[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 10:13:16 AM
> Subject: Re: [Bioc-devel] Error in citation info for SPAN.UPC
> 
> 
> 
> ----- 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",
> 

and

QuasR/inst/CITATION:	 doi="http://dx.doi.org/10.1186/gb-2009-10-3-r25",
QuasR/inst/CITATION:	 doi="http://dx.doi.org/10.1093/nar/gkq211",
Rbowtie/inst/CITATION:	 doi="http://dx.doi.org/10.1186/gb-2009-10-3-r25",
Rbowtie/inst/CITATION:	 doi="http://dx.doi.org/10.1093/nar/gkq211",


> Dan
> 
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