[BioC] help

[Steve Lianoglou]

Hi,

On Tue, Dec 27, 2011 at 9:30 AM, Roger [guest] <guest at bioconductor.org> wrote:
>
> 1) I've subsribed and confirmed.  Where's the url for the forum?  It would be nice to have the forum url listed on the page after one logs on.

What forum?

This is a mailing list, so .. no real forum to speak of.

The link for the archives of the list are found on the same page you
subscribed on. See the "Bioconductor Archives" link on this page:

https://stat.ethz.ch/pipermail/bioconductor/

You can also search the archives via the gmane here (which is somehow
forum like):

https://stat.ethz.ch/pipermail/bioconductor/

> 2) I've installed the new R 2.14.0.  Why are so many basic packages still not available?  (tcltk,bawse, stats, utils, SparceM, datasets, grDevices, graphics, ...)

I'm not sure what the "bawse" (did you mean "base"?) package is, but
most of what you mention (w/ the exception of tcltk and SparseM(?))
are already in your install.

None of these package have to do with bioconductor, though ... still
they are installable through the "normal" bioconductor means, if you
like, ie:

R> source("http://bioconductor.org/biocLite.R")
R> biocLite("SparseM")

How did you install R, btw? When you compile from source, there is a
flag that has something to do with "not installing recommended
packages" ... maybe you flipped that sucker on?

> 3) I tried to load the xcm from Bioconductor but it failed, message below:
>
>  -- output of sessionInfo():

I actually don't see any sessionInfo output, and I'm not sure how
helpful I can be even if it was included, but I'm *guessing* that you
are using linux, but not sure. Is that correct? What distro are you
on? What version of gcc, etc?

For what it's worth, `xcms` seems to compile OK on my OS X machine,
but ... that's not all that helpful for you, aside for it maybe
pointing to something wonky going on with your setup and not
R/bioconductor itself.

HTH,
-steve

>
>> source("http://bioconductor.org/biocLite.R")
> biocLite("xcms")
> BiocInstaller version 1.2.1, ?biocLite for help
>> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'xcms'
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/xcms_1.30. 3.tar.gz'
> Content type 'application/x-gzip' length 1949003 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
>
> * installing *source* package 'xcms' ...
> ** libs
> rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o m assifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/m at.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwa rp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o
> CC -library=stlport4 -I/usr/local/bin/R-2.14.0/include -I/usr/local/include -I/s w/include -D_LARGEFILE_SOURCE -I/usr/local/include    -Kpic  -xO5 -xlibmil -nofs tore -features=tmplrefstatic -m64 -c massifquant/xcms_massifquant.cpp -o massifq uant/xcms_massifquant.o
> "massifquant/DataKeeper.h", line 11: Error: __int64_t is not defined.
> "massifquant/DataKeeper.h", line 12: Error: __uint64_t is not defined.
> "massifquant/DataKeeper.h", line 13: Error: __int32_t is not defined.
> "massifquant/DataKeeper.h", line 14: Error: __uint32_t is not defined.
> "massifquant/DataKeeper.h", line 15: Error: __int16_t is not defined.
> "massifquant/DataKeeper.h", line 16: Error: __uint16_t is not defined.
> 6 Error(s) detected.
> *** Error code 2
> make: Fatal error: Command failed for target `massifquant/xcms_massifquant.o'
> ERROR: compilation failed for package 'xcms'
> * removing '/usr/local/bin/R-2.14.0/library/xcms'
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact