[BioC] Rsubread package not available? Warning resolved
Noah Dowell
noahd at ucla.edu
Thu Dec 8 16:44:37 CET 2011
Dear Wei,
Thanks for your response. I was going to use Rsubread with a small(ish) data set on a desktop with a little more memory than the standard laptop. I like the approach behind Rsubread and I wanted to do some comparisons with other aligners on small data sets before making a choice.
Of course I understand as a maintainer you have to make some careful choices where and what to put your effort into.
I should have a server up and running soon (at my new institute; not UCLA) and will consider using Rsubread at that time.
Best,
Noah
On Dec 8, 2011, at 4:41 AM, Robert Castelo wrote:
> Dear Wei,
>
> i think you might consider the following three reasons why it would be
> interesting to have Rsubread available in Mac OS X systems:
>
> 1. i've used Rsubread to teach my students about mapping reads without
> leaving the R console by using a small sample of reads (e.g. 1e5, 1e6),
> if eventually one makes a teaching course where students come with
> laptops, a significant fraction of them come now with mac. this could
> apply to all the BioC courses that take place throughout the world :)
>
> 2. apple not only sells laptops but also high-performance computing
> solutions. those users would also benefit of having Rsubread running in
> Mac OS X.
>
> 3. Mac OS X runs on top of a unix system, so it should not be all too
> difficult to have and maintain ANSI C code running in both, a linux and
> a Mac OS X system.
>
> cheers,
> robert.
>
> On Thu, 2011-12-08 at 21:06 +1100, Wei Shi wrote:
>> 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
>>>>
>>>> **********************************************************
>>>> 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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>>
>>
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