> 
> Cheers,
> Simon
> 
> 
> On Dec 13, 2011, at 6:17 PM, Jooil Kim wrote:
> 
> > Hello all,
> > 
> > I'm interested in calling some Fortran subroutines in R, and I have been 
> > trying out R CMD SHLIB.
> > 
> > I'm using R ver 2.14.0, and just installed the latest version of Xcode 
> > 4.2.1. I also downloaded and installed gfortran 4.2.3 (from the .dmg at 
> > http://cran.r-project.org/bin/macosx/tools/). My OS is Lion, with the 
> > latest updates (10.7.2) on a MacBook Pro about 2 years old.
> > 
> > So when I go to the command line and type the SHLIB command, I get:
> > 
> > $ R CMD SHLIB readgrid.f
> > gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib 
> > -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module 
> > -multiply_defined suppress -L/usr/local/lib -o readgrid.so readgrid.o 
> > -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> > -Wl,CoreFoundation
> > /bin/sh: gcc-4.2: command not found
> > make: *** [readgrid.so] Error 127
> > 
> > 
> > 
> > I think the problem is that the SHLIB command looks for "gcc-4.2" instead 
> > of "gcc". I also get a similar error ("gcc-4.2: command not found") when I 
> > try with a very simple "foo.c" program. I've tried looking through the 
> > documentation I could find, but didn't find any relevant info. Can someone 
> > give me advise on how to do this properly? Do I need to install another 
> > version of GCC on my mac?
> > 
> > 
> > Thanks,
> > 
> > Jooil
> > 
> > -- 
> > Jooil Kim
> > Postdoc Fellow
> > Scripps Institution of Oceanography, UC San Diego
> > Mailing address:
> > 9500 Gilman Drive # 0244
> > La Jolla, CA 92093-0244, USA
> > For FedEx/UPS:
> > 8675 Discovery Way, Vaughan Hall Rm. 447
> > La Jolla, CA 92037, USA
> > 
> > 
> > 
> > [[alternative HTML version deleted]]
> > 
> > ___
> > R-SIG-Mac mailing list
> > [email protected] (mailto:[email protected])
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > 
> 
> 
> 



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Re: [R-SIG-Mac] Help on using R CMD SHLIB for compiling shared libraries calling Fortran?

2011-12-13 Thread Simon Urbanek

Jooil,

most recent Xcode in Lion removes gcc-4.2, so you may want to install it from 
either from Xcode 4.0/4.1 or from
http://r.research.att.com/tools/

The direct link is
http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg

Also you can remove the Fortran you installed before (using gfortran-uninstall) 
since more recent Fortran is part of the above package.

Cheers,
Simon


On Dec 13, 2011, at 6:17 PM, Jooil Kim wrote:

> Hello all,
> 
> I'm interested in calling some Fortran subroutines in R, and I have been 
> trying out R CMD SHLIB.
> 
> I'm using R ver 2.14.0, and just installed the latest version of Xcode 4.2.1. 
> I also downloaded and installed gfortran 4.2.3 (from the .dmg at 
> http://cran.r-project.org/bin/macosx/tools/). My OS is Lion, with the latest 
> updates (10.7.2) on a MacBook Pro about 2 years old.
> 
> So when I go to the command line and type the SHLIB command, I get:
> 
> $ R CMD SHLIB readgrid.f
> gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names 
> -undefined dynamic_lookup -single_module -multiply_defined suppress 
> -L/usr/local/lib -o readgrid.so readgrid.o -lgfortran 
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> -Wl,CoreFoundation
> /bin/sh: gcc-4.2: command not found
> make: *** [readgrid.so] Error 127
> 
> 
> 
> I think the problem is that the SHLIB command looks for "gcc-4.2" instead of 
> "gcc". I also get a similar error ("gcc-4.2: command not found") when I try 
> with a very simple "foo.c" program. I've tried looking through the 
> documentation I could find, but didn't find any relevant info. Can someone 
> give me advise on how to do this properly? Do I need to install another 
> version of GCC on my mac?
> 
> 
> Thanks,
> 
> Jooil
> 
> -- 
> Jooil Kim
> Postdoc Fellow
> Scripps Institution of Oceanography, UC San Diego
> Mailing address:
> 9500 Gilman Drive # 0244
> La Jolla, CA 92093-0244, USA
> For FedEx/UPS:
> 8675 Discovery Way, Vaughan Hall Rm. 447
> La Jolla, CA 92037, USA
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> R-SIG-Mac mailing list
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> 
> 

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[R-SIG-Mac] Help on using R CMD SHLIB for compiling shared libraries calling Fortran?

2011-12-13 Thread Jooil Kim

Hello all,

I'm interested in calling some Fortran subroutines in R, and I have been trying 
out R CMD SHLIB.

I'm using R ver 2.14.0, and just installed the latest version of Xcode 4.2.1. I 
also downloaded and installed gfortran 4.2.3 (from the .dmg at 
http://cran.r-project.org/bin/macosx/tools/). My OS is Lion, with the latest 
updates (10.7.2) on a MacBook Pro about 2 years old.

So when I go to the command line and type the SHLIB command, I get:

$ R CMD SHLIB readgrid.f
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names 
-undefined dynamic_lookup -single_module -multiply_defined suppress 
-L/usr/local/lib -o readgrid.so readgrid.o -lgfortran 
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
-Wl,CoreFoundation
/bin/sh: gcc-4.2: command not found
make: *** [readgrid.so] Error 127



I think the problem is that the SHLIB command looks for "gcc-4.2" instead of 
"gcc". I also get a similar error ("gcc-4.2: command not found") when I try 
with a very simple "foo.c" program. I've tried looking through the 
documentation I could find, but didn't find any relevant info. Can someone give 
me advise on how to do this properly? Do I need to install another version of 
GCC on my mac?


Thanks,

Jooil

-- 
Jooil Kim
Postdoc Fellow
Scripps Institution of Oceanography, UC San Diego
Mailing address:
9500 Gilman Drive # 0244
La Jolla, CA 92093-0244, USA
For FedEx/UPS:
8675 Discovery Way, Vaughan Hall Rm. 447
La Jolla, CA 92037, USA



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Re: [R-SIG-Mac] Help rJava and imaplib.

2011-08-17 Thread Simon Urbanek


On Aug 17, 2011, at 8:15 AM, Bhima Pandava wrote:

> I am trying to teach myself a little R and recently I found an entry 
> over at R-Bloggers & Expansed, on how to create social graphs from your 
> email 
> , that 
> interested me.
> 
> I am using Mac OS Lion, so I installed the R-2.13.1pkg and the R.app 
> R-2.13-patched.  The script requires the Network, rJython, and rJava 
> libraries, so I installed these as binaries.  Mac OS Lion does not come 
> with a Java Development Kit installed,


It does (it will be installed the first time you try to use it). You may want 
to give it a shot - using MacPorts may be your problem.

Cheers,
Simon


> so I installed one from Mac Ports 
> and then I also tried building it from source based on the 
> instructions.  I then registered the JDK with R using "sudo R CMD 
> javareconf".  The script fails when executed with the following error:
> 
> Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :
>   Traceback (most recent call last):
>   File "", line 1, in 
>   File 
> "/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py",
>  
> line 437, in fetch
>   File 
> "/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py",
>  
> line 1055, in _simple_command
>   File 
> "/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py",
>  
> line 892, in _command_complete
> imaplib.error: FETCH command error: BAD ['Could not parse command']
> 
> I have tried many, many different things but I simply can not work out 
> how to make this work.  As other people sound like they have run this, 
> it is a mystery to me.  One of the things I have tried was trying the 
> same thing in a virtual instance of Linux running on my Mac and that 
> segfaults.  Another is installing the rJava library as source, so that 
> it would be compiled on my machine.  This fails due to R expecting a 
> different framework version.  The error returned is:
> 
> checking whether JNI programs can be compiled... configure: error: 
> Cannot compile a simple JNI program. See config.log for details.
> 
> and checking the log I find:
> 
> Dyld Error Message:
>   Library not loaded: 
> /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib
>   Referenced from: /Applications/R.app/Contents/MacOS/R
>   Reason: image not found
> 
> I am using Framework version 2.13, so I do not even have a directory for 
> version 2.12.  The file "libR.dylib" is in the right place for 2.13 but 
> I do not know how to configure R.app to use a particular version of the 
> Framework.  Or even if this is actually the root of the problem above.
> 
> If anyone has any suggestions I would appreciate it... or even if 
> someone could try the script Expansed published and see if it works for 
> them, I would appreciate that as well.
> 
> Thanks!
> 
>   [[alternative HTML version deleted]]
> 
> ___
> R-SIG-Mac mailing list
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 

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[R-SIG-Mac] Help rJava and imaplib.

2011-08-17 Thread Bhima Pandava

I am trying to teach myself a little R and recently I found an entry
over at R-Bloggers & Expansed, on how to create social graphs from your
email
, that
interested me.

I am using Mac OS Lion, so I installed the R-2.13.1pkg and the R.app
R-2.13-patched. The script requires the Network, rJython, and rJava
libraries, so I installed these as binaries. Mac OS Lion does not come
with a Java Development Kit installed, so I installed one from Mac Ports
and then I also tried building it from source based on the
instructions. I then registered the JDK with R using "sudo R CMD
javareconf". The script fails when executed with the following error:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
Traceback (most recent call last):
File "", line 1, in
File
"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py",

line 437, in fetch
File
"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py",

line 1055, in _simple_command
File
"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py",

line 892, in _command_complete
imaplib.error: FETCH command error: BAD ['Could not parse command']

I have tried many, many different things but I simply can not work out
how to make this work. As other people sound like they have run this,
it is a mystery to me. One of the things I have tried was trying the
same thing in a virtual instance of Linux running on my Mac and that
segfaults. Another is installing the rJava library as source, so that
it would be compiled on my machine. This fails due to R expecting a
different framework version. The error returned is:

checking whether JNI programs can be compiled... configure: error:
Cannot compile a simple JNI program. See config.log for details.

and checking the log I find:

Dyld Error Message:
Library not loaded:
/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib
Referenced from: /Applications/R.app/Contents/MacOS/R
Reason: image not found

I am using Framework version 2.13, so I do not even have a directory for
version 2.12. The file "libR.dylib" is in the right place for 2.13 but
I do not know how to configure R.app to use a particular version of the
Framework. Or even if this is actually the root of the problem above.

If anyone has any suggestions I would appreciate it... or even if
someone could try the script Expansed published and see if it works for
them, I would appreciate that as well.

Thanks!

[[alternative HTML version deleted]]

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