[R-pkg-devel] R-package did not pass the incoming checks automatically
Roy Mendelssohn - NOAA Federal
roy.mendelssohn at noaa.gov
Sat Jan 20 19:05:47 CET 2018
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]]
>
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**********************
"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.
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