[R-pkg-devel] R-package did not pass the incoming checks automatically

[Márcio Augusto Diniz]

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

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