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drd's Issues

About building with GitHub Actions

Hi, there are a few concerns about building with GitHub Actions.

  1. Since you don't specify the branch to be pushed as a trigger, rocker/drd:latest will be published even if you push to a non-default branch. I think it would be better to restrict the triggered branch. https://docs.github.com/es/actions/reference/events-that-trigger-workflows
  2. Since the PR trigger also pushes rocker/drd:latest, the contents before being merged into the default branch will be published as rocker/drd:latest. I think it is better to set it so that it will not be pushed if it is triggered by pull_request.
  3. I think that it is supposed to be automatically executed by schedule as the main trigger, but if the repository is not changed for 60 days, the workflow will be invalidated. Instead, set the base image to something like r-base: 4.1.1@sha256:7a55c99a48f8759a209c21c06cb2c44ec52d7bbe472957e31e5c29d497484db2 and use dependabot to create a PR every time the base image is updated and it will be built when the PR is merged. It may be convenient to do so because the update of the base image can be reflected immediately. https://docs.github.com/en/actions/managing-workflow-runs/disabling-and-enabling-a-workflow

drd/.github/workflows/docker.yaml

Lines 3 to 5 in 5f81f2a

on:
push:
pull_request:

drd/.github/workflows/docker.yaml

Lines 33 to 34 in 5f81f2a

push: true
tags: rocker/drd:latest

drd/Dockerfile

Line 4 in 5f81f2a

FROM r-base:latest

I think I can send these changes as a pull request if you like.

Can't start the latest build due libicuuc.so

May be this known issue, but...

docker run -t -i --rm rocker/drd:latest RDscript -e "print('hello')"
/usr/local/lib/R/bin/exec/R: error while loading shared libraries: libicuuc.so.67: cannot open shared object file: No such file or directory
$ docker image list | grep rocker/drd
rocker/drd                       latest              fb68afb72976        34 hours ago        1.57GB

The same with rocker/drp.

shared library directory between R-release and R-devel causes problems

The following sequence of commands:

docker run --name foo -ti --rm rocker/drd RD
# then in R-devel:
download.file("https://codeload.github.com/dtenenba/atestpackage/zip/master", './atestpackage.zip')
unzip("atestpackage.zip")
install.packages("atestpackage-master", repos=NULL)

Results in this:

...
** testing if installed package can be loaded
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'checkCompilerOptions' not found
Calls: ::: -> get
Execution halted
ERROR: loading failed

The reason is that .libPaths() includes /usr/lib/R/library which is a library tree for R-3.2.3 (not devel) and the old version of the compiler package is picked up during installation of this sample package which has ByteCompile: TRUE in its DESCRIPTION.

Removing /usr/lib/R/library or changing .libPaths() to exclude it works around this issue.

The issue is also present in rocker/rstudio-daily, but the docker command needs to be replaced with:

docker run -ti --rm rocker/rstudio-daily /usr/local/bin/R

warning: cannot resolve "libicui18n.so=70-64", a dependency of "ncmpcpp"

Hello,

today i check the usual system update via pacman and it output dependencies problem related to ncmpcpp.

❯ sudo pacman -Syu
:: Synchronizing package databases...
 system is up to date
 world is up to date
 galaxy is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
resolving dependencies...
warning: cannot resolve "libicui18n.so=70-64", a dependency of "ncmpcpp"
warning: cannot resolve "libicuuc.so=70-64", a dependency of "ncmpcpp"
:: The following package cannot be upgraded due to unresolvable dependencies:
      ncmpcpp

:: Do you want to skip the above package for this upgrade? [y/N] N
error: failed to prepare transaction (could not satisfy dependencies)
:: unable to satisfy dependency 'libicui18n.so=70-64' required by ncmpcpp
:: unable to satisfy dependency 'libicuuc.so=70-64' required by ncmpcpp
~ 8s
❯

ncmpcpp package is from artix community repo

❯ pacman -Ss ncmpcpp
community/ncmpcpp 0.9.2-4 [installed: 0.9.2-3]
    Almost exact clone of ncmpc with some new features

My system

❯ uname -a
Linux artix 5.15.3-zen1-1-zen #1 ZEN SMP PREEMPT Fri, 19 Nov 2021 12:15:06 +0000 x86_64 GNU/Linux
~

How do i resolve this? any help is appreciated, thanks

train function in caret package

Hi all,
I already installed caret package in R but when I want to use train function in this package I face this error:

Loading required package: class
Error in comp(expr, env = envir, options = list(suppressUndefined = TRUE)) : 
could not find function "mayCallBrowser"

I'm using version 3.2.5. Does anyone have any idea?! I need this train function for a feature selection task and I cannot understand the problem.
Thanks for any help!

Elahe

build errors on public build at hub.docker.com

From hub.docker.com:

Build failed: The command '/bin/sh -c apt-get update -qq && apt-get install -y -t unstable --no-install-recommends bash-completion bison debhelper default-jdk g++ gcc gfortran groff-base libblas-dev libbz2-dev libcairo2-dev/unstable libcurl4-openssl-dev/unstable libfreetype6-dev/unstable libharfbuzz-dev/unstable libjpeg-dev liblapack-dev liblzma-dev libncurses5-dev libpango1.0-dev/unstable libpcre3-dev libpng-dev libreadline-dev libtiff5-dev/unstable libx11-dev libxcb1-dev/unstable libxdmcp-dev/unstable libxt-dev mpack subversion tcl8.6-dev texinfo texlive-base texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-recommended tk8.6-dev x11proto-core-dev xauth xdg-utils xfonts-base xvfb zlib1g-dev && cd /tmp && svn co https://svn.r-project.org/R/trunk R-devel && cd /tmp/R-devel && R_PAPERSIZE=letter R_BATCHSAVE="--no-save --no-restore" R_BROWSER=xdg-open PAGER=/usr/bin/pager PERL=/usr/bin/perl R_UNZIPCMD=/usr/bin/unzip R_ZIPCMD=/usr/bin/zip R_PRINTCMD=/usr/bin/lpr LIBnn=lib AWK=/usr/bin/awk CFLAGS=$(R CMD config CFLAGS) CXXFLAGS=$(R CMD config CXXFLAGS) ./configure --enable-R-shlib --without-blas --without-lapack --with-readline --without-recommended-packages --program-suffix=dev && cd /tmp/R-devel && make && make install && rm -rf /tmp/R-devel /tmp/downloaded_packages/ /tmp/*.rds && echo "R_LIBS=\${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron && echo 'options("repos"="https://cran.rstudio.com")' >> /usr/local/lib/R/etc/Rprofile.site && cd /usr/local/bin && mv R Rdevel && mv Rscript Rscriptdevel && ln -s Rdevel RD && ln -s Rscriptdevel RDscript && dpkg --purge libblas-dev libbz2-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libglib2.0-dev libharfbuzz-dev libjpeg-dev liblapack-dev liblzma-dev libncurses5-dev libpango1.0-dev libpcre3-dev libpng12-dev libreadline-dev libtiff5-dev libxft-dev r-base-dev tcl8.6-dev texlive-base texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-recommended tk8.6-dev && apt-get autoremove -qy' returned a non-zero code: 1

Loved this docker image b/c it is small and useful for running in a VM. Not sure if you guys are still maintaining it elsewhere.

Switch to r2u as base

drd is meant to be a quick and easy helper to build with r-devel. Getting build-dependencies in easily is a good part of that, and r2u makes that a lot easier. So we are planning to switch this to be based on rocker/r2u 'soon'.

Can't build igraph package

Hi.

To reproduce:

docker run -ti rocker/drd:latest Rscript -e 'install.packages("igraph")'

Build process stopped with the following error:

/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status

Note: with RDscript the package installed successful.

Regards,
Artem

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