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

Hi M?rcio:

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, M?rcio 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,

--
M?rcio Diniz

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Jr.