[R-pkg-devel] Compiler warning using C versions of base R integrate function

[Devin Incerti]

Hi,

I'm attempting to submit a very minor update to my package where I replaced
a deprecated C++ function with an alternative. However, I'm receiving an
unrelated warning "*array subscript -1 is outside array bounds of ‘double
[52]’ [-Warray-bounds] *" on Debian during the CRAN pre-tests. I do not
receive this warning on my local OS X, Ubuntu 16.04 (on Travis-CI), with
Win-builder, or with R-hub builder. I also did not receive this warning on
previous submissions to CRAN, but it does now show up on the most recent CRAN
checks

.

The warning is related to the header file integrate.h
,
which is just integrate.c

from
R source with function pointers replaced by C++ functors. These integration
functions are needed so that the package can integrate at the C++ level.

I don't know how to avoid this warning. Is it perhaps related to the
particular version of GCC used during the CRAN checks. Any thoughts or
suggestions would be much appreciated.

Thank you!

Devin

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Re: [R-pkg-devel] compression of vignettes

[Dirk Eddelbuettel]

On 21 November 2019 at 16:43, Joris Meys wrote:
| The workflow as described in the manual :
| 
https://cran.r-project.org/doc/manuals/R-exts.html#Checking-and-building-packages
| 
| is as follows :
| 
| R CMD build pkg --compact-vignettes
| R CMD check pkg_x.y.z.tar.gz --as-cran
| 
| In a basic Travis script this can be used as:
| 
| script:
|   - R CMD build . --compact-vignettes=gs+qpdf
|   - R CMD check *tar.gz --as-cran
| 
| You find more information here : 
https://towardsdatascience.com/travis-ci-for-r-advanced-guide-719cb2d9e0e5

You can also call the base R helper functions directly.

I like having simple command-line wrapper, so I added one to `littler` which
I can call as `compactpdf.r`.  All it does (besides argument checking) is
loop over either the given pdf files (or those found in the current
directory) to then call

tools::compactPDF(f, gs_quality="ebook")

for each of them. That way you can simply compare 'before' and 'after'.

Similarly, I made compacting an option to the rendering script `render.r` I
often call directly from my editor when working on markdown files.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] compression of vignettes

[Joris Meys]

Dear Mark,

You rely on external packages like rcmdcheck and devtools, so if you insist on 
using those, you should contact the package authors.

The workflow as described in the manual :
https://cran.r-project.org/doc/manuals/R-exts.html#Checking-and-building-packages

is as follows :

R CMD build pkg --compact-vignettes
R CMD check pkg_x.y.z.tar.gz --as-cran

In a basic Travis script this can be used as:

script:
  - R CMD build . --compact-vignettes=gs+qpdf
  - R CMD check *tar.gz --as-cran

You find more information here : 
https://towardsdatascience.com/travis-ci-for-r-advanced-guide-719cb2d9e0e5

Cheers
Joris


--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: R-package-devel  on behalf of R. 
Mark Sharp 
Sent: Thursday, November 21, 2019 5:08 PM
To: R Package Devel
Subject: [R-pkg-devel] compression of vignettes

I have been unsuccessful with all of the following attempts to have compression 
of dynamically generated vignettes during the build on travis-ci and within 
RStudio. Help is appreciated.

I have tried the following travis-ci YAML to have vignettes compressed.
script:
  - R -e 'r <- rcmdcheck::rcmdcheck(".", args = c('--no-manual'), build_args = 
c('--compact-vignettes=both'); devtools::test(); quit(save = "no", status = if 
(length(c(r$errors, r$warnings)) > 0) { 1 } else { 0 }, runLast = FALSE)'

script:
  - R -e 'r <- rcmdcheck::rcmdcheck(".", args = c('--no-manual', 
'--compact-vignettes=gs+qpdf'); devtools::test(); quit(save = "no", status = if 
(length(c(r$errors, r$warnings)) > 0) { 1 } else { 0 }, runLast = FALSE)'

script:
  - R -e 'r <- rcmdcheck::rcmdcheck(".", args = c('--no-manual', 
'--compact-vignettes="gs+qpdf"'); devtools::test(); quit(save = "no", status = 
if (length(c(r$errors, r$warnings)) > 0) { 1 } else { 0 }, runLast = FALSE)'


I have tried the following build arguments in RStudio
--as-cran --compact-vignettes=gs+qpdf
--as-cran --compact-vignettes=both


R. Mark Sharp, Ph.D.
Data Scientist and Biomedical Statistical Consultant
7526 Meadow Green St.
San Antonio, TX 78251
mobile: 210-218-2868
rmsh...@me.com

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[R-pkg-devel] compression of vignettes

[R. Mark Sharp]

I have been unsuccessful with all of the following attempts to have compression 
of dynamically generated vignettes during the build on travis-ci and within 
RStudio. Help is appreciated.

I have tried the following travis-ci YAML to have vignettes compressed.
script:
  - R -e 'r <- rcmdcheck::rcmdcheck(".", args = c('--no-manual'), build_args = 
c('--compact-vignettes=both'); devtools::test(); quit(save = "no", status = if 
(length(c(r$errors, r$warnings)) > 0) { 1 } else { 0 }, runLast = FALSE)'

script:
  - R -e 'r <- rcmdcheck::rcmdcheck(".", args = c('--no-manual', 
'--compact-vignettes=gs+qpdf'); devtools::test(); quit(save = "no", status = if 
(length(c(r$errors, r$warnings)) > 0) { 1 } else { 0 }, runLast = FALSE)'

script:
  - R -e 'r <- rcmdcheck::rcmdcheck(".", args = c('--no-manual', 
'--compact-vignettes="gs+qpdf"'); devtools::test(); quit(save = "no", status = 
if (length(c(r$errors, r$warnings)) > 0) { 1 } else { 0 }, runLast = FALSE)'


I have tried the following build arguments in RStudio
--as-cran --compact-vignettes=gs+qpdf
--as-cran --compact-vignettes=both


R. Mark Sharp, Ph.D.
Data Scientist and Biomedical Statistical Consultant
7526 Meadow Green St.
San Antonio, TX 78251
mobile: 210-218-2868
rmsh...@me.com

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