[BioC] Rsubread package not available? Warning resolved

Thu Dec 8 11:06:38 CET 2011

Dear Noah,

We are still thinking about whether we should make Rsubread available on Mac or Windows laptops. I can certainly see the advantage of doing this. However, this will require considerable amount of work for developing and maintaining it because many functions in the package are written in C language and we are going to include more C functions into the package in the future. Moreover, the read alignment will consume most of the computational resources of a laptop and I do not think you can use your laptop for other work during the period of read mapping. So it might be best to run the read alignment on a server/supercomputer, rather on a laptop.

Cheers,
Wei

On Dec 6, 2011, at 8:29 AM, NDowell wrote:

> 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 ŒRsubread‚ ...
> ** 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 Œpthread_spinlock_t‚
> aligner.c:305: error: expected declaration specifiers or Œ...‚ before Œpthread_spinlock_t‚
> aligner.c: In function Œrun_search‚:
> aligner.c:349: error: Œinput_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 Œpthread_spin_lock‚
> aligner.c:415: warning: implicit declaration of function Œpthread_spin_unlock‚
> aligner.c: In function Œrun_search_thread‚:
> aligner.c:659: error: Œstruct gene_thread_data_transport‚ has no member named Œinit_lock‚
> aligner.c:661: error: Œstruct gene_thread_data_transport‚ has no member named Œinput_data_lock‚
> aligner.c:661: error: too many arguments to function Œrun_search‚
> aligner.c: In function Œrun_search_index‚:
> aligner.c:719: warning: passing argument 11 of Œrun_search‚ makes integer from pointer without a cast
> aligner.c:719: error: too many arguments to function Œrun_search‚
> aligner.c:725: error: Œpthread_spinlock_t‚ undeclared (first use in this function)
> aligner.c:725: error: expected Œ;‚ before Œdata_lock‚
> aligner.c:726: error: expected Œ;‚ before Œinit_lock‚
> aligner.c:736: error: Œstruct gene_thread_data_transport‚ has no member named Œinput_data_lock‚
> aligner.c:736: error: Œdata_lock‚ undeclared (first use in this function)
> aligner.c:737: error: Œstruct gene_thread_data_transport‚ has no member named Œinit_lock‚
> aligner.c:737: error: Œinit_lock‚ undeclared (first use in this function)
> aligner.c:743: warning: implicit declaration of function Œpthread_spin_init‚
> aligner.c:755: warning: implicit declaration of function Œpthread_spin_destroy‚
> aligner.c: At top level:
> gene-algorithms.h:27: warning: inline function Œadd_gene_vote_weighted‚ declared but never defined
> gene-algorithms.h:26: warning: inline function Œadd_gene_vote‚ declared but never defined
> make: *** [aligner.o] Error 1
> ERROR: compilation failed for package ŒRsubread‚
> * removing Œ/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsubread‚
> 
> The downloaded packages are in
> 	Œ/private/var/folders/14/14lHU6sYHXWDo48Jc3Lq++lgIs+/-Tmp-/Rtmp9gion7/downloaded_packages‚
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
> installation of package ŒRsubread‚ 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 ŒRsubread‚ 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 at 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
>> 
>> **********************************************************
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