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 at 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 at 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 at debian.org > | > > -- > dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >[[alternative HTML version deleted]]
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 at 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 at 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 at 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 at debian.org >> | >> >> -- >> dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >> >[[alternative HTML version deleted]]
On 7 June 2023 at 08:37, Johan Andresen wrote: | 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)? If you look (carefully) at the r2u docs (and maybe code) you will likely understand what it does and how. In order to do exactly that for Debian it would need ingredients that are not provided. No more, no less. r2u was effectively cooked up by my in two weekends as a first test, and then extended. (Arguably after spending 20 years laying groundwork and having code infrastructure for Debian packaging and package creation from R as myself and others had done three to four prior incantations.) It also relies on existing binaries (from RSPM/PPM) which simply do not exist for Debian. All that said it is of course possible for another motivated volunteer (or group of people) to fill in (all) gaps to make it happen on Debian. I am just saying it likely won't be me as I am busy enough with the projects I have ... and more than happy enough with the outsomes such as r2u on Ubuntu. Hth, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org