Re: [R-pkg-devel] doi confusion and Data codoc mismatches--AND THE VALUE OF GITHUB
Thanks to Duncan and Kurt for looking into this, recommending a patch
for my code, and implementing a change to codocData.
VALUE OF GITHUB: This exchange illustrates the value of GitHub:
1. It made it easier for Duncan to diagnose the problem and
recommend fixes both to me and to Kurt.
2. I missed this email when it arrived five days after my post but
found it after noticing a pull request from Duncan on GitHub. I
implemented it, and it worked! Then I checked for a reply to my earlier
post, and found Duncan's comment below.
Spencer
On 1/1/22 1:11 PM, Duncan Murdoch wrote:
On 26/12/2021 8:03 a.m., Duncan Murdoch wrote:
I've now submitted a bug report for R:
https://bugs.r-project.org/show_bug.cgi?id=18266 along with a suggested
patch to remove the first of these.
And this patch was committed to the trunk by Kurt Hornik, so it should
appear in R 4.2.0 or maybe some 4.1.x release. Thanks Kurt!
Duncan Murdoch
Duncan Murdoch
On 26/12/2021 5:55 a.m., Duncan Murdoch wrote:
On 26/12/2021 12:07 a.m., Spencer Graves wrote:
Hello, All:
The latest checks on
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true;
identify two problems I don't know how to fix:
FIRST: Data codoc mismatches from documentation object 'USnewspapers':
Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
Circ_G2012dollars Circ_currentGdollars GDP_G2012
GDP_nominalG
Population_M RevenuePerCap_2012 RevenuePerCap_nominal
Revenue_G2012dollars Revenue_currentGdollars Year
newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
Revenue_G2012dollars Revenue_currentGdollars
AdsProportion
Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
RevenuePerCap_2012 RevenuePerCap_nominal Year
newspapers_p_GDP
I believe that the column names in the data.frame 'USnewspapers'
match the names in the order given in the *.Rd file and the variable
list following "Code" here matches that following "Docs" using, e.g.,
sort(scan(what=character())).
You can debug this by running tools::codocData("Ecdat") after the
package is installed. It appears that some of the names in the docs are
picking up newlines, specifically the ones documented like this:
\item{Ads_currentGdollars,
Ads_G2012dollars,
Circ_currentGdollars,
Circ_G2012dollars,
Revenue_currentGdollars,
Revenue_G2012dollars}
I think that's a bug in codocData. A workaround is to put those all on
one line. You don't get a "line too long" warning, because they'll be
reformatted in the display.
SECOND: Found the following URLs which should use \doi (with the DOI
name only):
File 'AccountantsAuditorsPct.Rd':
https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
https://doi.org/10.18128/D010.V10.0
My concern here is that these two urls are in, e.g.,
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to
link to the doi url}. If it were, e.g.,
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with
\doi{10.18128/D010.V8.0}. However, if I do that, I don't know what to
do with the "text to display to click to link to the doi url".
The first of those links to a page with this version of the reference:
Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer,
Jose Pacas, and Matthew Sobek. Integrated Public Use Microdata Series:
Version 8.0 [dataset]. Minneapolis: University of Minnesota, 2018.
http://doi.org/10.18128/D010.V8.0
You'd get a format pretty close to that if you don't try to make the
title into a link, just enter it as
Steven Ruggles, Sarah Flood, Ronald Goeken,
Josiah Grover, Erin Meyer, Jose Pacas, and
Matthew Sobek (2018)
IPUMS
USA: Version 8.0 [dataset]. Minneapolis, MN:
IPUMS. \doi{10.18128/D010.V8.0}
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] doi confusion and Data codoc mismatches
On 26/12/2021 8:03 a.m., Duncan Murdoch wrote:
I've now submitted a bug report for R:
https://bugs.r-project.org/show_bug.cgi?id=18266 along with a suggested
patch to remove the first of these.
And this patch was committed to the trunk by Kurt Hornik, so it should
appear in R 4.2.0 or maybe some 4.1.x release. Thanks Kurt!
Duncan Murdoch
Duncan Murdoch
On 26/12/2021 5:55 a.m., Duncan Murdoch wrote:
On 26/12/2021 12:07 a.m., Spencer Graves wrote:
Hello, All:
The latest checks on
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true;
identify two problems I don't know how to fix:
FIRST: Data codoc mismatches from documentation object 'USnewspapers':
Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
Circ_G2012dollars Circ_currentGdollars GDP_G2012 GDP_nominalG
Population_M RevenuePerCap_2012 RevenuePerCap_nominal
Revenue_G2012dollars Revenue_currentGdollars Year
newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
Revenue_G2012dollars Revenue_currentGdollars AdsProportion
Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
RevenuePerCap_2012 RevenuePerCap_nominal Year newspapers_p_GDP
I believe that the column names in the data.frame 'USnewspapers'
match the names in the order given in the *.Rd file and the variable
list following "Code" here matches that following "Docs" using, e.g.,
sort(scan(what=character())).
You can debug this by running tools::codocData("Ecdat") after the
package is installed. It appears that some of the names in the docs are
picking up newlines, specifically the ones documented like this:
\item{Ads_currentGdollars,
Ads_G2012dollars,
Circ_currentGdollars,
Circ_G2012dollars,
Revenue_currentGdollars,
Revenue_G2012dollars}
I think that's a bug in codocData. A workaround is to put those all on
one line. You don't get a "line too long" warning, because they'll be
reformatted in the display.
SECOND: Found the following URLs which should use \doi (with the DOI
name only):
File 'AccountantsAuditorsPct.Rd':
https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
https://doi.org/10.18128/D010.V10.0
My concern here is that these two urls are in, e.g.,
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to
link to the doi url}. If it were, e.g.,
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with
\doi{10.18128/D010.V8.0}. However, if I do that, I don't know what to
do with the "text to display to click to link to the doi url".
The first of those links to a page with this version of the reference:
Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer,
Jose Pacas, and Matthew Sobek. Integrated Public Use Microdata Series:
Version 8.0 [dataset]. Minneapolis: University of Minnesota, 2018.
http://doi.org/10.18128/D010.V8.0
You'd get a format pretty close to that if you don't try to make the
title into a link, just enter it as
Steven Ruggles, Sarah Flood, Ronald Goeken,
Josiah Grover, Erin Meyer, Jose Pacas, and
Matthew Sobek (2018)
IPUMS
USA: Version 8.0 [dataset]. Minneapolis, MN:
IPUMS. \doi{10.18128/D010.V8.0}
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] doi confusion and Data codoc mismatches
I've now submitted a bug report for R:
https://bugs.r-project.org/show_bug.cgi?id=18266 along with a suggested
patch to remove the first of these.
Duncan Murdoch
On 26/12/2021 5:55 a.m., Duncan Murdoch wrote:
On 26/12/2021 12:07 a.m., Spencer Graves wrote:
Hello, All:
The latest checks on
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true;
identify two problems I don't know how to fix:
FIRST: Data codoc mismatches from documentation object 'USnewspapers':
Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
Circ_G2012dollars Circ_currentGdollars GDP_G2012 GDP_nominalG
Population_M RevenuePerCap_2012 RevenuePerCap_nominal
Revenue_G2012dollars Revenue_currentGdollars Year
newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
Revenue_G2012dollars Revenue_currentGdollars AdsProportion
Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
RevenuePerCap_2012 RevenuePerCap_nominal Year newspapers_p_GDP
I believe that the column names in the data.frame 'USnewspapers'
match the names in the order given in the *.Rd file and the variable
list following "Code" here matches that following "Docs" using, e.g.,
sort(scan(what=character())).
You can debug this by running tools::codocData("Ecdat") after the
package is installed. It appears that some of the names in the docs are
picking up newlines, specifically the ones documented like this:
\item{Ads_currentGdollars,
Ads_G2012dollars,
Circ_currentGdollars,
Circ_G2012dollars,
Revenue_currentGdollars,
Revenue_G2012dollars}
I think that's a bug in codocData. A workaround is to put those all on
one line. You don't get a "line too long" warning, because they'll be
reformatted in the display.
SECOND: Found the following URLs which should use \doi (with the DOI
name only):
File 'AccountantsAuditorsPct.Rd':
https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
https://doi.org/10.18128/D010.V10.0
My concern here is that these two urls are in, e.g.,
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to
link to the doi url}. If it were, e.g.,
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with
\doi{10.18128/D010.V8.0}. However, if I do that, I don't know what to
do with the "text to display to click to link to the doi url".
The first of those links to a page with this version of the reference:
Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer,
Jose Pacas, and Matthew Sobek. Integrated Public Use Microdata Series:
Version 8.0 [dataset]. Minneapolis: University of Minnesota, 2018.
http://doi.org/10.18128/D010.V8.0
You'd get a format pretty close to that if you don't try to make the
title into a link, just enter it as
Steven Ruggles, Sarah Flood, Ronald Goeken,
Josiah Grover, Erin Meyer, Jose Pacas, and
Matthew Sobek (2018)
IPUMS
USA: Version 8.0 [dataset]. Minneapolis, MN:
IPUMS. \doi{10.18128/D010.V8.0}
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] doi confusion and Data codoc mismatches-confusing check
Hello, All:
The latest checks on
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true;
identify two problems I don't know how to fix:
FIRST: Data codoc mismatches from documentation object 'USnewspapers':
Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
Circ_G2012dollars Circ_currentGdollars GDP_G2012 GDP_nominalG
Population_M RevenuePerCap_2012 RevenuePerCap_nominal
Revenue_G2012dollars Revenue_currentGdollars Year
newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
Revenue_G2012dollars Revenue_currentGdollars AdsProportion
Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
RevenuePerCap_2012 RevenuePerCap_nominal Year newspapers_p_GDP
I believe that the column names in the data.frame 'USnewspapers'
match the names in the order given in the *.Rd file and the variable
list following "Code" here matches that following "Docs" using, e.g.,
sort(scan(what=character())).
SECOND: Found the following URLs which should use \doi (with the DOI
name only):
File 'AccountantsAuditorsPct.Rd':
https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
https://doi.org/10.18128/D010.V10.0
My concern here is that these two urls are in, e.g.,
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to
link to the doi url}. If it were, e.g.,
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with
\doi{10.18128/D010.V8.0}. However, if I do that, I don't know what to
do with the "text to display to click to link to the doi url".
NOTE: I tried changing \href{}{} to \doi{}{} in
'AccountantsAuditorsPct.Rd' and got what I expected: First, I failed to
mention before that this complaint does NOT appear in R CMD check on my
local computer; see sessionInfo() below. when I checked how that doi
reference displayed in Ecdat-manual.pdf, I found that "doi:
10.18128/D010.V8.0" was displayed, followed by the "text to display to
click to link to the doi url".
Specifically, I got:
Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer,
Jose Pacas, and Matthew Sobek (2018) doi: 10.18128/D010.V8.0IPUMS USA:
Version 8.0 [dataset]. Minneapolis, MN: IPUMS.
With \href{}{}, "doi: 10.18128/D010.V8.0" does not appear, and I get
that URL by clicking on "IPUMS USA: Version 8.0 [dataset]. Minneapolis,
MN: IPUMS." With this version, clicking on "IPUMS USA: Version 8.0
[dataset]. Minneapolis, MN: IPUMS." does nothing, whild clicking on
"doi: 10.18128/D010.V8.0" takes me to that URL.
This looks like a change to how *.Rd files are rendered that has
appeared in the process on GitHub but not in my local computer. ???
Thanks,
Spencer Graves
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6.2
Matrix products: default
LAPACK:
/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] doi confusion and Data codoc mismatches
On 26/12/2021 12:07 a.m., Spencer Graves wrote:
Hello, All:
The latest checks on
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true;
identify two problems I don't know how to fix:
FIRST: Data codoc mismatches from documentation object 'USnewspapers':
Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
Circ_G2012dollars Circ_currentGdollars GDP_G2012 GDP_nominalG
Population_M RevenuePerCap_2012 RevenuePerCap_nominal
Revenue_G2012dollars Revenue_currentGdollars Year
newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
Revenue_G2012dollars Revenue_currentGdollars AdsProportion
Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
RevenuePerCap_2012 RevenuePerCap_nominal Year newspapers_p_GDP
I believe that the column names in the data.frame 'USnewspapers'
match the names in the order given in the *.Rd file and the variable
list following "Code" here matches that following "Docs" using, e.g.,
sort(scan(what=character())).
You can debug this by running tools::codocData("Ecdat") after the
package is installed. It appears that some of the names in the docs are
picking up newlines, specifically the ones documented like this:
\item{Ads_currentGdollars,
Ads_G2012dollars,
Circ_currentGdollars,
Circ_G2012dollars,
Revenue_currentGdollars,
Revenue_G2012dollars}
I think that's a bug in codocData. A workaround is to put those all on
one line. You don't get a "line too long" warning, because they'll be
reformatted in the display.
SECOND: Found the following URLs which should use \doi (with the DOI
name only):
File 'AccountantsAuditorsPct.Rd':
https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
https://doi.org/10.18128/D010.V10.0
My concern here is that these two urls are in, e.g.,
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to
link to the doi url}. If it were, e.g.,
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with
\doi{10.18128/D010.V8.0}. However, if I do that, I don't know what to
do with the "text to display to click to link to the doi url".
The first of those links to a page with this version of the reference:
Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer,
Jose Pacas, and Matthew Sobek. Integrated Public Use Microdata Series:
Version 8.0 [dataset]. Minneapolis: University of Minnesota, 2018.
http://doi.org/10.18128/D010.V8.0
You'd get a format pretty close to that if you don't try to make the
title into a link, just enter it as
Steven Ruggles, Sarah Flood, Ronald Goeken,
Josiah Grover, Erin Meyer, Jose Pacas, and
Matthew Sobek (2018)
IPUMS
USA: Version 8.0 [dataset]. Minneapolis, MN:
IPUMS. \doi{10.18128/D010.V8.0}
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] doi confusion and Data codoc mismatches
Hello, All:
The latest checks on
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true;
identify two problems I don't know how to fix:
FIRST: Data codoc mismatches from documentation object 'USnewspapers':
Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
Circ_G2012dollars Circ_currentGdollars GDP_G2012 GDP_nominalG
Population_M RevenuePerCap_2012 RevenuePerCap_nominal
Revenue_G2012dollars Revenue_currentGdollars Year
newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
Revenue_G2012dollars Revenue_currentGdollars AdsProportion
Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
RevenuePerCap_2012 RevenuePerCap_nominal Year newspapers_p_GDP
I believe that the column names in the data.frame 'USnewspapers'
match the names in the order given in the *.Rd file and the variable
list following "Code" here matches that following "Docs" using, e.g.,
sort(scan(what=character())).
SECOND: Found the following URLs which should use \doi (with the DOI
name only):
File 'AccountantsAuditorsPct.Rd':
https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
https://doi.org/10.18128/D010.V10.0
My concern here is that these two urls are in, e.g.,
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to
link to the doi url}. If it were, e.g.,
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with
\doi{10.18128/D010.V8.0}. However, if I do that, I don't know what to
do with the "text to display to click to link to the doi url".
Thanks,
Spencer Graves
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
