Gerber, Lauren J
2024-Jul-11 09:21 UTC
[R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest Version of R (R 4.4.1) to Docker Image
Hi Marco,
Thank you for the follow up email.
In the line below, do I replace $(lsb-release -cs) with jammy (Ubuntu 22.04) or
leave it alone:
Add-apt-repository ?deb https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/?
It?s good to know about installations for Bioconductor. I am not currently using
it, but I may need it in the future for other projects.
Br,
Lauren
--
Lauren J. Gerber
Bioinformatician
Precision Systems Medicine (Kallioniemi) Research Group
iCAN ? Digital Precision Cancer Medicine Flagship
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership for Molecular Medicine
Biomedicum Helsinki 2U, D301a1
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland
lauren.gerber at helsinki.fi
From: marcoblanchette at icloud.com <marcoblanchette at icloud.com>
Date: Wednesday, 10. July 2024 at 23.17
To: Gerber, Lauren J <lauren.gerber at helsinki.fi>, Dirk Eddelbuettel
<edd at debian.org>
Cc: Dirk Eddelbuettel <edd at debian.org>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Lauren, little oversight from my Dockerfile, if you want to follow the CRAN
steps and get the R from the cloud.r-project.org server, you want to replace
&& add-apt-repository -y "ppa:marutter/rrutter4.0"
With
&& add-apt-repository "deb
https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
The ppa repo is Michael Rutter personal repo on launchpad.net, which works just
fine but is not the CRAN sanctioned way of getting the R package.
Now, both AMD64 and ARM64 (Intel and Mac chip) binaries for Ubuntu are available
on cloud.r-project.org which will allow you to compile your Ubuntu based docker
image on either Intel or Mac chipset machines (few months ago only the Intel
built was available on cloud.r-project.org which necessitated us to use M.
Rutter PPA).
Here?s our current r-base Dockerfile which, as I said, also install a couple
commonly used libs in R packages and the step to install Bio Conductor base
package (if you don?t use BioC, delete it):
FROM ubuntu:22.04
USER root
ENV DEBIAN_FRONTEND noninteractive
# Configure Ubuntu for R install
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
software-properties-common \
gnupg2 \
wget \
build-essential \
libcurl4-openssl-dev \
libxml2-dev \
&& wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& add-apt-repository "deb
https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN apt-get update -y \
&& apt-get install -y r-base\
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/*
## Configure parallel options to use max CPUs by default and install BioC
RUN /usr/bin/R -e 'options(Ncpus = parallel::detectCores())'\
-e 'install.packages("BiocManager")' \
-e 'BiocManager::install()'
Marco
From: Gerber, Lauren J <lauren.gerber at helsinki.fi>
Date: Wednesday, July 10, 2024 at 9:43?AM
To: Dirk Eddelbuettel <edd at debian.org>
Cc: Dirk Eddelbuettel <edd at debian.org>, marcoblanchette at icloud.com
<marcoblanchette at icloud.com>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Hi Dirk,
Thank you so much for looking into this when you got home. I greatly appreciate
it.
I was actually in the midst of writing to everyone the following message:
?.
?.
?.
Hi All,
I have some good news. ? My docker image is now up-to-date with R version 4.4.1.
I first had to clear a bunch of unused data using docker system prune ?force.
Apparently, it cleared over 32.53 gigs of data, and seemed to have been
interfering with some of the package installations trying to take place.
Next, I tried using part of Marco?s dockerfile and it helped solve the issue:
RUN apt-get update \
&& apt install -y \
software-properties-common \
dirmngr \
gnupg2 \
wget \
build-essential \
libcurl4-openssl-dev \
libxml2-dev \
libasound2 \
python3 \
python3-pip \
python3.10-venv \
git-all \
lsb-release \
libxml-twig-perl \
libc6-dev \
&& wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& add-apt-repository -y "ppa:marutter/rrutter4.0"
RUN apt-get update -y \
&& apt-get install -y r-base\
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/*
Then I ran my Docker image in interactive mode to check it and it worked ?:
/# apt-cache policy r-base-core
r-base-core:
Installed: 4.4.1-1.2204.0
Candidate: 4.4.1-1.2204.0
Version table:
*** 4.4.1-1.2204.0 100
100 /var/lib/dpkg/status
This is great. Thank you all so much.
Br,
Lauren
--
Lauren J. Gerber
Bioinformatician
Precision Systems Medicine (Kallioniemi) Research Group
iCAN ? Digital Precision Cancer Medicine Flagship
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership for Molecular Medicine
Biomedicum Helsinki 2U, D301a1
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland
lauren.gerber at helsinki.fi
From: Dirk Eddelbuettel <edd at debian.org>
Date: Wednesday, 10. July 2024 at 19.09
To: Gerber, Lauren J <lauren.gerber at helsinki.fi>
Cc: Dirk Eddelbuettel <edd at debian.org>, marcoblanchette at icloud.com
<marcoblanchette at icloud.com>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Lauren,
I am now back home where looking into these things is a little easier. From
your first email to me, I started off with the selenium container you
mentioned as your starting point.
And that basically is your issue. It is a 'high-level' container, and it
sets
a user. (Essentially) all other Dockerfiles you have seen and been pointed at
are 'lower-level' and operate as root -- so you need to inject
'sudo' calls.
Otherwise it really is 'just' getting one key and adding one repo, but
it
helps to have had the same user <-> root issues before ...
So below is a working 'minimal' Dockerfile that gets me R 4.4.1
(validated
via 'docker exec -ti container_id_here bash' once built). Hope it helps.
Best, Dirk
FROM selenium/standalone-firefox:latest
## Following the standard rocker/r2u:jammy Dockerfile, and adapted slightly
RUN sudo apt update \
##
## We would normally do
## apt install --yes --no-install-recommends ca-certificates locales wget
## but these are already installed
##
## So we skip to the next step of adding the key and repo
&& wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& echo "deb [arch=amd64
signed-by=/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc]
https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" \
| sudo tee -a /etc/apt/sources.list.d/cran.list \
##
## Update again and install R
&& sudo apt update -qqq \
&& sudo apt install --yes --no-install-recommends r-base-core
--
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
[[alternative HTML version deleted]]
m@rcobi@@chette m@iii@g oii icioud@com
2024-Jul-11 17:03 UTC
[R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest Version of R (R 4.4.1) to Docker Image
Yes, keep the $(lsb-release -cs) there. This allows you to change the version of
the OS without having to change anything else (for instance we are migrating all
of our docker to 24.04 LTS right now, so we only have to modify the FROM entry
and all of our Dockerfile will still work).
From: Gerber, Lauren J <lauren.gerber at helsinki.fi>
Date: Thursday, July 11, 2024 at 2:21?AM
To: marcoblanchette at icloud.com <marcoblanchette at icloud.com>, Dirk
Eddelbuettel <edd at debian.org>
Cc: Dirk Eddelbuettel <edd at debian.org>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Hi Marco,
Thank you for the follow up email.
In the line below, do I replace $(lsb-release -cs) with jammy (Ubuntu 22.04) or
leave it alone:
Add-apt-repository ?deb https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/?
It?s good to know about installations for Bioconductor. I am not currently using
it, but I may need it in the future for other projects.
Br,
Lauren
--
Lauren J. Gerber
Bioinformatician
Precision Systems Medicine (Kallioniemi) Research Group
iCAN ? Digital Precision Cancer Medicine Flagship
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership for Molecular Medicine
Biomedicum Helsinki 2U, D301a1
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland
lauren.gerber at helsinki.fi
From: marcoblanchette at icloud.com <marcoblanchette at icloud.com>
Date: Wednesday, 10. July 2024 at 23.17
To: Gerber, Lauren J <lauren.gerber at helsinki.fi>, Dirk Eddelbuettel
<edd at debian.org>
Cc: Dirk Eddelbuettel <edd at debian.org>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Lauren, little oversight from my Dockerfile, if you want to follow the CRAN
steps and get the R from the cloud.r-project.org server, you want to replace
&& add-apt-repository -y "ppa:marutter/rrutter4.0"
With
&& add-apt-repository "deb
https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
The ppa repo is Michael Rutter personal repo on launchpad.net, which works just
fine but is not the CRAN sanctioned way of getting the R package.
Now, both AMD64 and ARM64 (Intel and Mac chip) binaries for Ubuntu are available
on cloud.r-project.org which will allow you to compile your Ubuntu based docker
image on either Intel or Mac chipset machines (few months ago only the Intel
built was available on cloud.r-project.org which necessitated us to use M.
Rutter PPA).
Here?s our current r-base Dockerfile which, as I said, also install a couple
commonly used libs in R packages and the step to install Bio Conductor base
package (if you don?t use BioC, delete it):
FROM ubuntu:22.04
USER root
ENV DEBIAN_FRONTEND noninteractive
# Configure Ubuntu for R install
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
software-properties-common \
gnupg2 \
wget \
build-essential \
libcurl4-openssl-dev \
libxml2-dev \
&& wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& add-apt-repository "deb
https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN apt-get update -y \
&& apt-get install -y r-base\
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/*
## Configure parallel options to use max CPUs by default and install BioC
RUN /usr/bin/R -e 'options(Ncpus = parallel::detectCores())'\
-e 'install.packages("BiocManager")' \
-e 'BiocManager::install()'
Marco
From: Gerber, Lauren J <lauren.gerber at helsinki.fi>
Date: Wednesday, July 10, 2024 at 9:43?AM
To: Dirk Eddelbuettel <edd at debian.org>
Cc: Dirk Eddelbuettel <edd at debian.org>, marcoblanchette at icloud.com
<marcoblanchette at icloud.com>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Hi Dirk,
Thank you so much for looking into this when you got home. I greatly appreciate
it.
I was actually in the midst of writing to everyone the following message:
?.
?.
?.
Hi All,
I have some good news. ? My docker image is now up-to-date with R version 4.4.1.
I first had to clear a bunch of unused data using docker system prune ?force.
Apparently, it cleared over 32.53 gigs of data, and seemed to have been
interfering with some of the package installations trying to take place.
Next, I tried using part of Marco?s dockerfile and it helped solve the issue:
RUN apt-get update \
&& apt install -y \
software-properties-common \
dirmngr \
gnupg2 \
wget \
build-essential \
libcurl4-openssl-dev \
libxml2-dev \
libasound2 \
python3 \
python3-pip \
python3.10-venv \
git-all \
lsb-release \
libxml-twig-perl \
libc6-dev \
&& wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& add-apt-repository -y "ppa:marutter/rrutter4.0"
RUN apt-get update -y \
&& apt-get install -y r-base\
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/*
Then I ran my Docker image in interactive mode to check it and it worked ?:
/# apt-cache policy r-base-core
r-base-core:
Installed: 4.4.1-1.2204.0
Candidate: 4.4.1-1.2204.0
Version table:
*** 4.4.1-1.2204.0 100
100 /var/lib/dpkg/status
This is great. Thank you all so much.
Br,
Lauren
--
Lauren J. Gerber
Bioinformatician
Precision Systems Medicine (Kallioniemi) Research Group
iCAN ? Digital Precision Cancer Medicine Flagship
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership for Molecular Medicine
Biomedicum Helsinki 2U, D301a1
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland
lauren.gerber at helsinki.fi
From: Dirk Eddelbuettel <edd at debian.org>
Date: Wednesday, 10. July 2024 at 19.09
To: Gerber, Lauren J <lauren.gerber at helsinki.fi>
Cc: Dirk Eddelbuettel <edd at debian.org>, marcoblanchette at icloud.com
<marcoblanchette at icloud.com>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Lauren,
I am now back home where looking into these things is a little easier. From
your first email to me, I started off with the selenium container you
mentioned as your starting point.
And that basically is your issue. It is a 'high-level' container, and it
sets
a user. (Essentially) all other Dockerfiles you have seen and been pointed at
are 'lower-level' and operate as root -- so you need to inject
'sudo' calls.
Otherwise it really is 'just' getting one key and adding one repo, but
it
helps to have had the same user <-> root issues before ...
So below is a working 'minimal' Dockerfile that gets me R 4.4.1
(validated
via 'docker exec -ti container_id_here bash' once built). Hope it helps.
Best, Dirk
FROM selenium/standalone-firefox:latest
## Following the standard rocker/r2u:jammy Dockerfile, and adapted slightly
RUN sudo apt update \
##
## We would normally do
## apt install --yes --no-install-recommends ca-certificates locales wget
## but these are already installed
##
## So we skip to the next step of adding the key and repo
&& wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& echo "deb [arch=amd64
signed-by=/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc]
https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" \
| sudo tee -a /etc/apt/sources.list.d/cran.list \
##
## Update again and install R
&& sudo apt update -qqq \
&& sudo apt install --yes --no-install-recommends r-base-core
--
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
[[alternative HTML version deleted]]
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