[BioC] Biostrings

Hervé Pagès hpages at fhcrc.org
Thu Feb 21 08:26:22 CET 2013


Hi Murli,

On 02/20/2013 08:12 PM, Murli Nair wrote:
> Dear Dr. Pages,
>
> I had a couple of clarifications regarding the Biostrings package. Are
> the methods |CharacterToFASTArecords and XStringSetToFASTArecords still
> part of the package?

No they are not.

> I was not able to get to them after I loaded the
> library. Also, when I searched the man pages posted in the URL below, I
> could not find them.
> (http://www.bioconductor.org/packages/2.11/bioc/manuals/Biostrings/man/Biostrings.pdf)

Because this is the manual for the current Biostrings and they are not
in the package anymore. I removed them more than 2 years ago after the
standard deprecated/defunct 1-year cycle.

> |
>
> ||
>
> |I installed in using biocLite(), it was not the most clean install,
> since I got a lot of warnings. I was not able to install it from the rpm
> or using “yum install R-Biostrings” |

You would need to check on the forums for your Linux distro why you were
not able to install via yum. The only installation procedure we support
on this mailing list is via biocLite(). However you're not showing me
the warnings you got when you use biocLite() so it's hard for me to
tell whether they're serious or not. Note that all the compilation
warnings that show up here (under the Biostrings.Rcheck/00install.out
section)

 
http://bioconductor.org/checkResults/2.11/bioc-LATEST/Biostrings/lamb1-checksrc.html

are well known and can be safely ignored (most of them are gcc false
positives).

>
> |I would appreciate any suggestions or help.|

I already tried to help a couple of days ago by answering your
questions on the mailing list. But now you are back with question
number 0. Did you see my last answer about how to go from strings
to DNAStringSet? If that is not what you need, please provide more
details about what you are trying to do exactly.

Thanks!
H.

>
> ||
>
> |Cheers../Murli|
>
> ============================
>
> Dr. Murli Nair,
>
> Associate Professor of Bioinformatics,
>
> Departments of Biological Sciences and Computer Science/Informatics
>
> Indiana University South Bend,
>
> South Bend, Indiana,
>
> http://bioinformatics.iusb.edu
>
> ============================
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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