Thanks Jim.

Yes, I had to do this a week or so ago with affxparser (and it usually works) but I am getting the error below.

Dan's quick response that there is not Mac or Windows binary explains the errors.

My fault for not reading to bottom of the Rsubread page.

I will have to look elsewhere.

Sorry for bothering ya'll before reading the complete web page.

Noah


> source("http://www.bioconductor.org/biocLite.R")
> biocLite("Rsubread", type= "source")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'Rsubread'
trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsubread_1.4.2.tar.gz'
Content type 'application/x-gzip' length 21848822 bytes (20.8 Mb)
opened URL
==================================================
downloaded 20.8 Mb

* installing *source* package ‘Rsubread’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -DMAKE_FOR_EXON -fPIC  -g -O2 -c R_wrapper.c -o R_wrapper.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -DMAKE_FOR_EXON -fPIC  -g -O2 -c aligner.c -o aligner.o
aligner.c:301: error: expected specifier-qualifier-list before ‘pthread_spinlock_t’
aligner.c:305: error: expected declaration specifiers or ‘...’ before ‘pthread_spinlock_t’
aligner.c: In function ‘run_search’:
aligner.c:349: error: ‘input_lock’ undeclared (first use in this function)
aligner.c:349: error: (Each undeclared identifier is reported only once
aligner.c:349: error: for each function it appears in.)
aligner.c:350: warning: implicit declaration of function ‘pthread_spin_lock’
aligner.c:415: warning: implicit declaration of function ‘pthread_spin_unlock’
aligner.c: In function ‘run_search_thread’:
aligner.c:659: error: ‘struct gene_thread_data_transport’ has no member named ‘init_lock’
aligner.c:661: error: ‘struct gene_thread_data_transport’ has no member named ‘input_data_lock’
aligner.c:661: error: too many arguments to function ‘run_search’
aligner.c: In function ‘run_search_index’:
aligner.c:719: warning: passing argument 11 of ‘run_search’ makes integer from pointer without a cast
aligner.c:719: error: too many arguments to function ‘run_search’
aligner.c:725: error: ‘pthread_spinlock_t’ undeclared (first use in this function)
aligner.c:725: error: expected ‘;’ before ‘data_lock’
aligner.c:726: error: expected ‘;’ before ‘init_lock’
aligner.c:736: error: ‘struct gene_thread_data_transport’ has no member named ‘input_data_lock’
aligner.c:736: error: ‘data_lock’ undeclared (first use in this function)
aligner.c:737: error: ‘struct gene_thread_data_transport’ has no member named ‘init_lock’
aligner.c:737: error: ‘init_lock’ undeclared (first use in this function)
aligner.c:743: warning: implicit declaration of function ‘pthread_spin_init’
aligner.c:755: warning: implicit declaration of function ‘pthread_spin_destroy’
aligner.c: At top level:
gene-algorithms.h:27: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26: warning: inline function ‘add_gene_vote’ declared but never defined
make: *** [aligner.o] Error 1
ERROR: compilation failed for package ‘Rsubread’
* removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsubread’

The downloaded packages are in
	‘/private/var/folders/14/14lHU6sYHXWDo48Jc3Lq++lgIs+/-Tmp-/Rtmp9gion7/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
 installation of package ‘Rsubread’ had non-zero exit status

On Dec 5, 2011, at 3:15 PM, James W. MacDonald wrote:

> Hi Noah,
> 
> On 12/5/2011 4:09 PM, Noah Dowell wrote:
>> Hello All,
>> 
>> I am trying to use the Rsubread package which is supposedly available but I am getting the following warning message.
> 
> It is only available as a source package. If you are set up to build packages from source, you can simply add the argument type="source" to your biocLite() call.
> 
> Otherwise,
> 
> http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Installation-of-source-packages
> 
> Best,
> 
> Jim
> 
> 
>> Thanks for your help.
>> 
>> Best,
>> 
>> Noah
>> 
>> 
>>> source("http://www.bioconductor.org/biocLite.R")
>> BiocInstaller version 1.2.1, ?biocLite for help
>>>    biocLite("Rsubread")
>> BioC_mirror: 'http://www.bioconductor.org'
>> Using R version 2.14, BiocInstaller version 1.2.1.
>> Installing package(s) 'Rsubread'
>> Warning message:
>> In getDependencies(pkgs, dependencies, available, lib) :
>>  package ‘Rsubread’ is not available (for R version 2.14.0)
>> 
>> 
>>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> 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   base
>> 
>> other attached packages:
>> [1] BiocInstaller_1.2.1
>> 
>> loaded via a namespace (and not attached):
>> [1] tools_2.14.0
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> 
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

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