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
I was delighted I with how fast (faster than a tickled toddler giggles) r2u
scarfed packages I. up my Pop!_OS (Ubuntu in party attire tuned for System76).
But, despite 40 years as my own sys admin (classic fool for a client?), I
bolluxed up, ending up with an install chain that was inferior to compiling from
source, despite having to occasionally track down system dependencies.
Absolutely no criticism of the Spidey Precept, and it?s hard to make things
foolproof because we fools are so ingenious.
I may be foolish but it?s possible that I?m more knowledgeable than the large
majority of R users, so I hope that the future of this brilliant tool lies in
easing the paths. Assuming, always, that it?s just not me.
Best regards,
Richard Careaga
On Jun 6, 2023, at 3:08 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
?
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
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R-SIG-Debian mailing list
R-SIG-Debian at r-project.org
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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]]