Re: [R-pkg-devel] FW: CRAN submission berryFunctions 1.8.0
Note that current devtools 1.8.0 attempts to use the spell checker when you say devtools::check(check_version = TRUE), and warns if no spell checker could be found. Perhaps a simpler option is to build on win-builder before submission (e.g., by running devtools::build_win() ), which is a good idea unless your package doesn't support Windows. Best regards Kirill On 03.06.2015 09:51, Uwe Ligges wrote: On 03.06.2015 09:48, Berry Boessenkool wrote: Hi, after submitting my package update, CRAN (Brian Ripley) found a couple of warnings / messages. URLs that are not longer existent, a non-ASCII character from copypasting, incorrect title case. Stuff that I should and could definitely solve before submitting. Why did the latest Rdevel (2015-06-01 r68455) CMD check --as-cran not find them? Your R was not libcurl enabled nor had you the spellchecker installed, I guess. Best, Uwe Ligges Below are the relevant excerpts. Thanks for any hints about what I may have done wrong, Berry - Found the following (possibly) invalid URLs: URL: http://cran.r-project.org/web/packages/denstrip (moved to http://cran.r-project.org/web/packages/denstrip/) From: man/betaPlot.Rd man/normPlot.Rd Status: 200 Message: OK CRAN URL not in canonical form URL: http://www.geolinde.musin.de/afrika/pic/klimamuenchen.gif From: man/climateGraph.Rd Status: 404 Message: Not Found [...] The canonical URL of the CRAN page for a package is http://cran.r-project.org/package=pkgname No package encoding and non-ASCII characters in the following R files: R/groupHist.R 19: # ignore messages like: argument col is not made use of The Title field should be in title case, current version then in title case: �Function Collection related to Plotting and Hydrology� �Function Collection Related to Plotting and Hydrology� [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] S3 method, useMethod and <-, using Roxygen
values -> value is a typo in the implementation of .default(). I'm not
sure you need to document the .default() function (the second @rdname
set_labels). If this doesn't help, you could try renaming set_labels()
to avoid collisions.
Best regards
Kirill
On 23.10.2015 10:30, Daniel Lüdecke wrote:
Hello,
I don't exactly know how to name my problem, so I try to describe it.
In my package (sjmisc), I have a function to set label attributes to
vectors:
set_labels <- function(x, labels, ...) {
...
}
Usage would be:
x <- set_labels(x, c("lo", "high"))
No I wanted to also add functionality to directly change a value:
set_labels(x) <- c("lo", "high")
So I added this to my package source:
#' @rdname set_labels
#' @export
`set_labels<-` <- function(x, force.labels = FALSE, force.values =
TRUE, value) {
UseMethod("set_labels<-")
}
#' @rdname set_labels
#' @export
`set_labels<-.default` <- function(x, force.labels = FALSE,
force.values = TRUE, value) {
x <- set_labels(x, values, force.labels, force.values)
x
}
However, running the check gives following note and warnings:
* checking R code for possible problems ... NOTE
set_labels<-.default: no visible binding for global variable 'values'
* 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
Functions or methods with usage in documentation object 'set_labels'
but not in code:
set_labels.default
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'set_labels':
'set_labels.default'
Bad \usage lines found in documentation object 'set_labels':
<- value
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
I don't know what to do here. Any help is appreciated!
Thanks in advance
Daniel
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Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr.
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Re: [R-pkg-devel] Problems with :::
On 28.01.2016 14:20, Duncan Murdoch wrote:
If the class is just "mytable", then you'll have to change it to
"ftable" before calling stats::format().
Side note: The following will fail, because format.ftable double-checks
the class of its argument:
format_ftable <- utils::getS3method("format", "ftable")
format_ftable(mytable)
-Kirill
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Re: [R-pkg-devel] Namespace error
It's difficult to tell without seeing the source code, but the NAMESPACE
you posted doesn't seem to contain "View". This file usually gets
updated when you call devtools::document() or roxygen2::roxygenize().
What happens if you run one of these functions?
-Kirill
On 16.02.2016 18:14, Glenn Schultz wrote:
All
I am not sure why I am getting this error and I cannot find anything
on the net other than try to restart R. I am
using Roxygen2 and it clearly says don't edit by hand at the top of
the namespace so I am stuck as what to do or look for.
Glenn
Error in namespaceExport(ns, exports) : undefined exports: View
Error: package or namespace load failed for ‘BondLab’
Execution halted
* checking whether the namespace can be loaded with stated
dependencies ... WARNING
Error in namespaceExport(ns, exports) : undefined exports: View
Calls: loadNamespace ... namespaceImportFrom -> asNamespace ->
loadNamespace -> namespaceExport
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Error: package or namespace load failed for ‘BondLab’
Call sequence:
2: stop(gettextf("package or namespace load failed for %s",
sQuote(package)), call. = FALSE, domain = NA)
Here is my namespace:
# Generated by roxygen2: do not edit by hand
export(AtomsData)
export(BeginBal)
export(Bond)
export(BondAnalytics)
export(BondBasisConversion)
export(BondCashFlows)
export(CDR.To.MDR)
export(CIRBondPrice)
export(CIRSim)
export(CPR.To.SMM)
export(CalibrateCIR)
export(CashFlowTable)
export(CollateralGroup)
export(CusipRecord)
export(DollarRoll)
export(DollarRollAnalytics)
export(Effective.Convexity)
export(Effective.Duration)
export(Effective.Measure)
export(EndingBal)
export(EstimYTM)
export(Forward.Rate)
export(ForwardPassThrough)
export(HPISim)
export(Interest)
export(MBS)
export(MakeBondDetails)
export(MakeCollateral)
export(MakeMBSDetails)
export(MakeModelTune)
export(MakeRAID)
export(MakeRDME)
export(MakeScenario)
export(MakeSchedule)
export(MakeTranche)
export(ModelTune)
export(Mortgage.Monthly.Payment)
export(Mortgage.OAS)
export(MortgageCashFlow)
export(MortgageCashFlowArray)
export(MortgageCashFlow_Array)
export(MortgageRate)
export(Mtg.Scenario)
export(MtgRate)
export(MtgTermStructure)
export(PPC.Ramp)
export(PassThroughOAS)
export(PaymentDate)
export(PrepaymentAssumption)
export(RDMEData)
export(RDMEFactor)
export(REMICDeal)
export(REMICGroupConn)
export(REMICSchedules)
export(REMICWaterFall)
export(Rates)
export(ReadRAID)
export(Remain.Balance)
export(RemicStructure)
export(SMM.To.CPR)
export(SMMVector.To.CPR)
export(SaveCollGroup)
export(SaveMBS)
export(SaveModelTune)
export(SaveRAID)
export(SaveRDME)
export(SaveREMIC)
export(SaveScenario)
export(SaveSchedules)
export(SaveTranche)
export(SaveTranches)
export(ScenarioCall)
export(Sched.Prin)
export(SwapRateData)
export(TermStructure)
export(TimeValue)
export(Tranches)
export(ULTV)
export(bondprice)
exportClasses(AtomsAnalytics)
exportClasses(AtomsData)
exportClasses(AtomsScenario)
exportClasses(BondCashFlows)
exportClasses(BondDetails)
exportClasses(BondTermStructure)
exportClasses(MBSDetails)
exportClasses(TermStructure)
import(data.tree)
import(methods)
import(optimx)
importFrom(lubridate,"%m+%")
importFrom(lubridate,day)
importFrom(lubridate,month)
importFrom(lubridate,year)
importFrom(lubridate,years)
importFrom(termstrc,create_cashflows_matrix)
importFrom(termstrc,create_maturities_matrix)
importFrom(termstrc,estim_cs)
importFrom(termstrc,estim_nss)
importFrom(termstrc,forwardrates)
importFrom(termstrc,spotrates)
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Re: [R-pkg-devel] Scripts to generate data objects
The devtools::use_data_raw() function creates a "data-raw" directory for this purpose, and adds it to .Rbuildignore so that it's not included in the built package. Your scripts can then write the data to the proper place using devtools::use_data(). -Kirill On 30.03.2016 14:03, Iago Mosqueira wrote: Hello, What is the best way of keeping R scripts that are used to generate the data files in the data/ folder? These are not meant to be available to the user, but I would like to keep them in the package itself. Right now I am storing them inside data/, for example PKG/data/datasetone.R to create PKG/data/dataseton.RData, and then adding those R files to .Rbuildignore. Are there any other sensible ways of doing this? Thanks, Iago [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] S3 dispatch for select()
Hi
When a package defines a select() generic, objects of type list seem to
be forcibly dispatched to utils::select.list(). This is not the case
when the generic is defined in a regular R script. I could define a
select__() generic and forward all select() calls to select__() first,
but I wonder if there's a better way. Thanks.
Examples below, the first needs the *select* package [1].
Best regards
Kirill
[1] https://github.com/krlmlr/select
# 1. From package:
library(select)
select(letters)
#> [1] "select.default"
select(1:3)
#> [1] "select.default"
select(list(1:3))
#> Error in select.list(list(1:3)): select.list() cannot be used
non-interactively
# 2. From script
select <- function(x, ...) UseMethod("select")
select.default <- function(x, ...) "select.default"
select.list <- function(x, ...) "select.list"
select(letters)
#> [1] "select.default"
select(1:3)
#> [1] "select.default"
select(list(1:3))
#> [1] "select.list"
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Re: [R-pkg-devel] active bindings in package namespace
Dear Jack
This doesn't answer your question, but I would advise against this design.
- Users do not expect side effects (such as network access) from
accessing a symbol.
- A function gives you much more flexibility to change the interface
later on. (Arguments for fetching the data, tokens for API access, ...)
- You already encountered a few quirks that make this an "interesting"
problem.
A function call only needs a pair of parentheses.
Best regards
Kirill
On 23.03.19 16:50, Jack O. Wasey wrote:
Dear all,
I am developing a package which is a front for various online data
(icd.data https://github.com/jackwasey/icd.data/ ). The current CRAN
version just has lazy-loaded data, but now the package encompasses far
more current and historic ICD codes from different countries, these
can't be included in the CRAN package even with maximal compression.
Other authors have solved this using functions to get the data, with
or without a local cache of the retrieved data. No CRAN or other
packages I have found after extensive searching use the attractive
active binding feature of R.
The goal is simple: for the user to refer to the data by its symbol,
e.g., 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be
downloaded and parsed transparently (if the user has already granted
permission, or after prompt if they haven't).
The bindings are set using commands alongside the function definitions
in R/*.R .E.g.
makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding,
environment())
lockBinding("icd10cm_latest", environment())
For non-interactive use, CI and CRAN tests, no data should be
downloaded, and no cache directory set up without user consent. For
interactive use, I ask permission to create a local data cache before
downloading data.
This works fine... until R CMD check. The following steps seems to
'get' or 'source' everything from the package namespace, which results
in triggering the active bindings, and this fails if I am unable to
get consent to download data, and want to 'stop' on this error condition.
- checking dependencies in R code
- checking S3 generic/method consistency
- checking foreign function calls
- checking R code for possible problems
Debugging CI-specific binding bugs is a nightmare because these occur
in different R sessions initiated by R CMD check.
There may be legitimate reasons to evaluate everything in the
namespace, but I've no idea what they are. Incidentally, Rstudio also
does 'mget' on the whole package namespace and triggers bindings
during autocomplete. https://github.com/rstudio/rstudio/issues/4414
Is this something I should raise as an issue with R? Or does anyone
have any idea of a sensible approach to this. Currently I have a set
of workarounds, but this complicates the code, and has taken an awful
lot of time. Does anyone know of any CRAN package which has active
bindings in the package namespace?
Any ideas appreciated.
Jack Wasey
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