Hi Jon.
Hmm, perhaps R-forge hasn't gotten all the R 2.12 binary builds done yet. If I
use type="source", FIRMAGene builds fine for me on Mac OS X ...
> sessionInfo()
R version 2.12.0 Patched (2010-10-19 r53373)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
[snip]
> install.packages("FIRMAGene", repos="http://R-Forge.R-project.org";,
> type="source")
trying URL 'http://R-Forge.R-project.org/src/contrib/FIRMAGene_0.9.5.tar.gz'
Content type 'application/x-gzip' length 9223 bytes
opened URL
==================================================
downloaded 9223 bytes
* installing *source* package ‘FIRMAGene’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include
-fPIC -g -O2 -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include
-fPIC -g -O2 -c mps.c -o mps.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o FIRMAGene.so init.o mps.o
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/FIRMAGene/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include
-fPIC -g -O2 -c init.c -o init.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include
-fPIC -g -O2 -c mps.c -o mps.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o FIRMAGene.so init.o mps.o
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/FIRMAGene/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include -fPIC -g -O2 -c init.c -o init.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include -fPIC -g -O2 -c mps.c -o mps.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o FIRMAGene.so init.o mps.o
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/FIRMAGene/libs/x86_64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (FIRMAGene)
The downloaded packages are in
‘/private/var/folders/8T/8TpdlpGXGzyAaNQm0Wp-zk++mHo/-Tmp-/Rtmph06hxm/downloaded_packages’
Updating HTML index of packages in '.Library'
and Linux:
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)
[snip]
> install.packages("FIRMAGene", repos="http://R-Forge.R-project.org";,
> type="source")
Warning in install.packages("FIRMAGene", repos =
"http://R-Forge.R-project.org";, :
'lib = "/usr/local/bioinfsoftware/R/R-2.12.0/library"' is not writable
Would you like to create a personal library
'~/R/x86_64-unknown-linux-gnu-library/2.12'
to install packages into? (y/n) y
trying URL 'http://R-Forge.R-project.org/src/contrib/FIRMAGene_0.9.5.tar.gz'
Content type 'application/x-gzip' length 9223 bytes
opened URL
==================================================
downloaded 9223 bytes
* installing *source* package ‘FIRMAGene’ ...
** libs
/usr/bin/cc -std=gnu99 -I/usr/local/bioinfsoftware/R/R-2.12.0/include
-I/usr/local/include -fpic -g -O2 -c init.c -o init.o
/usr/bin/cc -std=gnu99 -I/usr/local/bioinfsoftware/R/R-2.12.0/include
-I/usr/local/include -fpic -g -O2 -c mps.c -o mps.o
/usr/bin/cc -std=gnu99 -shared -L/usr/local/lib64 -o FIRMAGene.so init.o mps.o
installing to
/export/share/disk501/lab0605/mrobinson/R/x86_64-unknown-linux-gnu-library/2.12/FIRMAGene/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (FIRMAGene)
So, I'm inclined to think the error has to do with your system. Unfortunately,
I can't help with the actual errors you are getting -- libSystem.dylib
malformed object. A google search popped up a link that may help:
http://hintsforums.macworld.com/archive/index.php/t-273.html
Also, you might check that you have an appropriate version of Dev Tools:
http://developer.apple.com/technologies/tools/
Hope that helps.
Mark
On 2010-10-27, at 1:52 PM, Jon Tang wrote:
> Hi,
>
> I'm having problems installing FIRMAGene on my computer either with the
> install.packages command in R or with the R Package Installer. I keep getting
> the warning message that FIRMAGene is not available. Is there another
> location to get this package? Thanks.
>
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> When I try to install by using the install.packages command, it says the
> package is unavailable:
> > install.packages("FIRMAGene", repos="http://R-Forge.R-project.org";)
> Warning: unable to access index for repository
> http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.12
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
> package ‘FIRMAGene’ is not available
>
>
> If I try to install the package using the R Package Installer, I get the
> following warnings:
> > install.packages("FIRMAGene", repos="http://R-Forge.R-project.org";)
> Warning: unable to access index for repository
> http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.12
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
> package ‘FIRMAGene’ is not available
> trying URL 'http://R-Forge.R-project.org/src/contrib/FIRMAGene_0.9.5.tar.gz'
> Content type 'application/x-gzip' length 9223 bytes
> opened URL
> ==================================================
> downloaded 9223 bytes
>
> * installing *source* package ‘FIRMAGene’ ...
> ** libs
> *** arch - i386
> gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386
> -I/usr/local/include -fPIC -g -O2 -c init.c -o init.o
> gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386
> -I/usr/local/include -fPIC -g -O2 -c mps.c -o mps.o
> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/usr/local/lib -o FIRMAGene.so init.o mps.o
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> /usr/bin/libtool: for architecture ppc7400 object:
> /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libSystem.dylib malformed
> object (unknown load command 7)
> /usr/bin/libtool: for architecture: (null) file: -lSystem is not an object
> file (not allowed in a library)
> /usr/bin/libtool: for architecture ppc64 object:
> /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libSystem.dylib malformed
> object (unknown load command 7)
> make: *** [FIRMAGene.so] Error 1
> ERROR: compilation failed for package ‘FIRMAGene’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/2.12/Resources/library/FIRMAGene’
>
> The downloaded packages are in
>
> ‘/private/var/folders/pQ/pQBxScbYEACZOn2BER6xiE+++TI/-Tmp-/RtmpzEsz6S/downloaded_packages’
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobin...@wehi.edu.au
e: m.robin...@garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------
______________________________________________________________________
The information in this email is confidential and intended solely for the
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You must not disclose, forward, print or use it without the permission of the
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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