[Bioc-devel] Fwd: readGAlignmentsFromBam function

Hervé Pagès hpages at fredhutch.org
Thu Feb 19 23:37:37 CET 2015

Hi Karolis,

Please use the bioc-devel mailing list (to which you should
be subscribed) to ask this type of question.

If you manually run the example in your package (using BioC devel,
which requires R-3.2), you'll get:

   > prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping)
   Inferred name for CDF package: HGU133Plus2_mapping.txt -> hgu133plus2cdf

   [1] "Finished: 
   [1] "Finished: 
   Note: Some probe IDs contain duplicates.

   Estimated values for Bayesian prior:



   Note: 41457 probe sequences are missing in _mapping.txt file.

   Calculating Expression
   Warning messages:
   1: 'readGAlignmentsFromBam' is deprecated.
   Use 'readGAlignments' instead.
   See help("Deprecated")
   2: 'readGAlignmentsFromBam' is deprecated.
   Use 'readGAlignments' instead.
   See help("Deprecated")

Hope this helps. Too bad 'R CMD check' truncates the deprecation
message :-/


On 02/19/2015 01:15 PM, Michael Lawrence wrote:
> ---------- Forwarded message ----------
> From: "Karolis Uziela" <karolis.uziela at scilifelab.se>
> Date: Feb 19, 2015 9:22 AM
> Subject: readGAlignmentsFromBam function
> To: "Michael Lawrence" <lawrence.michael at gene.com>
> Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Hi,
> I have looked at R check results for the devel version of Bioconductor and
> I noticed that the package I developed ("prebs") gives this warning:
> Warning: 'readGAlignmentsFromBam' is deprecated.
> What is the new function that should be used instead of
> readGAlignmentsFromBam (GenomicAlignments package)? Do the changes
> affect readGAlignmentPairs function, too?
> Regards,
> Karolis

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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