[R-pkg-devel] correcting errors in an existing package
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Tue Apr 4 16:04:05 CEST 2023
Your message is posted using HTML, which mangles a lot of it. For
example, the NAMESPACE file you posted has URLs mixed in with the text.
But if I can guess correctly what was in those files, it looks as though
the package being checked doesn't have those files in it. I don't know
exactly what devtools::check does, but it's probably your problem.
I'd suggest this: build the tarball, and check the tarball.
Duncan Murdoch
On 04/04/2023 9:41 a.m., Dennis Boos wrote:
> Thanks so much to all of you. If you have time, I'm getting really
> contradictory results.
>
> 1. It first seemed to have passed the check in Rstudio (I used
> device::build() in the R window and then clicked on check in the drop
> down menu under build).
>
> ==> devtools::check(document = FALSE, args = c('--as-cran'))
>
> ── R CMD check results Monte.Carlo.se <http://Monte.Carlo.se> 0.1.1
> ────Duration: 56.6s 0 errors ✔| 0 warnings ✔| 0 notes ✔R CMD check succeeded
>
> However, I then couldn't find the tar.gz where it was supposed to be. It
> was just gone.
>
>
> Here is my namespace. It says not to edit, but I had been told to add
> the importFrom. So I didn't use
> devtools::document() for fear roxygen2 would get rid of it.
>
> # Generated by roxygen2: do not edit by hand
> importFrom("stats", "cor", "sd", "var")
> export(boot.se <http://boot.se>)
> export(jack.se <http://jack.se>)
> export(mc.se.matrix)
> export(mc.se.vector)
> export(pairwise.se <http://pairwise.se>)
> export(sim.samp)
>
> 4.Here is my DESCRIPTION file
>
> Package:Monte.Carlo.se <http://Monte.Carlo.se>
> Type: Package
> Title: Monte Carlo Standard Errors
> Version: 0.1.1
> Author: Dennis Boos, Kevin Matthew, Jason Osborne
> Maintainer: Dennis Boos <boos using ncsu.edu <mailto:boos using ncsu.edu>>
> Description: Computes Monte Carlo standard errors for summaries of Monte Carlo output. Summaries and their standard errors are based on columns of Monte Carlo simulation output. Dennis D. Boos and Jason A. Osborne (2015) <doi:10.1111/insr.12087>.
> License: GPL-3
> Encoding: UTF-8
> RoxygenNote: 7.2.3
> Suggests: knitr, rmarkdown
> Imports: stats
> VignetteBuilder: knitr
>
> 5.And because of your advice: " It sounds as though you're using Roxygen2 to generate your NAMESPACE file.
> ff so, you need @imports directives in the comments
> (conventionally before the function that uses the import, but I think it
> doesn't really matter where)."
>
> So I put "@imports" in the function that had trouble
>
> #' @examples
> #' \donttest{
> #' # Using the output data matrix hold generated in vignette Example3,
> #' # calculate jackknife and bootstrap standard errors
> #' # for the differences and ratios of the CV estimates.
> #' # First get the components of hold needed.
> #'
> #' @imports
> #'
> #' trim20 <- function(x){mean(x,.2)} # 20% trimmed mean function
>
> Was that the correct thing to do?
>
> 6.And here are the failed check results. I'm clueless at this point.
>
>
> ==> devtools::check(document = FALSE, args = c('--as-cran'))
> ══Building════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════Setting env vars:• CFLAGS : -Wall -pedantic -fdiagnostics-color=always• CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always• CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always• CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always• CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always──R CMD build─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────✔checking for file 'C:\Users\boos\Dropbox\My PC (boos-home)\Desktop\dennis\R.packages\Monte.Carlo.se.March.2023/DESCRIPTION'... ─preparing 'Monte.Carlo.se <http://Monte.Carlo.se>':✔checking DESCRIPTION meta-information... ─installing the package to build vignettes✔creating vignettes(3.6s)─checking for LF line-endings in source and make files and shell scripts─checking for empty or unneeded directories─building 'Monte.Carlo.se_0.1.1.tar.gz'══Checking════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════Setting env vars:• _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE• _R_CHECK_CRAN_INCOMING_ : FALSE• _R_CHECK_FORCE_SUGGESTS_ : FALSE• _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE• NOT_CRAN : true── R CMD check ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────using log directory 'C:/Users/boos/Dropbox/My PC (boos-home)/Desktop/dennis/R.packages/Monte.Carlo.se.Rcheck'(793ms)─using R version 4.2.3 (2023-03-15 ucrt)─ using platform: x86_64-w64-mingw32 (64-bit)─ using session charset: UTF-8─using options '--no-manual --as-cran'(653ms)✔checking for file 'Monte.Carlo.se/DESCRIPTION <http://Monte.Carlo.se/DESCRIPTION>'─ checking extension type ... Package─ this is package 'Monte.Carlo.se <http://Monte.Carlo.se>' version '0.1.1'─ package encoding: UTF-8✔checking package namespace information✔checking package dependencies(3.2s)✔checking if this is a source package✔checking if there is a namespace✔checking for executable files(491ms)✔checking for hidden files and directories... ✔checking for portable file names✔checking serialization versions✔checking whether package 'Monte.Carlo.se <http://Monte.Carlo.se>' can be installed(2.9s)✔checking installed package size... ✔checking package directory... ✔checking for future file timestamps... ✔checking 'build' directory✔checking DESCRIPTION meta-information... ✔checking top-level files... ✔checking for left-over files✔checking index information... ✔checking package subdirectories... ✔checking R files for non-ASCII characters... ✔checking R files for syntax errors... ✔checking whether the package can be loaded... ✔checking whether the package can be loaded with stated dependencies... ✔checking whether the package can be unloaded cleanly... ✔checking whether the namespace can be loaded with stated dependencies... ✔checking whether the namespace can be unloaded cleanly... ✔checking loading without being on the library search path... N checking dependencies in R code... Namespace in Imports field not imported from: 'stats' All declared Imports should be used. ✔checking S3 generic/method consistency(422ms)✔checking replacement functions... ✔checking foreign function calls... N checking R code for possible problems(3s)boot.se <http://boot.se>: no visible global function definition for 'sd' boot.var: no visible global function definition for 'var' corr: no visible global function definition for 'cor' cv: no visible global function definition for 'sd' ratio.mean.sdhat.sd <http://ratio.mean.sdhat.sd>: no visible global function definition for 'sd' ratio.mean.vhat.var: no visible global function definition for 'var' ratio.sd <http://ratio.sd>: no visible global function definition for 'sd' ratio.var: no visible global function definition for 'var' varn: no visible global function definition for 'var' Undefined global functions or variables: cor sd var Consider adding importFrom("stats", "cor", "sd", "var") to your NAMESPACE file. ✔checking Rd files... ✔checking Rd metadata... ✔checking Rd line widths... ✔checking Rd cross-references... ✔checking for missing documentation entries... ✔checking for code/documentation mismatches(562ms)✔checking Rd \usage sections(661ms)✔checking Rd contents... ✔checking for unstated dependencies in examples... ✔checking installed files from 'inst/doc'W checking files in 'vignettes'... Files in the 'vignettes' directory newer than same file in 'inst/doc': 'Brief-Overview.Rmd' ✔checking examples(573ms)─checking examples with --run-donttest ... [24s] OK(24.7s)✔checking for unstated dependencies in vignettes... ✔checking package vignettes in 'inst/doc'... ✔checking re-building of vignette outputs(6.8s)✔checking for non-standard things in the check directory... ✔checking for detritus in the temp directorySee 'C:/Users/boos/Dropbox/My PC (boos-home)/Desktop/dennis/R.packages/Monte.Carlo.se.Rcheck/00check.log' for details. ── R CMD check results ─────────────────────────────────────────────────────────────────────────────────── Monte.Carlo.se <http://Monte.Carlo.se> 0.1.1 ────Duration: 51.5s ❯ checking files in 'vignettes' ... WARNINGFiles in the 'vignettes' directory newer than same file in 'inst/doc': 'Brief-Overview.Rmd' ❯ checking dependencies in R code ... NOTENamespace in Imports field not imported from: 'stats' All declared Imports should be used. ❯ checking R code for possible problems ... NOTEboot.se <http://boot.se>: no visible global function definition for 'sd' boot.var: no visible global function definition for 'var' corr: no visible global function definition for 'cor' cv: no visible global function definition for 'sd' ratio.mean.sdhat.sd <http://ratio.mean.sdhat.sd>: no visible global function definition for 'sd' ratio.mean.vhat.var: no visible global function definition for 'var' ratio.sd <http://ratio.sd>: no visible global function definition for 'sd' ratio.var: no visible global function definition for 'var' varn: no visible global function definition for 'var' Undefined global functions or variables: cor sd var Consider adding importFrom("stats", "cor", "sd", "var") to your NAMESPACE file. 0 errors ✔| 1 warning ✖| 2 notes ✖Error: R CMD check found WARNINGs Execution halted Exited with status 1.
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> On Sat, Apr 1, 2023 at 5:34 PM Duncan Murdoch <murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>> wrote:
>
> On 31/03/2023 4:51 p.m., Dennis Boos wrote:
> > Recently I got a message from CRAN that my package Monte.Carlo.se
> <http://Monte.Carlo.se> (on CRAN
> > for the last few years) does not pass current testing. There
> seemed to be
> > 2 problems:
> >
> >
> ***************************************************************************************************************
> >
> > 1. * checking LazyData ... NOTE
> > 'LazyData' is specified without a 'data' directory
> >
> > I have this line in my DESCRIPTION file:
> >
> > LazyData: true
> >
> > Should I remove that?
> >
> >
> *****************************************************************************************************************
> >
> > 2. * checking examples with --run-donttest ... [42s/42s] ERROR
> > Running examples in ‘Monte.Carlo.se-Ex.R’ failed
> > The error most likely occurred in:
> >
> >> pairwise.se <http://pairwise.se>(hold,xcol=10:12,summary.f=cv)
> > Error: object 'hold' not found
> > Execution halted
> >
> >
> ***************************************************************************************
> >
> > So, I put in the R code to generate the data matrix *hold. *But that
> > brought a host of other errors when checking in Rstudio with
> >
> >>
> devtools::check("S:/Documents/srcis/a.projects/Monte.Carlo.isr.and.package/Monte.Carlo.se.March.2023")
> >
> > I started seeing the following list about standard functions like sd.
> >
> > N checking R code for possible problems (3.4s)
> > boot.se <http://boot.se>: no visible global function definition
> for 'sd'
> > boot.var: no visible global function definition for 'var'
> > corr: no visible global function definition for 'cor'
> > cv: no visible global function definition for 'sd'
> > ratio.mean.sdhat.sd <http://ratio.mean.sdhat.sd>: no visible
> global function definition for 'sd'
> > ratio.mean.vhat.var: no visible global function definition
> for 'var'
> > ratio.sd <http://ratio.sd>: no visible global function definition
> for 'sd'
> > ratio.var: no visible global function definition for 'var'
> > varn: no visible global function definition for 'var'
> > Undefined global functions or variables:
> > cor sd var
> > Consider adding
> > importFrom("stats", "cor", "sd", "var")
> > to your NAMESPACE file.
> >
> > But you can't add those functions to NAMESPACE. Well I did but
> >
> > devtools::build()
> >
> >
> > gets rid of it. Also, I keep getting the message in the Rstudio check
> >
> > WARNING
> > 'qpdf' is needed for checks on size reduction of PDFs
> >
> >
> > but I got the latest versions of R and Rstudio and was able to get
> > qpdf to install and loaded with library(qpdf), but Rstudio still
> gives
> > that message.
> >
>
> It sounds as though you're using Roxygen2 to generate your NAMESPACE
> file. If so, you need @imports directives in the comments
> (conventionally before the function that uses the import, but I
> think it
> doesn't really matter where).
>
> Duncan Murdoch
>
>
>
> --
> Dennis Boos email: dennis_boos using ncsu.edu
> <mailto:dennis_boos using ncsu.edu>
> Department of Statistics Phone: 919-515-1918
> NC State University Fax: 919-515-1169
> Raleigh, NC 27695-8203 http://www4.stat.ncsu.edu/~boos
> <http://www4.stat.ncsu.edu/~boos>
>
> Aim for kindness, tolerance, and humility.
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