Bioconductor/bioconductor_docker issues and pull requests

#122 - Add anvil-rstudio container based on Terra Jupyter

Pull Request - State: closed - Opened by almahmoud 3 months ago

#121 - Galaxy extension

Pull Request - State: closed - Opened by almahmoud 3 months ago

#120 - Formalize "extensions" concept

Issue - State: open - Opened by almahmoud 4 months ago

#119 - Push of arm64 docker image to dockerhub failing, resulting in missing recent arm64 builds of bioconductor_docker

Issue - State: closed - Opened by seandavi 4 months ago - 6 comments

#118 - Add nginx need by usegalaxy

Pull Request - State: closed - Opened by afgane 4 months ago - 5 comments

#117 - Add default packages fro the Galaxy extension

Pull Request - State: closed - Opened by afgane 5 months ago

#116 - Add arch to container name

Pull Request - State: open - Opened by almahmoud 5 months ago

#115 - apt install python packages

Pull Request - State: closed - Opened by almahmoud 5 months ago

#114 - Allow format-security errors for devel

Pull Request - State: closed - Opened by jwokaty 8 months ago

#113 - Singularity image for bioconductor 3.20

Issue - State: open - Opened by reshu23 8 months ago - 11 comments

#112 - EBImage failing in 3.20

Issue - State: open - Opened by almahmoud 9 months ago - 4 comments

#111 - [Auto] Bumping RELEASE_3_20 branch to R 4.4.2

Pull Request - State: closed - Opened by almahmoud 9 months ago
Labels: auto-bump

#110 - [Auto] Bumping RELEASE_3_19 branch to R 4.4.2

Pull Request - State: closed - Opened by almahmoud 9 months ago
Labels: auto-bump

#109 - Move CUDA image to noble

Pull Request - State: closed - Opened by almahmoud 9 months ago

#108 - [Auto] Bumping RELEASE_3_19 branch to R 4.4.2

Pull Request - State: closed - Opened by almahmoud 9 months ago
Labels: auto-bump

#107 - Update devel all to rocker and 4.4.1

Pull Request - State: closed - Opened by almahmoud about 1 year ago

#106 - Bumping RELEASE_3_19 branch to R 4.4.1 and changing all to rocker base

Pull Request - State: closed - Opened by almahmoud about 1 year ago
Labels: auto-bump

#105 - [Auto] Bumping RELEASE_3_19 branch to R 4.4.0

Pull Request - State: closed - Opened by almahmoud about 1 year ago
Labels: auto-bump

#104 - [Auto] Bumping RELEASE_3_19 branch to R 4.4.0

Pull Request - State: closed - Opened by almahmoud about 1 year ago
Labels: auto-bump

#103 - [Auto] Bumping RELEASE_3_19 branch to R 4.4.0

Pull Request - State: closed - Opened by almahmoud about 1 year ago
Labels: auto-bump

#102 - Auto-update "latest" tag to latest released tag for each image base

Pull Request - State: closed - Opened by almahmoud about 1 year ago

#101 - Start 3.20 devel build

Pull Request - State: closed - Opened by almahmoud about 1 year ago

#100 - Add check for specific version

Pull Request - State: closed - Opened by almahmoud about 1 year ago

#99 - Unable to start container process: exec: "/init": stat /init: no such file or directory: unknown

Issue - State: closed - Opened by smartinez-yatiribio over 1 year ago - 4 comments

#98 - [Auto] Bumping RELEASE_3_18 branch to R 4.4.0

Pull Request - State: closed - Opened by almahmoud over 1 year ago
Labels: auto-bump

#97 - Lighter bioconductor container in the future?

Issue - State: closed - Opened by JihedC over 1 year ago - 2 comments

#96 - Fixes the bug for automatic R version switch from devel to patched

Pull Request - State: closed - Opened by almahmoud over 1 year ago

#95 - [Auto] Bumping RELEASE_3_18 branch to R 4.3.3

Pull Request - State: closed - Opened by almahmoud over 1 year ago
Labels: auto-bump

#94 - Auto bump R version and create PR

Pull Request - State: closed - Opened by almahmoud over 1 year ago

#93 - Turn compilation formatting error into warning

Pull Request - State: closed - Opened by almahmoud over 1 year ago - 2 comments

#92 - Cannot install packages with BiocManager::install during docker build

Issue - State: closed - Opened by usu-imeg over 1 year ago - 3 comments

#91 - Update bioconductor_docker images for consistency w/ upstream Rocker images

Issue - State: open - Opened by nathanweeks over 1 year ago - 1 comment

#90 - update README

Issue - State: open - Opened by LiNk-NY over 1 year ago

#89 - Automatic R devel version fix

Pull Request - State: closed - Opened by almahmoud over 1 year ago

#88 - Update install_bioc_sysdeps.sh

Pull Request - State: closed - Opened by LiNk-NY almost 2 years ago

#87 - Prepare for devel becoming 3.19

Pull Request - State: closed - Opened by almahmoud almost 2 years ago

#86 - Move 3.17 to R 4.3.1

Pull Request - State: closed - Opened by almahmoud almost 2 years ago

#85 - fix: update curl to secured http link

Pull Request - State: closed - Opened by js2264 almost 2 years ago - 1 comment

#84 - Install preprocessCore manually to disable threading

Pull Request - State: closed - Opened by almahmoud almost 2 years ago

#83 - Add shiny flavor to devel

Pull Request - State: closed - Opened by almahmoud about 2 years ago

#82 - 'binary' package shared objects are not compatible with the docker container

Issue - State: closed - Opened by mtmorgan about 2 years ago - 4 comments

#81 - container defaults to installing packages from source, rather than binary

Issue - State: closed - Opened by mtmorgan about 2 years ago - 2 comments

#80 - README continues to mention AnVIL::

Issue - State: closed - Opened by vjcitn about 2 years ago - 2 comments

#79 - Fix TARGET* ARGS & remove binaries for arm64

Pull Request - State: closed - Opened by almahmoud about 2 years ago

#78 - RELEASE_3_17: *.so shared objects from container_packages in /usr/local/lib/R/site-library packages not loading

Issue - State: closed - Opened by lima1 over 2 years ago - 9 comments

#77 - New rocker builds

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#76 - Add R version tags

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#75 - Change free space action and add schedule defaults

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#74 - R 4.2.2 to 4.2.3

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#73 - Update weekly builder GHA

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#72 - Incorrect references to `rockerdev` Rocker organization in release process document

Issue - State: closed - Opened by noamross over 2 years ago - 1 comment

#71 - Add Dockerhub target to GHA build

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#70 - Strange issue running image fedora 36 vs 37 - rocker/rstudio::devel works, as does home build

Issue - State: open - Opened by r-cheologist over 2 years ago - 9 comments

#69 - Add more bases

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#68 - Add libs for Rsymphony

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#67 - Issue #64: Build Linux ARM64 image in addition to x86_64 (for GHCR)

Pull Request - State: closed - Opened by martin-g over 2 years ago - 4 comments

#66 - libpath to put the custom lib folder in the front

Issue - State: closed - Opened by crazyhottommy over 2 years ago - 11 comments

#65 - Unable to install additional Bioconductor packages.

Issue - State: closed - Opened by usu-imeg over 2 years ago - 2 comments

#64 - Make an ARM image available

Issue - State: closed - Opened by Adafede over 2 years ago - 10 comments

#63 - Push PR #62 forward to devel

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#62 - Add BIOCONDUCTOR_USE_CONTAINER_REPOSITORY=FALSE before installations

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#61 - Errors with release 3.16

Issue - State: closed - Opened by fortune9 over 2 years ago - 3 comments

#60 - sed IS_BIOC_BUILD_MACHINE to false

Pull Request - State: closed - Opened by almahmoud over 2 years ago - 3 comments

#59 - Issue with the stringi package in RELEASE_3_16

Issue - State: closed - Opened by grimbough over 2 years ago - 20 comments

#58 - Update 3.16 to 4.2.2

Pull Request - State: closed - Opened by almahmoud over 2 years ago - 1 comment

#57 - Add GHCR to 3_16

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#56 - Update devel for 3.17

Pull Request - State: closed - Opened by almahmoud over 2 years ago

#55 - Add base image and tag to gha

Pull Request - State: closed - Opened by almahmoud over 2 years ago - 2 comments

#54 - leidenalg for Bioc pkg scBubbletree

Issue - State: open - Opened by jwokaty almost 3 years ago
Labels: enhancement

#53 - Add libarchive-dev apt package

Pull Request - State: closed - Opened by zeehio almost 3 years ago

#52 - MCR doesn't host bioconductor images anymore

Pull Request - State: open - Opened by nturaga almost 3 years ago - 1 comment
Labels: documentation

#51 - Could not connect to the R session on RStudio Server

Issue - State: closed - Opened by rgaiacs almost 3 years ago - 1 comment

#50 - Update R to 4.2.1 as per build system

Pull Request - State: closed - Opened by nturaga almost 3 years ago

#49 - Major update: Add gpu support to Bioconductor containers [WIP]

Pull Request - State: open - Opened by nturaga about 3 years ago
Labels: enhancement

#48 - Update to R4.2.1

Issue - State: closed - Opened by jwokaty about 3 years ago - 1 comment

#47 - Add python3.8-venv in the docker image

Pull Request - State: closed - Opened by nturaga about 3 years ago

#46 - Add python3.8-venv to the bioconductor_docker container?

Issue - State: closed - Opened by mtmorgan about 3 years ago
Labels: enhancement

#45 - Pip install torch

Issue - State: open - Opened by jwokaty about 3 years ago - 3 comments
Labels: enhancement

#44 - Bioconductor docker devel update

Pull Request - State: closed - Opened by nturaga over 3 years ago

#43 - Update to R-4.1.3

Pull Request - State: closed - Opened by nturaga over 3 years ago - 1 comment

#42 - Add libgdal-dev to RELEASE_3_14

Pull Request - State: closed - Opened by nturaga over 3 years ago

#41 - Patch reinstall anvil package

Pull Request - State: closed - Opened by nturaga over 3 years ago

#40 - Separate out system dependencies of Bioconductor.

Pull Request - State: closed - Opened by nturaga over 3 years ago - 6 comments
Labels: enhancement

#39 - R/Rstudio version conflict

Issue - State: open - Opened by bschilder over 3 years ago - 7 comments

#38 - Failed bioconductor package installations do not cause docker builds to stop

Issue - State: open - Opened by pmoris over 3 years ago - 3 comments

#37 - Conflicting definitions of "devel"/"release" between actual Bioconductor and bioconductor_docker

Issue - State: closed - Opened by bschilder almost 4 years ago - 12 comments

#36 - Remove python2 completely from Dockerfile.

Pull Request - State: closed - Opened by nturaga almost 4 years ago - 2 comments
Labels: enhancement

#35 - R graphics engine version 14 is not supported by this version of RStudio

Issue - State: open - Opened by lgatto almost 4 years ago - 4 comments

#34 - Missing `checkbashisms` script creates warning from running check

Issue - State: open - Opened by omsai almost 4 years ago

#33 - volume setup for caching basilisk infrastructure?

Issue - State: open - Opened by vjcitn almost 4 years ago - 1 comment

#32 - Move dependencies out of Dockerfile

Pull Request - State: open - Opened by jwokaty about 4 years ago - 9 comments
Labels: enhancement

#31 - Move apt dependencies out of Dockerfile

Pull Request - State: closed - Opened by jwokaty about 4 years ago - 1 comment

#30 - Error in .install_repos, argument "force" is missing, with no default

Issue - State: closed - Opened by jwokaty about 4 years ago - 3 comments
Labels: bug

#29 - Update `latest` version to be the same as `RELEASE_3_13`

Issue - State: closed - Opened by nuno-agostinho about 4 years ago - 5 comments
Labels: enhancement, good first issue

#28 - Install parallel BLAS on bioconductor_docker image

Issue - State: open - Opened by nturaga about 4 years ago
Labels: enhancement, question

#27 - Any call to `ggplot2` in the current `bioconductor_docker:devel` image makes `R`/`Rstuido` CRASH

Issue - State: open - Opened by r-cheologist over 4 years ago - 4 comments

#26 - Add experimental docker compose file

Pull Request - State: closed - Opened by nturaga over 4 years ago - 1 comment
Labels: enhancement

#25 - Use http for RStudio URL

Pull Request - State: closed - Opened by rushtehrani over 4 years ago - 1 comment

#24 - bug: new library path auto added to .libPaths() upon mounting a volume

Issue - State: closed - Opened by nturaga over 4 years ago - 1 comment

#23 - Create new versioning system

Pull Request - State: closed - Opened by nturaga over 4 years ago

GitHub / Bioconductor/bioconductor_docker issues and pull requests