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

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.

Thanks,

-Ryan Thompson

	[[alternative HTML version deleted]]

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).

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",

Dan