Hi Matt

Installation of Bioconductor packages works fine with biocLite.  When I tried to install an R package, RMySQL, I got an error related to tcltk:  

> options(pkgType="source")
> install.packages(pkgs ="RMySQL",type ="source", lib ="/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64")
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/Library/Frameworks/R.framework/Resources/library/tcltk/libs/x86_64/tcltk.so':
  dlopen(/Library/Frameworks/R.framework/Resources/library/tcltk/libs/x86_64/tcltk.so, 10): Library not loaded: /usr/local/X11R7/lib/libX11.6.dylib
  Referenced from: /usr/local/lib/libtk8.4.dylib
  Reason: image not found
Error: .onLoad failed in 'loadNamespace' for 'tcltk'
> 
I tried to install tcltk but I got the same error.
I googled this error but I did not get anywhere; can you please help me to solve this issue?
Thanks

> sessionInfo()
R version 2.8.0 Under development (unstable) (2008-07-24 r46120) 
i386-apple-darwin9.4.0 
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
> 

Joseph



----- Original Message ----
From: Matthew Keller <mckellercran@gmail.com>
To: joseph <jdsandjd@yahoo.com>
Sent: Sunday, July 27, 2008 5:46:21 PM
Subject: Re: [R] 64-bit R on Mac OS X 10.5.4

Joseph,

You tell R where the packages are in two ways.
1) see ?library. use the lib.loc argument
2) or set it in options. see my webpage.

The command to tell if it is 32 or 64
.Machine$sizeof.pointer

if it is 4 it is 32-bit and if 8 is 64

Best,

Matt


On Sun, Jul 27, 2008 at 5:10 PM, joseph <jdsandjd@yahoo.com> wrote:
> Hi Matt
> I successfully installed the Bioconductor packages in RLib64 by doing the
> following:
> export PATH=$PATH:/usr/local/bin
> R --arch=x86_64
> source("http://bioconductor.org/biocLite.R")
> biocLite(type="source",lib="/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64")
>
> However, I got an error when I tried to load one of the packages:
>
>> library(affy)
> Error in library(affy) : there is no package called 'affy'
>> sessionInfo()
> R version 2.8.0 Under development (unstable) (2008-07-24 r46120)
> i386-apple-darwin9.4.0
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>
>
> How do you tell R that the packages are in RLib64?
> Also, what command do you use to check that your are running the 64-bit and
> not the 32-bit? I noticed that sessionInfo() does not tell you that.
> Thank you,
> Joseph
>
>
>
> ----- Original Message ----
> From: Matthew Keller <mckellercran@gmail.com>
> To: joseph <jdsandjd@yahoo.com>
> Sent: Sunday, July 27, 2008 1:25:08 PM
> Subject: Re: [R] 64-bit R on Mac OS X 10.5.4
>
> Hi Joseph,
>
> I am no UNIX whiz so take my suggestions with a grain of salt.
>
> From this message ("make: gcc-4.2: Command not found"), it looks like
> either a) you don't have gcc-4.2 installed or b) it is installed but
> your OS isn't aware of where it is.
>
> I would go here to install all compilers (gcc, gfortran, xcode
> development tools) that you'll be needing from here on out in order to
> compile stuff on your own: http://r.research.att.com/tools/
>
> Once compilers are installed, you'll need to 'let your OS know' to
> look in the directory where these compilers live (thus, make sure you
> note where they're being installed). If they are installed in
> /usr/local/bin, then:
> export PATH=$PATH:/usr/local/bin
>
> For whatever reason (I can't remember why) my fortran compilers are in
> /usr/local/bin and my Gnu Compiler Collection (gcc) are in /usr/bin.
> Thus I also did this:
> export PATH=$PATH:/usr/local/bin
>
> To see what directories are already in your path, type this into terminal:
> $PATH
>
> OK - so I've tried to help you out. Could you return the favor by
> letting me know what ended up working? I'll post it all on my webpage,
>
> Matt
>
>
>
>
>
>
> On Sun, Jul 27, 2008 at 1:39 PM, joseph <jdsandjd@yahoo.com> wrote:
>>
>> Hi Matt
>> Your method is the easiest way for me to install the 64-bit R.  I followed
>> the directions on your web site and then did the following:
>> R --arch=x86_64
>> source("http://bioconductor.org/biocLite.R")
>> biocLite(type = "source",lib =
>> "/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64")
>>
>> I got many errors and warnings which I copied to the attached file.
>> Any suggestions on how to fix the errors will be appreciated.
>> Thank you for your help
>> Joseph
>>
>>
>>> sessionInfo()
>> R version 2.8.0 Under development (unstable) (2008-07-24 r46120)
>> i386-apple-darwin9.4.0
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> attached base packages:
>> [1] stats    graphics  grDevices utils    datasets  methods  base
>> loaded via a namespace (and not attached):
>> [1] tools_2.8.0
>>
>> This is the computer I am using:
>> Hardware Overview:
>>  Model Name:    Mac Pro
>>  Model Identifier:    MacPro1,1
>>  Processor Name:    Dual-Core Intel Xeon
>>  Processor Speed:    2.66 GHz
>>  Number Of Processors:    2
>>  Total Number Of Cores:    4
>>  L2 Cache (per processor):    4 MB
>>  Memory:    20 GB
>>  Bus Speed:    1.33 GHz
>>  Boot ROM Version:    MP11.005C.B08
>>  SMC Version:    1.7f10
>>  Serial Number:    G87052SGUPZ
>>
>> System Software Overview:
>>  System Version:    Mac OS X 10.5.4 (9E17)
>>  Kernel Version:    Darwin 9.4.0
>>  Boot Volume:    Macintosh HD
>>  Boot Mode:    Normal
>>
>> ----- Original Message ----
>> From: Matthew Keller <mckellercran@gmail.com>
>> To: Steven McKinney <smckinney@bccrc.ca>
>> Cc: joseph <jdsandjd@yahoo.com>; r-help@r-project.org
>> Sent: Saturday, July 26, 2008 9:15:41 AM
>> Subject: Re: [R] 64-bit R on Mac OS X 10.4.5
>>
>> Hi Joseph,
>>
>> For what it is worth (which might not be that much!), I have written
>> down step by step instructions on my website for getting 64 bit R
>> working under Leopard - it should be much different with Tiger:
>> http://www.matthewckeller.com/html/64_bit_r_on_mac.html. I think it'll
>> work but there may be some mistakes in there. I'd be happy to take
>> suggestions...
>>
>> Matt
>>
>> On Fri, Jul 25, 2008 at 7:23 PM, Steven McKinney <smckinney@bccrc.ca>
>> wrote:
>>>
>>> Hello
>>>
>>> I haven't found better instructions, it's just
>>> not an easy thing to do.
>>>
>>> You might also consider joining the r-sig-mac group
>>> and reviewing threads there for additional information.
>>>
>>> Rather than try to configure, make and install with
>>> one giant command, I'd suggest breaking the task down
>>> until you have worked out all the details.  Then you
>>> can build more routinely with giant commands such as
>>> the one you report below.
>>>
>>> Note that the page of the URL you posted says this:
>>> "R on Mac OS X 10.5 (Leopard)"
>>>
>>> so look around the r.research.att.com
>>> website for older 10.4 related instructions.
>>> OS X 10.5 is different enough from 10.4 that
>>> copying and pasting the 10.5 instructions
>>> will not work everywhere.
>>>
>>> You don't say what kind of computer you have
>>> (Intel or PowerPC), if you have a power pc
>>> then -arch x86_64 is not right.  So do
>>> report your hardware configuration as well
>>> as your operating system configuration.
>>>
>>> Try breaking up the build process into steps
>>> and review the messages generated at each step.
>>>
>>> e.g. the configure step:  Just do these bits
>>>
>>> cd rd64
>>> ../R-devel/configure SHELL='/bin/bash' \
>>> r_arch=x86_64 \
>>> CC="gcc -arch x86_64 -std=gnu99" \
>>> CXX="g++ -arch x86_64" \
>>> OBJC="gcc -arch x86_64" \
>>> F77="gfortran -arch x86_64" \
>>> FC="gfortran -arch x86_64" \
>>> --with-system-zlib \
>>> --with-blas='-framework vecLib' \
>>> --with-lapack 1> configure.R.txt 2>&1
>>>
>>> The end bits of this version of the
>>> configure command redirect output and
>>> error messages to a file that you can then
>>> read, to see which bits you are missing and
>>> which bits cause problems.  It's tough to catch those
>>> as they scroll by in a terminal window.
>>>
>>> If configure runs without any signs of trouble,
>>> try the make.
>>>
>>> make 1> make.R.txt 2>&1
>>>
>>> Then you can review all the make output for signs
>>> of problems and error messages.
>>>
>>>
>>> Here's a configure command that worked for me to
>>> build a 64-bit R on 10.4 a while back:
>>>
>>>
>>> ./configure --host=powerpc64-apple-darwin8.10.0
>>> --build=powerpc64-apple-darwin8.10.0 \
>>> --prefix=/usr/local/lib64 'CC=gcc-4.0 -arch ppc64' 'CXX=g++ -arch ppc64'
>>> \
>>> 'FC=gfortran-4.0 -arch ppc64' 'F77=gfortran-4.0 -arch ppc64' \
>>> 'CFLAGS=-g -O3 -mtune=G5 -mcpu=G5' 'FFLAGS=-g -O3 -mtune=G5 -mcpu=G5' \
>>> 'LDFLAGS=-arch ppc64 -m64 -L/usr/local/lib' 'CXXFLAGS=-g -O3 -mtune=G5
>>> -mcpu=G5' \
>>> 'FCFLAGS=-g -O3 -mtune=G5 -mcpu=G5' --disable-R-framework
>>> --enable-R-shlib
>>> \
>>> '--with-blas=-framework vecLib' --with-lapack --without-iconv 1>
>>> configure.R.txt 2>&1
>>>
>>>
>>> and also note that you need to have root privileges when doing the
>>> make install, so you either need to run the command as root
>>> (not so common on Mac OS X) or run
>>>
>>> sudo make install
>>>
>>> and enter your password etc.
>>>
>>> HTH
>>>
>>> Steve McKinney
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: r-help-bounces@r-project.org on behalf of joseph
>>> Sent: Fri 7/25/2008 5:07 PM
>>> To: r-help@r-project.org
>>> Cc: r-help@r-project.org
>>> Subject: [R] 64-bit R on Mac OS X 10.4.5
>>>
>>> Hello
>>> I have a Mac OS X 10.4.5.  I am trying to build a 64-bit R by following
>>> the directions on this page: http://r.research.att.com/building.html
>>>
>>> r_arch=x86_64 \
>>> CC="gcc -arch x86_64 -std=gnu99" \
>>> CXX="g++ -arch x86_64" \
>>> OBJC="gcc -arch x86_64" \
>>> F77="gfortran -arch x86_64" \
>>> FC="gfortran -arch x86_64"
>>>
>>> PATH=/usr/X11/bin:/usr/local/bin:$PATH
>>> export PATH
>>> LANG=C
>>> export LANG
>>> svn co https://svn.r-project.org/R/trunk R-devel
>>> # you may have to accept a certificate here
>>> cd R-devel
>>> tools/rsync-recommended
>>> cd ..
>>> # got the sources, on to building 64-bit R
>>> mkdir rd64
>>> cd rd64
>>> ../R-devel/configure SHELL='/bin/bash' \
>>> r_arch=x86_64 \
>>> CC="gcc -arch x86_64 -std=gnu99" \
>>> CXX="g++ -arch x86_64" \
>>> OBJC="gcc -arch x86_64" \
>>> F77="gfortran -arch x86_64" \
>>> FC="gfortran -arch x86_64" \
>>> --with-system-zlib \
>>> --with-blas='-framework vecLib' --with-lapack && \
>>> make -j4 && \
>>> make check && \
>>> make install
>>> cd ..when I try to run it by typing R, it gives me the following error:
>>> -bash: R: command not found
>>>
>>>
>>> Can any body help me to solve this problem or direct me to better
>>> step-by-step instructions.
>>> Thanks
>>> Joseph
>>>
>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>>
>> --
>> Matthew C Keller
>> Asst. Professor of Psychology
>> University of Colorado at Boulder
>> www.matthewckeller.com
>>
>>
>
>
>
> --
> Matthew C Keller
> Asst. Professor of Psychology
> University of Colorado at Boulder
> www.matthewckeller.com
>
>



-- 
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com



      
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