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

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Ryan" <rct at thompsonclan.org>
> Cc: "bioC-devel" <bioc-devel at stat.math.ethz.ch>, "stephen piccolo" <stephen_piccolo at byu.edu>
> Sent: Friday, February 6, 2015 10:06:40 AM
> Subject: Re: [Bioc-devel] Error in citation info for SPAN.UPC
> 
> 
> 
> ----- 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).
> 

The following packages also need to be fixed in this way:


$ grep "doi = " */inst/CITATION|grep -i "http"
MiRaGE/inst/CITATION:         doi = "http://dx.doi.org/10.3390/ijms12129265",
RCytoscape/inst/CITATION:         doi = "http://dx.doi.org/10.1186/1471-2105-14-217",
SCAN.UPC/inst/CITATION:         doi = "http://dx.doi.org/10.1016/j.ygeno.2012.08.003",
SCAN.UPC/inst/CITATION:         doi = "http://dx.doi.org/10.1016/j.ygeno.2012.08.003",
affy/inst/CITATION:         doi = "http://dx.doi.org/10.1093/bioinformatics/btg405",
affypdnn/inst/CITATION:#         doi = "http://",
charm/inst/CITATION:         doi = "http://dx.doi.org/10.1093/biostatistics/kxq055",
oligo/inst/CITATION:         doi = "http://dx.doi.org/10.1093/bioinformatics/btq431",
pcaGoPromoter/inst/CITATION:         doi = "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032394",
plgem/inst/CITATION:  doi = "http://dx.doi.org/10.1186/1471-2105-5-203",

Dan