Re: [R-pkg-devel] package CatDataAnalysis
That's where the copyright violation comes in. Copying descriptions from the book is clear copyright violation unless it is so minimal as to be "fair use" and I have no idea where that line is. Even Alan may not be free to add such descriptions. I have no idea what his contract with Wiley says. So like I said in my original posting, good idea in an alternative universe where copyright law does not exist. On Sun, Jun 28, 2020 at 1:13 PM Jeff Newmiller wrote: > Just describe the nature of the data sets literally as though the book was > inaccessible. They are not asking you to describe how one should analyze > the the data, so there really shouldn't be any conflict with the book > content that your agreement with the author has not already resolved. > > If you feel you are being held to a higher standard than others have > been... that is life. As a user of packages I agree with the CRAN that > package documention should be usable on its own. > > On June 28, 2020 10:58:15 AM PDT, Charles Geyer > wrote: > >CRAN did not just ask for an expanded Description field. They > >instructed > >"Tell the users what the datasets are about and what they contain so > >they > >can use them even when they haven't read your book". AFAIK no CRAN > >package > >that goes with a book satisfies that. > > > >On Sun, Jun 28, 2020 at 12:52 PM Max Turgeon > >wrote: > > > >> Fair enough. But CRAN is clearly asking for a more detailed > >Description > >> field. I simply offered one suggestion for expanding it. Keep in mind > >> that users will typically see the DESCRIPTION file first, and not the > >help > >> pages. > >> > >> > >> Max Turgeon > >> Assistant Professor > >> Department of Statistics > >> Department of Computer Science > >> University of Manitoba > >> maxturgeon.ca > >> > >> > >> -- > >> *From:* Charles Geyer > >> *Sent:* June 28, 2020 12:48:06 PM > >> *To:* Max Turgeon > >> *Cc:* R Package Development > >> *Subject:* Re: [R-pkg-devel] package CatDataAnalysis > >> > >> *Caution:* This message was sent from outside the University of > >Manitoba. > >> The link to Alan's web site is on every help page (in the source > >> section). That's where the source is supposed to be. > >> > >> I have no problem with adding the source to the DESCRIPTION file, but > >that > >> is not what CRAN asked me to do. > >> > >> On Sun, Jun 28, 2020 at 12:16 PM Max Turgeon > > > >> wrote: > >> > >>> For what it's worth, I'd be inclined to interpreting CRAN's response > >>> *very* literally, i.e. your Description field is not descriptive > >enough. > >>> According to what I can see in the Github repo, you only have > >>> > >>> > >>> "Datasets used in the book Categorical Data Analysis by Agresti but > >not > >>> printed in the book." > >>> > >>> > >>> Which is not much more than what the Title field says. One glaring > >>> omission (IMO) from the Description field is any mention of > >Agresti's > >>> website, where the data comes from. > >>> > >>> > >>> In contrast, looking at the "woolridge" package, I can see from the > >>> Description field that it contains 111 datasets (well, that's in the > >Title > >>> field), it's about econometrics, and the purpose of the package is > >to make > >>> it easier for students to work with these datasets. > >>> > >>> > >>> Max Turgeon > >>> Assistant Professor > >>> Department of Statistics > >>> Department of Computer Science > >>> University of Manitoba > >>> maxturgeon.ca > >>> > >>> > >>> > >>> > >>> -- > >>> *From:* R-package-devel on > >>> behalf of Charles Geyer > >>> *Sent:* June 28, 2020 11:38 AM > >>> *To:* Neal Fultz > >>> *Cc:* R Package Development > >>> *Subject:* Re: [R-pkg-devel] package CatDataAnalysis > >>> > >>> **** > >>> Caution: This message was sent from outside the University of > >Manitoba. > >>> > >>> > >>> Actually the wool
Re: [R-pkg-devel] package CatDataAnalysis
That's a good idea about adding some licence info to the web page, but note that Agresti is not the original source of any of this data. Some of it was published in subject matter papers by the scientists involved. For some perhaps (I don't know) Alan got the whole data set via consulting and the whole data (as opposed to summary statistics) was never published. This is the case for almost all real data that statisticians re-analyze for examples. There is no "licence" and AFAIK (IANAL) none is needed. If there were most textbooks and most papers in statistics would be in violation of law. On Sun, Jun 28, 2020 at 1:08 PM Ivan Krylov wrote: > On Sun, 28 Jun 2020 11:07:46 -0500 > Charles Geyer wrote: > > >Please note that I made Alan Agresti (with his acquiescence) the > >author of the package > > Sorry to derail this, but is it possible for Alan Agresti to add a line > to the page [*] allowing redistribution of the data, preferably under > the terms of a well-known license such as CC BY-NC [**] or ODbL [***]? > As it stands, CRAN only has your word (and the fact that this whole > thread is Cc: to Prof. Agresti) that Alan Agresti agreed to have the > data published as an R package. It might be needed to allow creating > derivative works to make creating such a package feasible, though > (otherwise I would assume that only literal redistribution is allowed). > > With that done, you could be much more comfortable providing the > requested description for the package, no? > > -- > Best regards, > Ivan > > [*] http://www.stat.ufl.edu/~aa/cda/data.html > [**] https://creativecommons.org/licenses/ > [***] https://opendatacommons.org/licenses/ > -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package CatDataAnalysis
CRAN did not just ask for an expanded Description field. They instructed "Tell the users what the datasets are about and what they contain so they can use them even when they haven't read your book". AFAIK no CRAN package that goes with a book satisfies that. On Sun, Jun 28, 2020 at 12:52 PM Max Turgeon wrote: > Fair enough. But CRAN is clearly asking for a more detailed Description > field. I simply offered one suggestion for expanding it. Keep in mind > that users will typically see the DESCRIPTION file first, and not the help > pages. > > > Max Turgeon > Assistant Professor > Department of Statistics > Department of Computer Science > University of Manitoba > maxturgeon.ca > > > -- > *From:* Charles Geyer > *Sent:* June 28, 2020 12:48:06 PM > *To:* Max Turgeon > *Cc:* R Package Development > *Subject:* Re: [R-pkg-devel] package CatDataAnalysis > > *Caution:* This message was sent from outside the University of Manitoba. > The link to Alan's web site is on every help page (in the source > section). That's where the source is supposed to be. > > I have no problem with adding the source to the DESCRIPTION file, but that > is not what CRAN asked me to do. > > On Sun, Jun 28, 2020 at 12:16 PM Max Turgeon > wrote: > >> For what it's worth, I'd be inclined to interpreting CRAN's response >> *very* literally, i.e. your Description field is not descriptive enough. >> According to what I can see in the Github repo, you only have >> >> >> "Datasets used in the book Categorical Data Analysis by Agresti but not >> printed in the book." >> >> >> Which is not much more than what the Title field says. One glaring >> omission (IMO) from the Description field is any mention of Agresti's >> website, where the data comes from. >> >> >> In contrast, looking at the "woolridge" package, I can see from the >> Description field that it contains 111 datasets (well, that's in the Title >> field), it's about econometrics, and the purpose of the package is to make >> it easier for students to work with these datasets. >> >> >> Max Turgeon >> Assistant Professor >> Department of Statistics >> Department of Computer Science >> University of Manitoba >> maxturgeon.ca >> >> >> >> >> -- >> *From:* R-package-devel on >> behalf of Charles Geyer >> *Sent:* June 28, 2020 11:38 AM >> *To:* Neal Fultz >> *Cc:* R Package Development >> *Subject:* Re: [R-pkg-devel] package CatDataAnalysis >> >> >> Caution: This message was sent from outside the University of Manitoba. >> >> >> Actually the wooldridge package does not seem to satisfy any of the >> specific requests CRAN asked me for. I have checked several other CRAN >> packages for textbooks and they don't seem to satisfy those requirements >> either. So this seems to be a new idea from CRAN. >> >> On Sun, Jun 28, 2020 at 11:32 AM Neal Fultz wrote: >> >> > I'm not sure exactly what cran is asking for, but the wooldridge >> > package is a good example of a text book data set package, so maybe >> > you can use the same format they did. >> > >> > https://cran.r-project.org/web/packages/wooldridge/index.html >> > >> > Best, >> > >> > Neal >> > >> > On Sun, Jun 28, 2020 at 9:08 AM Charles Geyer >> > wrote: >> > > >> > > I have a package that has the datasets for Categorical Data Analysis >> by >> > > Agresti that do not appear in the book. The whole package is a github >> > repo >> > > https://github.com/cjgeyer/CatDataAnalysis. All of the data were >> > > translated mechanically using the R script foo.R included in the repo >> > (but >> > > not in the package) from Agresti's web site >> > > http://www.stat.ufl.edu/~aa/cda/data.html. >> > > >> > > This package seems to be a useful service to students and teachers. >> The >> > > data >> > > are much simpler to use with this package than trying to get the data >> > from >> > > Agresti's web page (foo.R has 277 lines of code). >> > > >> > > When I submitted the package to CRAN, I got the following response. >> > > >> > > > The Description field of the DESCRIPTION file is intended to be a >> (one >> > >
Re: [R-pkg-devel] package CatDataAnalysis
The link to Alan's web site is on every help page (in the source section). That's where the source is supposed to be. I have no problem with adding the source to the DESCRIPTION file, but that is not what CRAN asked me to do. On Sun, Jun 28, 2020 at 12:16 PM Max Turgeon wrote: > For what it's worth, I'd be inclined to interpreting CRAN's response > *very* literally, i.e. your Description field is not descriptive enough. > According to what I can see in the Github repo, you only have > > > "Datasets used in the book Categorical Data Analysis by Agresti but not > printed in the book." > > > Which is not much more than what the Title field says. One glaring > omission (IMO) from the Description field is any mention of Agresti's > website, where the data comes from. > > > In contrast, looking at the "woolridge" package, I can see from the > Description field that it contains 111 datasets (well, that's in the Title > field), it's about econometrics, and the purpose of the package is to make > it easier for students to work with these datasets. > > > Max Turgeon > Assistant Professor > Department of Statistics > Department of Computer Science > University of Manitoba > maxturgeon.ca > > > > > -- > *From:* R-package-devel on behalf > of Charles Geyer > *Sent:* June 28, 2020 11:38 AM > *To:* Neal Fultz > *Cc:* R Package Development > *Subject:* Re: [R-pkg-devel] package CatDataAnalysis > > > Caution: This message was sent from outside the University of Manitoba. > > > Actually the wooldridge package does not seem to satisfy any of the > specific requests CRAN asked me for. I have checked several other CRAN > packages for textbooks and they don't seem to satisfy those requirements > either. So this seems to be a new idea from CRAN. > > On Sun, Jun 28, 2020 at 11:32 AM Neal Fultz wrote: > > > I'm not sure exactly what cran is asking for, but the wooldridge > > package is a good example of a text book data set package, so maybe > > you can use the same format they did. > > > > https://cran.r-project.org/web/packages/wooldridge/index.html > > > > Best, > > > > Neal > > > > On Sun, Jun 28, 2020 at 9:08 AM Charles Geyer > > wrote: > > > > > > I have a package that has the datasets for Categorical Data Analysis by > > > Agresti that do not appear in the book. The whole package is a github > > repo > > > https://github.com/cjgeyer/CatDataAnalysis. All of the data were > > > translated mechanically using the R script foo.R included in the repo > > (but > > > not in the package) from Agresti's web site > > > http://www.stat.ufl.edu/~aa/cda/data.html. > > > > > > This package seems to be a useful service to students and teachers. > The > > > data > > > are much simpler to use with this package than trying to get the data > > from > > > Agresti's web page (foo.R has 277 lines of code). > > > > > > When I submitted the package to CRAN, I got the following response. > > > > > > > The Description field of the DESCRIPTION file is intended to be a > (one > > > > paragraph) description of what the package does and why it may be > > > > useful. Please elaborate. Tell the users what the datasets are about > > and > > > > what they contain so they can use them even when they haven't read > your > > > > book. > > > > > > > Please fix and resubmit, and document what was changed in the > > submission > > > > comments. > > > > > > In an alternate universe without copyright law this seems a reasonable > > > request. In this universe it seems to be asking for trouble. I know > > about > > > fair use, but I am not a lawyer and do not want to walk the borderline > > > between fair use and copyright violation. > > > > > > The package as it is seems OK because it comes from the author's public > > web > > > site and these data were never in the book. > > > > > > Please note that I made Alan Agresti (with his acquiescence) the author > > of > > > the package because it is his book and his data, but I (or rather > foo.R) > > > did all the work. > > > > > > I replied to cran.r-project.org, but that was apparently sent to > > /dev/null. > > > > > > This book is IMHO the authoritative textbook on the subject. Amazon > >
Re: [R-pkg-devel] package CatDataAnalysis
As I said in my original post, I have asked Alan Agresti and he agreed. There is no problem about authorship. On Sun, Jun 28, 2020 at 12:12 PM Hugh Parsonage wrote: > If you’re not the author of the data, you can’t submit it as such. The > website has a copyright message on it which, while not definitive, doesn’t > suggest the use you’re proposing would be allowed. > > Bear in mind that you may expose CRAN not just yourself to liability if > you try to conceal true authorship. > > I’d recommend asking the author of that website for permission. Either he > says that’s fine in which case you have permission, or he doesn’t and you > dodge a bullet. > > > On Mon, 29 Jun 2020 at 2:45 am, Charles Geyer > wrote: > >> Actually the wooldridge package does not seem to satisfy any of the >> specific requests CRAN asked me for. I have checked several other CRAN >> packages for textbooks and they don't seem to satisfy those requirements >> either. So this seems to be a new idea from CRAN. >> >> On Sun, Jun 28, 2020 at 11:32 AM Neal Fultz wrote: >> >> > I'm not sure exactly what cran is asking for, but the wooldridge >> > package is a good example of a text book data set package, so maybe >> > you can use the same format they did. >> > >> > https://cran.r-project.org/web/packages/wooldridge/index.html >> > >> > Best, >> > >> > Neal >> > >> > On Sun, Jun 28, 2020 at 9:08 AM Charles Geyer >> > wrote: >> > > >> > > I have a package that has the datasets for Categorical Data Analysis >> by >> > > Agresti that do not appear in the book. The whole package is a github >> > repo >> > > https://github.com/cjgeyer/CatDataAnalysis. All of the data were >> > > translated mechanically using the R script foo.R included in the repo >> > (but >> > > not in the package) from Agresti's web site >> > > http://www.stat.ufl.edu/~aa/cda/data.html. >> > > >> > > This package seems to be a useful service to students and teachers. >> The >> > > data >> > > are much simpler to use with this package than trying to get the data >> > from >> > > Agresti's web page (foo.R has 277 lines of code). >> > > >> > > When I submitted the package to CRAN, I got the following response. >> > > >> > > > The Description field of the DESCRIPTION file is intended to be a >> (one >> > > > paragraph) description of what the package does and why it may be >> > > > useful. Please elaborate. Tell the users what the datasets are about >> > and >> > > > what they contain so they can use them even when they haven't read >> your >> > > > book. >> > > >> > > > Please fix and resubmit, and document what was changed in the >> > submission >> > > > comments. >> > > >> > > In an alternate universe without copyright law this seems a reasonable >> > > request. In this universe it seems to be asking for trouble. I know >> > about >> > > fair use, but I am not a lawyer and do not want to walk the borderline >> > > between fair use and copyright violation. >> > > >> > > The package as it is seems OK because it comes from the author's >> public >> > web >> > > site and these data were never in the book. >> > > >> > > Please note that I made Alan Agresti (with his acquiescence) the >> author >> > of >> > > the package because it is his book and his data, but I (or rather >> foo.R) >> > > did all the work. >> > > >> > > I replied to cran.r-project.org, but that was apparently sent to >> > /dev/null. >> > > >> > > This book is IMHO the authoritative textbook on the subject. Amazon >> > sales >> > > rank agrees. The book is used for many courses. So this package >> would >> > be >> > > very helpful as is to many students and teachers. >> > > >> > > So what to do? Is there any way to get this package on CRAN? >> > > >> > > -- >> > > Charles Geyer >> > > Professor, School of Statistics >> > > Resident Fellow, Minnesota Center for Philosophy of Science >> > > University of Minnesota >> > > char...@stat.umn.edu >> > > >> > > [[alternative HTML version deleted]] >> > > >> > > __ >> > > R-package-devel@r-project.org mailing list >> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > >> >> >> -- >> Charles Geyer >> Professor, School of Statistics >> Resident Fellow, Minnesota Center for Philosophy of Science >> University of Minnesota >> char...@stat.umn.edu >> >> [[alternative HTML version deleted]] >> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package CatDataAnalysis
Actually the wooldridge package does not seem to satisfy any of the specific requests CRAN asked me for. I have checked several other CRAN packages for textbooks and they don't seem to satisfy those requirements either. So this seems to be a new idea from CRAN. On Sun, Jun 28, 2020 at 11:32 AM Neal Fultz wrote: > I'm not sure exactly what cran is asking for, but the wooldridge > package is a good example of a text book data set package, so maybe > you can use the same format they did. > > https://cran.r-project.org/web/packages/wooldridge/index.html > > Best, > > Neal > > On Sun, Jun 28, 2020 at 9:08 AM Charles Geyer > wrote: > > > > I have a package that has the datasets for Categorical Data Analysis by > > Agresti that do not appear in the book. The whole package is a github > repo > > https://github.com/cjgeyer/CatDataAnalysis. All of the data were > > translated mechanically using the R script foo.R included in the repo > (but > > not in the package) from Agresti's web site > > http://www.stat.ufl.edu/~aa/cda/data.html. > > > > This package seems to be a useful service to students and teachers. The > > data > > are much simpler to use with this package than trying to get the data > from > > Agresti's web page (foo.R has 277 lines of code). > > > > When I submitted the package to CRAN, I got the following response. > > > > > The Description field of the DESCRIPTION file is intended to be a (one > > > paragraph) description of what the package does and why it may be > > > useful. Please elaborate. Tell the users what the datasets are about > and > > > what they contain so they can use them even when they haven't read your > > > book. > > > > > Please fix and resubmit, and document what was changed in the > submission > > > comments. > > > > In an alternate universe without copyright law this seems a reasonable > > request. In this universe it seems to be asking for trouble. I know > about > > fair use, but I am not a lawyer and do not want to walk the borderline > > between fair use and copyright violation. > > > > The package as it is seems OK because it comes from the author's public > web > > site and these data were never in the book. > > > > Please note that I made Alan Agresti (with his acquiescence) the author > of > > the package because it is his book and his data, but I (or rather foo.R) > > did all the work. > > > > I replied to cran.r-project.org, but that was apparently sent to > /dev/null. > > > > This book is IMHO the authoritative textbook on the subject. Amazon > sales > > rank agrees. The book is used for many courses. So this package would > be > > very helpful as is to many students and teachers. > > > > So what to do? Is there any way to get this package on CRAN? > > > > -- > > Charles Geyer > > Professor, School of Statistics > > Resident Fellow, Minnesota Center for Philosophy of Science > > University of Minnesota > > char...@stat.umn.edu > > > > [[alternative HTML version deleted]] > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] package CatDataAnalysis
I have a package that has the datasets for Categorical Data Analysis by Agresti that do not appear in the book. The whole package is a github repo https://github.com/cjgeyer/CatDataAnalysis. All of the data were translated mechanically using the R script foo.R included in the repo (but not in the package) from Agresti's web site http://www.stat.ufl.edu/~aa/cda/data.html. This package seems to be a useful service to students and teachers. The data are much simpler to use with this package than trying to get the data from Agresti's web page (foo.R has 277 lines of code). When I submitted the package to CRAN, I got the following response. > The Description field of the DESCRIPTION file is intended to be a (one > paragraph) description of what the package does and why it may be > useful. Please elaborate. Tell the users what the datasets are about and > what they contain so they can use them even when they haven't read your > book. > Please fix and resubmit, and document what was changed in the submission > comments. In an alternate universe without copyright law this seems a reasonable request. In this universe it seems to be asking for trouble. I know about fair use, but I am not a lawyer and do not want to walk the borderline between fair use and copyright violation. The package as it is seems OK because it comes from the author's public web site and these data were never in the book. Please note that I made Alan Agresti (with his acquiescence) the author of the package because it is his book and his data, but I (or rather foo.R) did all the work. I replied to cran.r-project.org, but that was apparently sent to /dev/null. This book is IMHO the authoritative textbook on the subject. Amazon sales rank agrees. The book is used for many courses. So this package would be very helpful as is to many students and teachers. So what to do? Is there any way to get this package on CRAN? -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] check --as-cran error on Rd file
Sorry for the late reply. I am getting ready to have courses on-line only. Executive summary. Problem fixed, solution at bottom after some wandering around. sped.Rcheck/00install.out says (among other blather, no warnings or errors) byte-compile and prepare package for lazy loading so that doesn't appear to be the issue. Moreover changing "data(alberta)" in the example on the help page to just "alberta" (no "data") does not make the error go away. Moreover, when I run the package installed by R CMD check I get no errors blurfle$ ~/local/devel/bin/R --vanilla R Under development (unstable) (2020-03-10 r77920) -- "Unsuffered Consequences" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(sped, lib.loc = "sped.Rcheck") > data(alberta) > head(alberta) ind pa ma [1,] 58 11 12 [2,] 100 39 40 [3,] 101 39 40 [4,] 103 39 40 [5,] 107 39 100 [6,] 113 17 18 Oh. I see. I need to change "alberta" (with no "data") to "data(alberta)" in the usage section and in the examples section. Then the problem goes away. Thanks for the help. On Wed, Mar 11, 2020 at 3:57 PM Duncan Murdoch wrote: > > On 11/03/2020 11:44 a.m., Charles Geyer wrote: > > blurfle$ cat sped.Rcheck/00check.log > > * using log directory ‘/home/geyer/Software/sped/package/sped.Rcheck’ > > * using R Under development (unstable) (2020-03-10 r77920) > > * using platform: x86_64-pc-linux-gnu (64-bit) > > * using session charset: UTF-8 > > * using option ‘--as-cran’ > > * checking for file ‘sped/DESCRIPTION’ ... OK > > * this is package ‘sped’ version ‘0.1’ > > * checking CRAN incoming feasibility ... NOTE > > Maintainer: ‘Charles J. Geyer ’ > > > > New submission > > * checking package namespace information ... OK > > * checking package dependencies ... OK > > * checking if this is a source package ... OK > > * checking if there is a namespace ... OK > > * checking for executable files ... OK > > * checking for hidden files and directories ... OK > > * checking for portable file names ... OK > > * checking for sufficient/correct file permissions ... OK > > * checking serialization versions ... OK > > * checking whether package ‘sped’ can be installed ... OK > > * checking installed package size ... OK > > * checking package directory ... OK > > * checking for future file timestamps ... OK > > * checking DESCRIPTION meta-information ... OK > > * checking top-level files ... OK > > * checking for left-over files ... OK > > * checking index information ... OK > > * checking package subdirectories ... OK > > * checking R files for non-ASCII characters ... OK > > * checking R files for syntax errors ... OK > > * checking whether the package can be loaded ... OK > > * checking whether the package can be loaded with stated dependencies ... OK > > * checking whether the package can be unloaded cleanly ... OK > > * checking whether the namespace can be loaded with stated dependencies ... > > OK > > * checking whether the namespace can be unloaded cleanly ... OK > > * checking loading without being on the library search path ... OK > > * checking use of S3 registration ... OK > > * checking dependencies in R code ... OK > > * checking S3 generic/method consistency ... OK > > * checking replacement functions ... OK > > * checking foreign function calls ... OK > > * checking R code for possible problems ... OK > > * checking Rd files ... OK > > * checking Rd metadata ... OK > > * checking Rd line widths ... OK > > * checking Rd cross-references ... OK > > * checking for missing documentation entries ... OK > > * checking for code/documentation mismatches ... WARNING > > Variables with usage in documentation object 'alberta' but not in code: > >‘alberta’ > > > > * checking Rd \usage sections ... OK > > * checking Rd contents ... OK > > * checking for unstated dependencies in examples ... OK > > * checking contents of ‘data’ directory ... OK > > * checking data for non-ASCII characters ... OK > > * ch
[R-pkg-devel] check --as-cran error on Rd file
blurfle$ cat sped.Rcheck/00check.log
* using log directory ‘/home/geyer/Software/sped/package/sped.Rcheck’
* using R Under development (unstable) (2020-03-10 r77920)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘sped/DESCRIPTION’ ... OK
* this is package ‘sped’ version ‘0.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Charles J. Geyer ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘sped’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ...
OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Variables with usage in documentation object 'alberta' but not in code:
‘alberta’
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
Running ‘foo.R’
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 1 NOTE
blurfle$
I do not get this warning when --as-cran is omitted. I have never seen the
warning before. The Rd file is
blurfle$ cat sped/man/alberta.Rd
\name{alberta}
\docType{data}
\alias{alberta}
\title{Pedigree Data on Equus przewalskii in Alberta}
\description{
Pedigree of Asian wild horse (also called Mongolian wild horse)
\emph{Equus przewalskii} individuals living in Alberta, Canada in 1988.
}
\usage{alberta}
\format{
A matrix with 69 rows giving (individual, father, mother) triplets.
The column labels are \code{ind}, \code{pa}, and \code{ma}.
The names (which are numbers) are studbook numbers.
There are 82 individuals in this pedigree in all.
There are \eqn{82 - 69 = 13} founders.
}
\examples{
library(sped)
data(alberta)
}
\keyword{datasets}
blurfle$
And this is AFAICS what Section 2.1.2 of Writing R Extensions (R-devel
version) says it should be.
So what is this warning about?
--
Charles Geyer
Professor, School of Statistics
Resident Fellow, Minnesota Center for Philosophy of Science
University of Minnesota
char...@stat.umn.edu
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] registering native routines
Sorry. I am a moron. It was an illusion. I was checking R package foo with the Makevars for R package fooRegister via the R_MAKEVARS_USER mechanism and got confused. In fact R package foo, when checked with --as-cran only gives warnings not errors about registering native routines. So AFAICS, CRAN warns against not using registration of native routines but that is not yet an ERROR. So that is what I am going to tell the students. All of my CRAN packages properly register native routines, and I teach this to my advisees and students. But my github packages I use as teaching examples don't (except for the aforementioned fooRegister) and I was suddenly worried about them. On Sat, Feb 16, 2019 at 9:41 PM Avraham Adler wrote: > > https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html > > On Sat, Feb 16, 2019 at 3:22 PM Charles Geyer wrote: > > > > I just noticed that R package foo in the github repo > > https://github.com/cjgeyer/foo no longer passes R CMD check --as-cran. The > > problem seems to be that it does not register native routines and thus the > > C routines cannot be found. It does pass R CMD check (without --as-cran). > > The version of the package that does register native routines (package > > fooRegister) in the same repo passes with or without --as-cran. So did I > > miss the announcement? Is registration of native routines now mandatory > > for CRAN? > > > > Just asking because I am currently teaching about R packages in PhD level > > statistical confusing and don't want to provide erroneous info. > > > > These packages are toy packages to introduce the class to R packages. I > > don't actually want to put them on CRAN. > > > > -- > > Charles Geyer > > Professor, School of Statistics > > Resident Fellow, Minnesota Center for Philosophy of Science > > University of Minnesota > > char...@stat.umn.edu > > > > [[alternative HTML version deleted]] > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] registering native routines
I just noticed that R package foo in the github repo https://github.com/cjgeyer/foo no longer passes R CMD check --as-cran. The problem seems to be that it does not register native routines and thus the C routines cannot be found. It does pass R CMD check (without --as-cran). The version of the package that does register native routines (package fooRegister) in the same repo passes with or without --as-cran. So did I miss the announcement? Is registration of native routines now mandatory for CRAN? Just asking because I am currently teaching about R packages in PhD level statistical confusing and don't want to provide erroneous info. These packages are toy packages to introduce the class to R packages. I don't actually want to put them on CRAN. -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R_registerRoutines, R_useDynamicSymbols
There are several other things to do. You might find the toy package fooRegister I use for teaching helpful. https://github.com/cjgeyer/foo/tree/master/package/fooRegister -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Determine subset from glm object
I think your second option sounds better because this is all happening inside one function I'm writing so users won't be able mess with the glm object. Many thanks. On Sun, Jul 8, 2018, 12:10 PM Duncan Murdoch wrote: > On 08/07/2018 11:48 AM, Charles Geyer wrote: > > I need to find out from an object returned by R function glm with > argument > > x = TRUE > > what the subsetting was. It appears that if gout is that object, then > > > > as.integer(rownames(gout$x)) > > > > is a subset vector equivalent to the one actually used. > > You don't want the "as.integer". If the dataframe had rownames to start > with, the x component of the fit will have row labels consisting of > those labels, so as.integer may fail. Even if it doesn't, the rownames > aren't necessarily sequential integers. You can index the dataframe by > the character versions of the default numbers, so simply > rownames(gout$x) should always work. > > More generally, I'm not sure your question is well posed. What do you > mean by "the subsetting"? If you have something like > > df <- data.frame(letters, x = 1:26, y = rbinom(26, 1, 0.5)) > > df1 <- subset(df, letters > "b" & letters < "y") > > gout <- glm(y ~ x, data = df1, subset = letters < "q", x = TRUE) > > the rownames(gout$x) are going to be numbers for rows of df, because df1 > will get a subset of those as row labels. > > > > I do also have the call to glm (as a call object) so can determine the > > actual subset argument, but this seems to be not so useful because I > don't > > know the length of the original variables before subsetting. > > You should be able to evaluate the subset expression in the environment > of the formula, i.e. > > eval(gout$call$subset, envir = environment(gout$formula)) > > This may give incorrect results if the variables used in subsetting > aren't in the dataframe and have changed since glm() was called. > > > > So now my questions. Is this idea above (using rownames) OK even though > I > > cannot find where (if anywhere) it is documented? Is there a better way? > > One more guaranteed to be correct in the future? > > > > I would trust evaluating the subset more than grabbing row labels from > gout$x, but I don't know for sure it is likely to be more robust. > > Duncan Murdoch > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Determine subset from glm object
I need to find out from an object returned by R function glm with argument x = TRUE what the subsetting was. It appears that if gout is that object, then as.integer(rownames(gout$x)) is a subset vector equivalent to the one actually used. I do also have the call to glm (as a call object) so can determine the actual subset argument, but this seems to be not so useful because I don't know the length of the original variables before subsetting. So now my questions. Is this idea above (using rownames) OK even though I cannot find where (if anywhere) it is documented? Is there a better way? One more guaranteed to be correct in the future? -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN upload and prechecking confusion (Johannes Graumann)
You can precompute long running things in vignettes. See CRAN package mcmc for examples that do this reproducibly. -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Problems with Notes for Package IncDTW
I modified a toy package I use for teaching to do the registration right (to serve as an example). See https://github.com/cjgeyer/foo/tree/master/package where packages foo and fooRegister do the same thing except for registration. Diffing them shows what is needed. -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
