[R-pkg-devel] Get an empty note for "checking DESCRIPTION meta-information" when I run devtools::build_win()
Martin Maechler
m@echler @ending from @t@t@m@th@ethz@ch
Thu Jul 26 17:39:37 CEST 2018
>>>>> Eggleston, Barry
>>>>> on Wed, 25 Jul 2018 21:53:30 +0000 writes:
> This is great news Roman.
> The "rth" role stands for "Research team head", and I got it from the http://www.loc.gov/marc//relators/relaterm.html website.
and it *IS* a correct role also in R, using non-API function
(non-API: do *not* use it in reproducible code, pkgs, etc !) :
> utils:::.canonicalize_person_role("rth")
[1] "rth"
tells us that this is a correct role,
whereas these are not :
> utils:::.canonicalize_person_role("Rth")
character(0)
Warning message:
In utils:::.canonicalize_person_role("Rth") :
Invalid role specification: ‘Rth’.
> utils:::.canonicalize_person_role("Foobar")
character(0)
Warning message:
In utils:::.canonicalize_person_role("Foobar") :
Invalid role specification: ‘Foobar’.
>
So the bug is really in the Windows version of R that was
running for you when you've used devtools::build_win() or in
build_win() itself.
"rth" is a correct role and you should *NOT* replace it by
something less appropriate ...
Martin Maechler
ETH Zurich and R Core Team
> This issue here is Diane Catellier provided the funds and management for us to develop this package. I did not know about the person() function. When I looked at the help page for person(), I see that I can use "fnd" for funder and that will define Diane's role sufficiently well. I'll make the change and run through my checks again.
> Thank you,
> Barry
> -----Original Message-----
> From: Roman Flury <roman.flury using math.uzh.ch>
> Sent: Wednesday, July 25, 2018 5:27 PM
> To: Eggleston, Barry <beggleston using rti.org>
> Cc: Hugh Parsonage <hugh.parsonage using gmail.com>; r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] Get an empty note for "checking DESCRIPTION meta-information" when I run devtools::build_win()
> Barry,
> sorry did not anticipate the behaving of the emailer. I could reproduce your error with the DESCRIPTION file below with a helloworld pkg
> Package: test
> Type: Package
> Title: What the Package Does (Title Case)
> Version: 0.1.0
> Authors using R: c(person("Roman", "Flury", email = "roman.flury using math.uzh.ch", role = c("aut", "cre")),
> person("Test", "person", email = "testmail using test.org", role = c("fnd", "rth")))
> Description: Short description to describe this package.
> Depends: R (>= 3.5.0)
> License: GPL-3
> Encoding: UTF-8
> LazyData: true
> Imports: eha (>= 2.5.1),
> ggplot2 (>= 2.2.1),
> survival (>= 2.41-3),
> reshape2 (>= 1.4.3),
> stats (>= 3.5.0)
> RoxygenNote: 6.0.1
> this passes R CMD check --as-cran on a unix system, but not on windwos.
> The problem seems to be the role "rth", which is also not listed in ?person. What does this role stand for?
> best, Roman
> On 25.07.2018 16:21, Eggleston, Barry wrote:
>> Roman,
>>
>> Not sure why my emailer added all those <mailto:aaa using bbb.ccc> items, but none of them are in my original DESCRIPTION file. So my Maintainer line, for example, simply reads Barry Eggleston <email address>, where email address is simply beggleston using rti.org.
>>
>> Thanks for the observation,
>> Barry
>>
>>
>> -----Original Message-----
>> From: Roman Flury <roman.flury using math.uzh.ch>
>> Sent: Wednesday, July 25, 2018 9:42 AM
>> To: Eggleston, Barry <beggleston using rti.org>
>> Cc: Hugh Parsonage <hugh.parsonage using gmail.com>;
>> r-package-devel using r-project.org
>> Subject: Re: [R-pkg-devel] Get an empty note for "checking DESCRIPTION
>> meta-information" when I run devtools::build_win()
>>
>> Hello,
>>
>> after https://cran.r-project.org/doc/manuals/r-release/R-exts.html the ‘Maintainer’ field should give a single name followed by a valid (RFC 2822) email address in angle brackets.
>> but beggleston using rti.org<mailto:beggleston using rti.org> is not a valid RFC
>> 2822 email address, you could check this for instance with
>> https://proxy2.de/email-validation.php
>>
>> you could omit the 'Maintainer' field, since a suitable ‘Authors using R’ field is given..
>> does this solve your problem?
>>
>> best, Roman
>>
>> ----- Original Message -----
>> From: "Eggleston, Barry" <beggleston using rti.org>
>> To: "Hugh Parsonage" <hugh.parsonage using gmail.com>
>> Cc: r-package-devel using r-project.org
>> Sent: Wednesday, July 25, 2018 3:00:35 PM
>> Subject: Re: [R-pkg-devel] Get an empty note for "checking DESCRIPTION
>> meta-information" when I run devtools::build_win()
>>
>> Below is a copy of my DESCRIPTION file:
>>
>> Package: BayesCTDesign
>> Type: Package
>> Title: Two Arm Bayesian Clinical Trial Design with and Without
>> Historical Control Data
>> Version: 1.0.0
>> Authors using R: c(
>> person("Barry", "Eggleston", email = "beggleston using rti.org<mailto:beggleston using rti.org>", role = c("cre", "aut")),
>> person("Doug", "Wilson", email = "doug.roy.wilson using gmail.com<mailto:doug.roy.wilson using gmail.com>", role = c("aut")),
>> person("Becky", "McNeil", email = "rmcneil using rti.org<mailto:rmcneil using rti.org>", role = c("aut")),
>> person("Joseph", "Ibrahim", email = "jibrahim using email.unc.edu<mailto:jibrahim using email.unc.edu>", role = c("aut")),
>> person("Diane", "Catellier", email =
>> "dcatellier using rti.org<mailto:dcatellier using rti.org>", role = c("fnd",
>> "rth")))
>> Maintainer: Barry Eggleston
>> <beggleston using rti.org<mailto:beggleston using rti.org>>
>> Description: A set of functions to help clinical trial researchers calculate power and sample size for two-arm Bayesian randomized clinical trials that do or do not incorporate historical control data. At some point during the design process, a clinical trial researcher who is designing a basic two-arm Bayesian randomized clinical trial needs to make decisions about power and sample size within the context of hypothesized treatment effects. Through simulation, the \code{simple_sim()} function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about treatment effect,control group characteristics, and outcome. If the clinical trial researcher has access to historical control data, then the researcher can design a two-arm Bayesian randomized clinical trial that incorporates the historical data. In such a case, the researcher needs to work through the potential consequences of historical and randomiz ed control differences on trial characteristics, in addition to working through issues regarding power in the context of sample size, treatment effect size, and outcome. If a researcher designs a clinical trial that will incorporate historical control data, the researcher needs the randomized controls to be from the same population as the historical controls. What if this is not the case when the designed trial is implemented? During the design phase, the researcher needs to investigate the negative effects of possible historic/randomized control differences on power, type one error, and other trial characteristics. Using this information, the researcher should design the trial to mitigate these negative effects. Through simulation, the \code{historic_sim()} function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about historical and randomized control differences as well as treatment effec ts and outcomes. The results from \code{historic_sim()} and \code{simple_sim()} can be printed with \code{print_table()} and graphed with \code{plot_table()} methods. Outcomes considered are Gaussian, Poisson, Bernoulli, Lognormal, Weibull, and Piecewise Exponential.
>> Depends: R (>= 3.5.0)
>> License: GPL-3
>> Encoding: UTF-8
>> LazyData: true
>> Imports: eha (>= 2.5.1),
>> ggplot2 (>= 2.2.1),
>> survival (>= 2.41-3),
>> reshape2 (>= 1.4.3),
>> stats (>= 3.5.0)
>> RoxygenNote: 6.0.1
>>
>>
>> From: Hugh Parsonage <hugh.parsonage using gmail.com>
>> Sent: Tuesday, July 24, 2018 10:12 PM
>> To: Eggleston, Barry <beggleston using rti.org>
>> Cc: r-package-devel using r-project.org
>> Subject: Re: [R-pkg-devel] Get an empty note for "checking DESCRIPTION
>> meta-information" when I run devtools::build_win()
>>
>> Thank you. Could you provide the contents of DESCRIPTION too? That might provide the richest clue. If you have a link to an online copy of the package that could be helpful too.
>> On Wed, 25 Jul 2018 at 12:01 Eggleston, Barry <beggleston using rti.org<mailto:beggleston using rti.org>> wrote:
>> I am working through my first package submission. When I checked my package using devtools::build_win(), I got no errors and two notes. One note is simply the expected note that my package is a new submission. My second note involves DESCRIPTION meta-information, but nothing is printed so I don't know what to focus on. I have copied the important parts of my 00check.log from CRAN below for context. What areas of my DESCRIPTION file might create such an empty note? Thanks in advance for any help you might give me.
>>
>> * checking CRAN incoming feasibility ... NOTE
>> Maintainer: 'Barry Eggleston <beggleston using rti.org<mailto:beggleston using rti.org><mailto:beggleston using rti.org<mailto:beggleston using rti.org>>>'
>>
>> 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 hidden files and directories ... OK
>> * checking for portable file names ... OK
>> * checking whether package 'BayesCTDesign' can be installed ... OK
>> * checking installed package size ... OK
>> * checking package directory ... OK
>> * checking DESCRIPTION meta-information ... NOTE
>>
>> * 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
>> * loading checks for arch 'i386'
>> ** 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
>> * loading checks for arch 'x64'
>> ** 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 ... [41s] 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 ... OK
>> * checking Rd \usage sections ... OK
>> * checking Rd contents ... OK
>> * checking for unstated dependencies in examples ... OK
>> * checking examples ...
>> ** running examples for arch 'i386' ... [19s] OK
>> ** running examples for arch 'x64' ... [22s] OK
>> * checking PDF version of manual ... OK
>> * DONE
>> Status: 2 NOTEs
>>
>> Barry
>>
>>
>> [[alternative HTML version deleted]]
>>
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