[R-sig-Debian] Fwd: package interflex

[Johan Andresen]

Btw Dirk, can I help package interflex for apt? Please be welcome to refer
me to guidelines/a manual for doing so if you can imagine it happening.

Johan

Den ons. 7. jun. 2023 kl. 08.37 skrev Johan Andresen <
johan.andresen using gmail.com>:

> I can understand why it changes the game.
>
> It would be sweet if we could do something like r2u for Debian, but for now
>> we can't.  Switching between Debian and Ubuntu is not that onerous though.
>
>
> Do you mind clarifying what you do here? Do you operate Ubuntu when
> working in R? Or do you somehow operate Ubuntu to manage R packages and
> dependencies, and then switch back into Debian to carry out the R work? And
> what is required on Debian for something like this to function, and what
> are the prospects (next stable or longer)?
>
> Den ons. 7. jun. 2023 kl. 00.03 skrev Dirk Eddelbuettel <edd using debian.org>:
>
>>
>> On 6 June 2023 at 23:33, Johan Andresen wrote:
>> | Cheers - my response mixes up the order of things:
>> |
>> | The suggested apt way INSTALLED INTERFLEX nicely. Lesson learned:
>> install
>> | dependencies from apt if a package/library isn't in apt search.
>> |
>> | Yes I also tried install.packages('interflex'). RStudio console
>> complained
>> | about the same packages like this:
>> | ERROR: dependency 'xyz' is not available for package ''abc"
>> | * removing '/home/............/4.3/abc'
>> | Warning in install.packages :
>> |  installation of package 'abc' had non-zero exit status.
>>
>> That can happen when a compile-from-source fails for lack of a (for
>> compilation from source) needed -dev packages.
>>
>> Which is why _reliable_ and _complete_ provision of binaries is such a
>> game
>> changer. I have been at this for 20+ years (as it was that long ago that
>> injected the first few r-cran-* packages into Debian).
>>
>> And having r2u is a complete gamechanger.
>>
>> I can drop into a random code repository (as today for work), run my
>> `installDeps.r` helper to install everything, or in the demo for you just
>> do
>> `install.r interflex` (or, if one prefers run it as an R command via eg a
>> simple `Rscript -e 'install.packages("interflex")'`).
>>
>> And getting all of that in under 30 seconds _reliably_ is pure magic.
>>
>> | ok, AFAIU, wanting to manage R dependencies as easily as possible
>> suggests
>> | using Ubuntu with r2u instead of Debian. Be my guest to evaluate this
>> | interpretation.
>>
>> It would be sweet if we could do something like r2u for Debian, but for
>> now
>> we can't.  Switching between Debian and Ubuntu is not that onerous though.
>>
>> Cheers, Dirk
>>
>> | Johan
>> |
>> |
>> |
>> |
>> | Den tirs. 6. jun. 2023 kl. 19.58 skrev Dirk Eddelbuettel <
>> edd using debian.org>:
>> |
>> |
>> |     On 6 June 2023 at 19:37, Johan Andresen wrote:
>> |     | I'd like input on how to install interflex
>> |     | <https://github.com/xuyiqing/interflex> (note the instructions
>> on its
>> |     | github).
>> |
>> |     It says   install.packages("interflex")   -- did you try that?
>> |
>> |     | The installation failed on stable/bullseye, also when I updated
>> to the
>> |     | newer R version 4.3.0 through secure apt and the additional
>> source.list
>> |     | <https://cran.r-project.org/bin/linux/debian/#secure-apt>
>> element.
>> |     | 1. $ `sudo apt r-base-dev`
>> |     | 2. RStudio install.packages('pacman')
>> |     | 3. RStudio pacman::p_load('interflex')
>> |
>> |     Sorry but that is non-standard and not what a) the R documentation
>> suggests
>> |     or b) the package itself suggests.  You're on your own there; maybe
>> try the
>> |     RStudio / posit help forums for pacman.
>> |
>> |     My preference these days is r2u (on Ubuntu 22.04) and a quick
>> |
>> |        $ time docker run --rm -ti rocker/r2u:22.04 install.r interflex
>> |
>> |     succeeded in 22 seconds (!!) installing a total of 91 (!!)
>> different .deb
>> |     packages. I like r2u a _lot_ for this ease, speed and reliability
>> of fully
>> |     dependency-declared .deb packages (for Ubuntu 22.04 and 20.04, NOT
>> for
>> |     Debian).  See   https://eddelbuettel.github.io/r2u/   for more.
>> |
>> |     | Warning messages:
>> |     |
>> |     | > 1: In utils::install.packages(package, ...) :
>> |     | >  installation of package 'nloptr' had non-zero exit status
>> |     | > 2: In utils::install.packages(package, ...) :
>> |     | >  installation of package 'lme4' had non-zero exit status
>> |     | > 3: In utils::install.packages(package, ...) :
>> |     | >  installation of package 'pbkrtest' had non-zero exit status
>> |     | > 4: In utils::install.packages(package, ...) :
>> |     | >  installation of package 'car' had non-zero exit status
>> |     | > 5: In utils::install.packages(package, ...) :
>> |     |
>> |     |  installation of package 'AER' had non-zero exit status
>> |     | > 6: In utils::install.packages(package, ...) :
>> |     | >  installation of package 'interflex' had non-zero exit status
>> |     | > 7: In p_install(package, character.only = TRUE, ...) :
>> |     | > 8: In library(package, lib.loc = lib.loc, character.only = TRUE,
>> |     | > logical.return = TRUE, :
>> |     | >  there is no package called 'interflex'
>> |     | > 9: In pacman::p_load("interflex") : Failed to install/load:
>> |     | >  interflex
>> |
>> |     There is a saying that you try to walk before you run. _Many_ of
>> those
>> |     packages failing to install from source (== harder, you need
>> dependencies,
>> |     and also slower) are in fact available as r-cran-xyz package for
>> |     Debian. Try 'apt-cache search r-cran-xyz' for different values of
>> xyz.
>> |
>> |     Cheers, Dirk
>> |
>> |     --
>> |     dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>> |
>>
>> --
>> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>>
>

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