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/m an/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