----- Original Message ----- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Ryan" <r...@thompsonclan.org> > Cc: "bioC-devel" <bioc-de...@stat.math.ethz.ch>, "stephen piccolo" > <stephen_picc...@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" <dtene...@fredhutch.org> > > To: "Ryan" <r...@thompsonclan.org> > > Cc: "bioC-devel" <bioc-de...@stat.math.ethz.ch>, "stephen piccolo" > > <stephen_picc...@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" <r...@thompsonclan.org> > > > To: "stephen piccolo" <stephen_picc...@byu.edu> > > > Cc: "bioC-devel" <bioc-de...@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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
