[R-pkg-devel] R-package did not pass the incoming checks automatically
Hugh Parsonage
hugh.parsonage at gmail.com
Sat Jan 20 20:31:49 CET 2018
Use the url at the bottom of the linked page, i.e.
https://cran.r-project.org/package=ewoc
On Sun, 21 Jan 2018 at 5:06 am, Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:
> Hi Márcio:
>
> I do not have solutions to your specific problems, but the errors do
> appear to be coming from the development version of R. When you run
> devtools::build_win(), run it twice, once as:
>
> devtools::build_win(version = "R-release")
>
> and once with
>
> devtools::build_win(version = "R-devel")
>
> which is then more likely to produce the CRAN results before you submit.
> Also, as Henrik Bengtsson explained on this list a few weeks ago:
>
> > As far as I understand it, the new R-devel tests basically tests your
> > package with the minimal setup of packages (a "sandboxed" .libPaths())
> > inferred from you DESCRIPTION (by excluding Suggests of the packages
> > you depend on, which is where I think 'webshot' lives).
>
> So R-devel can give different results, and you need to make certain that
> your Imports and Suggests includes anything that might not be loaded.
>
> Hope this helps some.
>
> -Roy
>
> > On Jan 20, 2018, at 9:47 AM, Márcio Augusto Diniz <dnz.marcio at gmail.com>
> wrote:
> >
> > Hello all,
> >
> > I submitted my package (
> > https://cran.r-project.org/web/packages/ewoc/index.html) to CRAN and it
> did
> > not pass the automatic checks of win_builder. However, I did not have
> the
> > same error or warning messages when I ran devtools::win_builder() and
> > devtools::run_examples() before. I had the same notes, though.
> >
> > See message from win_builder() CRAN:
> >
> > * using log directory 'd:/RCompile/CRANincoming/R-devel/ewoc.Rcheck'
> > * using R Under development (unstable) (2018-01-19 r74138)
> > * using platform: x86_64-w64-mingw32 (64-bit)
> > * using session charset: ISO8859-1
> > * checking for file 'ewoc/DESCRIPTION' ... OK
> > * checking extension type ... Package
> > * this is package 'ewoc' version '0.1.1'
> > * checking CRAN incoming feasibility ... NOTE
> > Maintainer: 'Marcio A. Diniz <marcio.diniz at cshs.org>'
> >
> > Found the following (possibly) invalid URLs:
> > URL: https://cran.rstudio.com/web/packages/ewoc/index.html
> > From: README.md
> > Status: 200
> > Message: OK
> > CRAN URL not in canonical form
> > Canonical CRAN.R-project.org URLs use https.
> > * 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 serialized R objects in the sources ... OK
> > * checking whether package 'ewoc' can be installed ... OK
> > * checking installed package size ... OK
> > * checking package directory ... 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
> > * 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 ... WARNING
> > Error: package or namespace load failed for 'ewoc' in namespaceExport(ns,
> > exports):
> > undefined exports: iter, nextElem, isplit, irnorm, irunif, irbinom,
> > irnbinom, irpois, icount, idiv, ireadLines, iread.table, icountn, iapply
> > In addition: Warning message:
> > S3 methods 'iter.default', 'iter.iter', 'iter.matrix', 'iter.data.frame',
> > 'iter.function', 'nextElem.containeriter', 'nextElem.matrixiter',
> > 'nextElem.dataframeiter', 'nextElem.funiter', 'nextElem.abstractiter',
> > 'as.list.iter', 'isplit.default', 'isplit.data.frame' were declared in
> > NAMESPACE but not found
> > Execution halted
> >
> > It looks like this package has a loading problem when not on .libPaths:
> > see the messages for details.
> > ** 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 ... [15s] 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' ... [51s] NOTE
> > Examples with CPU or elapsed time > 10s
> > user system elapsed
> > ewoc_simulation 1.65 0.01 17.4
> > ** running examples for arch 'x64' ... ERROR
> > Running examples in 'ewoc-Ex.R' failed
> > The error most likely occurred in:
> >
> >> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> >> ### Name: optimal_toxicity
> >> ### Title: Percent of doses in relation the optimal toxicity interval
> >> ### Aliases: optimal_toxicity
> >>
> >> ### ** Examples
> >>
> >> ## Don't show:
> >> DLT <- 0
> >> dose <- 30
> >> step_zero <- ewoc_d1classic(DLT ~ dose, type = 'discrete',
> > + theta = 0.33, alpha = 0.25,
> > + min_dose = 0, max_dose = 100,
> > + dose_set = seq(0, 100, 20),
> > + rho_prior = matrix(1, ncol = 2, nrow = 1),
> > + mtd_prior = matrix(1, ncol = 2, nrow = 1),
> > + rounding = "nearest")
> > Warning in limits_d1nocov(first_dose = first_dose, last_dose =
> last_dose, :
> > 'first_dose' and 'last_dose' were defined as the first and last
> elements
> > of 'dose_set', respectively.
> > Compiling model graph
> > Resolving undeclared variables
> > Allocating nodes
> > Graph information:
> > Observed stochastic nodes: 1
> > Unobserved stochastic nodes: 2
> > Total graph size: 32
> >
> > Initializing model
> >
> >> response_sim <- response_d1classic(rho = 0.05, mtd = 20, theta = 0.33,
> > + min_dose = 10, max_dose = 50)
> >> pdlt_sim <- pdlt_d1classic(rho = 0.05, mtd = 20, theta = 0.33,
> > + min_dose = 10, max_dose = 50)
> >> sim <- ewoc_simulation(step_zero = step_zero,
> > + n_sim = 1, sample_size = 2,
> > + alpha_strategy = "increasing",
> > + response_sim = response_sim,
> > + ncores = 2)
> > Error in { : task 1 failed - "could not find function "feasibility""
> > Calls: ewoc_simulation ... ewoc_simulation.ewoc_d1classic -> %dopar% ->
> > <Anonymous>
> > Execution halted
> > * checking PDF version of manual ... OK
> > * DONE
> > Status: 1 ERROR, 1 WARNING, 2 NOTEs
> >
> >
> > Any thoughts?
> >
> > Thank you,
> >
> > --
> > Márcio Diniz
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-package-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> **********************
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
> ______________________________________________
> R-package-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
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