[Bioc-devel] Error in citation info for SPAN.UPC

[Dan Tenenbaum]

----- Original Message -----
> From: "Ryan" <rct at thompsonclan.org>
> To: "stephen piccolo" <stephen_piccolo at byu.edu>
> Cc: "bioC-devel" <bioc-devel at stat.math.ethz.ch>
> Sent: Friday, February 6, 2015 9:37:24 AM
> Subject: [Bioc-devel] Error in citation info for SPAN.UPC
> 
> Hi Stephen,
> 
> I noticed that there's a mistake in the citation info for SCAN.UPC,
> as
> seen here:
> http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html
> 
> Specifically, the URLs for the citations are broken because "
> http://dx.doi.org/" is repeated twice. I'm guessing the system
> auto-prepends this to the DOI, and you also manually included it?
> Just
> wanted to let you know so you could fix it for the next release.
> 
> I've also cc'd bioC-devel because they might be interested in adding
> code to auto-detect and trim this duplicated prefix during package
> building, if that's possible.
> 

Here's the fix:

$ svn diff inst/CITATION 
Index: inst/CITATION
===================================================================
--- inst/CITATION	(revision 99134)
+++ inst/CITATION	(working copy)
@@ -9,7 +9,7 @@
          year = "2012",
          issn = "",
          pages = "337-344",
-         doi = "http://dx.doi.org/10.1016/j.ygeno.2012.08.003",
+         doi = "10.1016/j.ygeno.2012.08.003",
          publisher = "Elsevier",
          address = "Oxford, UK",
          textVersion = "Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, and Johnson WE. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics, 2012, 100(6), 337-44. "
@@ -24,7 +24,7 @@
          year = "2013",
          issn = "",
          pages = "17778-17783",
-         doi = "http://dx.doi.org/10.1016/j.ygeno.2012.08.003",
+         doi = "10.1016/j.ygeno.2012.08.003",
          publisher = "",
          address = "",
          textVersion = "Piccolo SR, Withers MR, Francis OE, Bild AH and Johnson WE. Multi-platform single-sample estimates of transcriptional activation. Proceedings of the National Academy of Sciences of the United States of America, 2013, in press."

Basically remove "http://dx.doi.org/" from "doi" fields.

You can test this by running
x <- readCitationFile("SCAN.UPC/inst/CITATION")
print(x, style="html")

And see if the links look ok (you can copy the output to an html file and open it in your browser and click on the links, if eyeballing isn't enough).

Dan



> Thanks,
> 
> -Ryan Thompson
> 
> 	[[alternative HTML version deleted]]
> 
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