[BioC] Rsubread package not available? Warning resolved

Fri Dec 9 00:03:36 CET 2011

Hi all,

On Thu, Dec 8, 2011 at 12:10 PM, Noah Dowell <noahd at ucla.edu> wrote:
> TIm,
>
> Thanks for providing your experiences on using different aligners.  I used R/Bioconductor for tiling and expression arrays as a grad student but now I am using next generation sequencing as a postdoc so I am getting up to speed with some new packages like Rsubread.
>
> Yes, I have the Xcode developer tools installed and have installed from source recently for other packages with no errors.
>

Wei can correct me if I am wrong, but I believe it's not as simple as
building Rsubread from source on Mac (or Windows). If it were,
Bioconductor would provide a binary package on those platforms.

I believe the problem is that certain constructs (e.g. phtread) are
used in such a way that is not portable to Mac OS X or Windows,

Dan

> Best,
> Noah
> On Dec 8, 2011, at 11:31 AM, Tim Triche, Jr. wrote:
>
>> One other thing Noah, do you have Xcode and the R tools for Mac OSX installed?  I'm using my wife's Macbook Air at this particular instant, and I'm tempted to try compiling Rsubread, but I don't really have time to debug something for fun right now.  Still -- it would be interesting to see if that resolved your issues.  It's not like laptops are being produced with less RAM and smaller processors as time goes by, and there are old-but-still-very-useful RNAseq datasets out there.  And Rsubread is *FAST* so it's by far the most sensible choice for a laptop.
>>
>>
>> On Thu, Dec 8, 2011 at 9:28 AM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
>> FWIW, I've had pretty good results with some older 36-cycle Illumina RNAseq data using Rsubread, just aligning it on my laptop (granted it's a dual-core i7 with 16GB of RAM and 2 SSDs).  For some of the RNAseq data from CD34+CD38- cells and neutrophils that Andrew Smith was kind enough to send, it took about 30 minutes, and I was able to do other things at the same time.  Again, that might have something to do with my using 7.4GB for the index, having another 8.6GB for other processes, and running Linux.  But mostly the RAM, I think.
>>
>> YMMV... Rsubread has some terrific features, I am torn between using it all the time, using BowTie/TopHat/Cufflinks/cummeRbund all the time, or both.  Last time I just used both, but with our RNAseq/QC pipeline, if I want to re-align against hg18 I either have to use bedtools and liftOver, re-run the pipeline, or use Rsubread.  The latter is more convenient, even if the former does have some more tools for removing PCR dupes, looking at alternative splicing, etc.
>>
>> Either one runs fine on our servers, of course, and both go a lot faster with 24 cores and 48GB of RAM :-)
>>
>>
>> On Thu, Dec 8, 2011 at 7:44 AM, Noah Dowell <noahd at ucla.edu> wrote:
>> 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 åRsubreadÇ ...
>> >>> ** 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 åpthread_spinlock_tÇ
>> >>> aligner.c:305: error: expected declaration specifiers or å...Ç before åpthread_spinlock_tÇ
>> >>> aligner.c: In function årun_searchÇ:
>> >>> aligner.c:349: error: åinput_lockÇ 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 åpthread_spin_lockÇ
>> >>> aligner.c:415: warning: implicit declaration of function åpthread_spin_unlockÇ
>> >>> aligner.c: In function årun_search_threadÇ:
>> >>> aligner.c:659: error: åstruct gene_thread_data_transportÇ has no member named åinit_lockÇ
>> >>> aligner.c:661: error: åstruct gene_thread_data_transportÇ has no member named åinput_data_lockÇ
>> >>> aligner.c:661: error: too many arguments to function årun_searchÇ
>> >>> aligner.c: In function årun_search_indexÇ:
>> >>> aligner.c:719: warning: passing argument 11 of årun_searchÇ makes integer from pointer without a cast
>> >>> aligner.c:719: error: too many arguments to function årun_searchÇ
>> >>> aligner.c:725: error: åpthread_spinlock_tÇ undeclared (first use in this function)
>> >>> aligner.c:725: error: expected å;Ç before ådata_lockÇ
>> >>> aligner.c:726: error: expected å;Ç before åinit_lockÇ
>> >>> aligner.c:736: error: åstruct gene_thread_data_transportÇ has no member named åinput_data_lockÇ
>> >>> aligner.c:736: error: ådata_lockÇ undeclared (first use in this function)
>> >>> aligner.c:737: error: åstruct gene_thread_data_transportÇ has no member named åinit_lockÇ
>> >>> aligner.c:737: error: åinit_lockÇ undeclared (first use in this function)
>> >>> aligner.c:743: warning: implicit declaration of function åpthread_spin_initÇ
>> >>> aligner.c:755: warning: implicit declaration of function åpthread_spin_destroyÇ
>> >>> aligner.c: At top level:
>> >>> gene-algorithms.h:27: warning: inline function åadd_gene_vote_weightedÇ declared but never defined
>> >>> gene-algorithms.h:26: warning: inline function åadd_gene_voteÇ declared but never defined
>> >>> make: *** [aligner.o] Error 1
>> >>> ERROR: compilation failed for package åRsubreadÇ
>> >>> * removing å/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RsubreadÇ
>> >>>
>> >>> The downloaded packages are in
>> >>>     å/private/var/folders/14/14lHU6sYHXWDo48Jc3Lq++lgIs+/-Tmp-/Rtmp9gion7/downloaded_packagesÇ
>> >>> Warning message:
>> >>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>> >>> installation of package åRsubreadÇ 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 åRsubreadÇ 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
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>> >>>>
>> >>>> --
>> >>>> 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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>>
>> --
>> If people do not believe that mathematics is simple,
>> it is only because they do not realize how complicated life is.
>> John von Neumann
>>
>>
>>
>>
>>
>> --
>> If people do not believe that mathematics is simple,
>> it is only because they do not realize how complicated life is.
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