[R-pkg-devel] Two (newbie/luser) questions about adding CI to github hosted package

Tue, Mar 16, 2021 6:22 AM

Hi everybody,

I would like to take a minute to address the language used in the initial
e-mail, notably the "newbie/luser" terminology.
It was given in both the subject (" Two (newbie/luser) questions") as well
as the body ("...  robust R package that might be useful (mainly to R
newbies/lusers of even lower R/programming skills than mine).").

Personally I find the term "luser" (as of a "loser user") very
condescending, whether it is about yourself (because you are not an
experienced programmer) or others (because you perceive them as
inexperienced programmers).
To put it short, using such a condescending term inhibits yourself and,
especially, others. Its use is simply unwarranted. Using the term about the
users of your package, regardless of their experience, is derogatory.

If you are writing to this mailing list with issues developing an
R-package, you are neither a newbie nor a loser, and we collectively will
do our best to help you. So no need in derograting yourself.

Kind regards,
Stefan

Den tir. 16. mar. 2021 kl. 14.05 skrev Chris Evans <chrishold at psyctc.org>:

Hugely appreciated Duncan.

----- Original Message -----

From: "Duncan Murdoch" <murdoch.duncan at gmail.com>
To: "Chris Evans" <chrishold at psyctc.org>, "r-package-devel" <

r-package-devel at r-project.org>

Sent: Tuesday, 16 March, 2021 10:48:50
Subject: Re: [R-pkg-devel] Two (newbie/luser) questions about adding CI

to github hosted package

On 16/03/2021 5:58 a.m., Chris Evans wrote:

I would be very grateful of help as I seem to be making very heavy

weather of

all the intricacies of creating a
robust R package that might be useful (mainly to R newbies/lusers of

even lower

R/programming skills than mine).

I am making a lot of progress and am awed by the work so many have put

in to

make things possible: huge gratitude
to too many to name. However, I seem to be hitting a wall on adding CI

to my

package.

1) I am sure that linting my package will help me but there are some

defaults in

lintr/superlinter that I am want
to take a personal stand and not use: allowing myself not always to use

perfect

camelCase because I think it will
confuse my end users and the line length limit which at the default of

80 seems

to me, on a modern set up, to make
my code far less readable than if I allow some long lines. My problem

is that I

am failing to work out how to override
the defaults. I thought that putting in /TEMPLATES/.lintr in my package
directory and having it contain:

# linters: with_defaults(object_usage_linter = NULL)
linters: with_defaults(
   line_length_linter(120),
   cyclocomp_linter(25),
   object_name_linter = NULL
   )
would override the defaults (I'm working on the cyclocomp complaint!)

Can

anyone, perhaps looking at my
https://github.com/cpsyctc/CECPfuns/ package, tell me what I'm doing

wrong and

how to get it right?!


I use lintr, and put my .lintr file in the main directory of the package.

OK.  I have removed the TEMPLATES directory and moved .lintr to the
package root.

I think I am better keeping lintr local and having moved .lintr using

lintr::lint_package()

locally is working fine, flagging up cosmetics I can see are all
improvements so I
can sort those out without wasting github power.  Which takes to the next
stage ...

2) I work on a machine running Ubuntu 20.04 in Rstudio and everything

checks and

tests fine there but I wanted
to use the github actions to check the package out on Windows and Mac

and,

rather more by luck I think than really
understanding how I got there, I seem to have achieved that.  Rather

bizarrely,

the code (it's only R source)
passes on Windows and Mac but fails in the Ubuntu test systems with

errors like:

?? R CMD build

?????????????????????????????????????????????????????????????????

* checking for file ?.../DESCRIPTION? ... OK
* preparing ?CECPfuns?:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
       -----------------------------------
* installing *source* package ?CECPfuns? ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object
   '/home/runner/work/_temp/Library/stringi/libs/stringi.so':
   libicui18n.so.55: cannot open shared object file: No such file or

directory

Calls: <Anonymous> ... namespaceImport -> loadNamespace ->

library.dynam ->

dyn.load
Execution halted
ERROR: lazy loading failed for package ?CECPfuns?

I _think_ these are just changes in the stirngi package that seem to

failing on

the test machine
and OK on my machine. That made me think that I can see a lot of logic

in my

checking things on
the various default versions of R in Ubuntu 16.04, Windows and MacOS

but perhaps

it is unnecessary
and wasting resources to check the release version of R on Ubuntu 20.04

as it

seems safe enough to
assume that the package built on my local machine in the release

version of R

and on Ubuntu 20.04
that fails like this will only be transient (or that successes on my

machine

will only be ... but
at least I'll see them and not waste github resources!)

The catch is that I am baffled by how to configure github actions to

change the

lint defaults and
to change the selection of releases and platforms.  I think that may

because I

may have created
a mess in my github actions workflows.

Would anyone be willing to help or even to look at it and point me to

the

explanations I am failing
to find?!

You have 5 workflows, and their current content doesn't appear to match
the results on your actions page.  Pick one, run it, and I'll see if I
can spot the reason for a failure.

That is so appreciated Duncan. One stupid question: is there a way to run a
workflow other than by making an upload/push (or a pull request)?

I think I have discovered that the workflows are controlled by the yaml
files
in .github/workflows so I have deleted all except R-CMD-check.yaml and I
think
that when I now commit and push this that should delete the other
workflows
on github and trigger this one to run.  If you could look at that one then
that would be hugely appreciated.  I see it says:

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: windows-latest, r: '3.6'}
          - {os: ubuntu-18.04,   r: 'devel', rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest",
http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu
x86_64 linux-gnu) on GitHub Actions" }
          - {os: ubuntu-18.04,   r: 'release', rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
          - {os: ubuntu-18.04,   r: '3.5',     rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
          - {os: ubuntu-18.04,   r: '3.4',     rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
          - {os: ubuntu-18.04,   r: '3.3',     rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}


Some questions as I, I think, make some progress:

1) Why is windows-latest pointing at 3.6?  I am on 4.0.4 locally for
windows.  I assume this is because I have copied or pulled in
a template that is out of date.  Can I just replace that '3.6' with
'release'

2) My guts say that at this point it is sensible for me to test against
devel, release and oldrel but that after the next
release I could stop testing against oldrel?  Is that sensible?

3) I see tests against 3.3, 3.4 and 3.5 there for ubuntu 18.04 and no
20.04.  Am I correct that I could replace the above
with this:

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-18.04,   r: 'devel', rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest",
http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu
x86_64 linux-gnu) on GitHub Actions" }
          - {os: ubuntu-18.04,   r: 'release', rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "
https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
          - {os: ubuntu-20.04,   r: 'devel',     rspm: "
https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-20.04,   r: 'release',     rspm: "
https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-20.04,   r: 'oldrel',     rspm: "
https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}

[I have changed the windows '3.6' to 'release' and the last three ubuntu
calls to 20.04 and the R versions to 'devel', 'release'
 and 'oldrel' and the repositories to point at xenial not bionic.  I have
only done this here in the Email, not on disc!]

It would be nice to check all that occasionally but I am sure that at the
frequency I'm pushing up new functions and tweaks,
so my colleagues can check things, I am putting far too much work on
github with all those.  Could I just check windows
and macOS release and devel by commenting out lines there.  Or is it
better to have different yaml files and just to put
the one you want in .github/workflows for each particular push?  No great
difference?

OK.  I have pushed these changes with the commit comment "More work to get
continuous integration testing ..." and the
actions seem to be running and I seem to have succeeded in pruning things
down to that one action.

Wonderful if you can find the time to have a look at these questions and
the run ... now I'm off to the dentist.
Hm: dentist ... bad day with R ... dentist ... OK, I'll take bad day with
R any day!

Thanks (and to all),

Chris

Duncan Murdoch

--
Small contribution in our coronavirus rigours:

https://www.coresystemtrust.org.uk/home/free-options-to-replace-paper-core-forms-during-the-coronavirus-pandemic/

Chris Evans <chris at psyctc.org> Visiting Professor, University of
Sheffield <chris.evans at sheffield.ac.uk>
I do some consultation work for the University of Roehampton <
chris.evans at roehampton.ac.uk> and other places
but <chris at psyctc.org> remains my main Email address.  I have a work web
site at:
   https://www.psyctc.org/psyctc/
and a site I manage for CORE and CORE system trust at:
   http://www.coresystemtrust.org.uk/
I have "semigrated" to France, see:
   https://www.psyctc.org/pelerinage2016/semigrating-to-france/

https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/

If you want an Emeeting, I am trying to keep them to Thursdays and my
diary is at:
   https://www.psyctc.org/pelerinage2016/ceworkdiary/
Beware: French time, generally an hour ahead of UK.

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[R-pkg-devel] Two (newbie/luser) questions about adding CI to github hosted package

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