[BioC] Rsubread package not available? Warning resolved
Robert Castelo
robert.castelo at upf.edu
Thu Dec 8 11:41:25 CET 2011
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
> >>
> >> **********************************************************
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> >
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