search for: marcoblanchette

...is basically following the steps from https://cloud.r-project.org/bin/linux/ubuntu/ as Lauren was trying to do but start by installing the pre-requisites needed to deploy the r-base package on a Ubuntu 22.04 Docker image (which is NOT a base 22.04 but a minimally striped version of 22.04). From: marcoblanchette at icloud.com <marcoblanchette at icloud.com> Date: Monday, July 8, 2024 at 12:21?PM To: Dirk Eddelbuettel <edd at debian.org> Cc: Gerber, Lauren J <lauren.gerber at helsinki.fi>, r-sig-debian at r-project.org <r-sig-debian at r-project.org> Subject: Re: [R-sig-Debian] Issue...

Hmm? It?s picking up the pre-made binary from ppa:marutter/rrutter4.0 using apt-get install. Isn?t it what Lauren?s trying to do? From: Dirk Eddelbuettel <edd at debian.org> Date: Monday, July 8, 2024 at 11:57?AM To: marcoblanchette at icloud.com <marcoblanchette at icloud.com> Cc: Gerber, Lauren J <lauren.gerber at helsinki.fi>, 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 O...

Oh, again, sorry for the spam but the problem Lauren is seeing is when she is trying to sign the key. Installing gnugpg usually takes care of that problem. From: marcoblanchette at icloud.com <marcoblanchette at icloud.com> Date: Monday, July 8, 2024 at 12:26?PM To: Dirk Eddelbuettel <edd at debian.org> Cc: Gerber, Lauren J <lauren.gerber at helsinki.fi>, r-sig-debian at r-project.org <r-sig-debian at r-project.org> Subject: Re: [R-sig-Debian] Issue...

...out 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 Versio...

...) 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-pro...

...#39;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 g...

On 8 July 2024 at 16:37, marcoblanchette at icloud.com wrote: | Lauren, here?s my Dockerfile I use to build r-base from the repos, it builds on both Arm64 (Mac with Apple M2 chip) and Amd64 (AWS m5.4xlarge instance running Ubuntu 24.04). I rebuilt the docker image this morning and it builds fine with R 4.4.1 That's very kind but reca...

On 8 July 2024 at 19:32, marcoblanchette at icloud.com wrote: | Oh, again, sorry for the spam but the problem Lauren is seeing is when she is | trying to sign the key. Installing gnugpg usually takes care of that problem. I am not sure about that. For jammy, my current (and used) rocker/r2u:jammy Dockerfile is https://github.com/roc...

...to add a C/C++ compiler to the base (hence build-essential) for downstream package installation as well as frequently used libs in R packages (hence libcurl4-openssl-dev and libxml2-dev). Just my 2 cents. From: Dirk Eddelbuettel <edd at debian.org> Date: Monday, July 8, 2024 at 12:50?PM To: marcoblanchette at icloud.com <marcoblanchette at icloud.com> Cc: Dirk Eddelbuettel <edd at debian.org>, Gerber, Lauren J <lauren.gerber at helsinki.fi>, 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 Lat...

...1 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...

...ecular 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: Tuesday, 9. July 2024 at 9.13 To: marcoblanchette at icloud.com <marcoblanchette at icloud.com> Cc: Dirk Eddelbuettel <edd at debian.org>, Gerber, Lauren J <lauren.gerber at helsinki.fi>, 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 Lat...

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

Lauren, here?s my Dockerfile I use to build r-base from the repos, it builds on both Arm64 (Mac with Apple M2 chip) and Amd64 (AWS m5.4xlarge instance running Ubuntu 24.04). I rebuilt the docker image this morning and it builds fine with R 4.4.1 The last RUN is for installing a bit of custom configuration as well as the base of Bio Conductor. Hope this helps (I also have a Dockerfile for