Hi Joesph, 1. The RELEASE_3_11 and devel images do not have any installed packages. You are free to install the packages within these images. Please read the help http://bioconductor.org/help/docker/ <http://bioconductor.org/help/docker/>. The goal behind these images is to provide an image where all Bioconductor packages can be installed. Once you install the MultiAssayExperiment package it will load just fine.
2. The RELEASE_3_11 image is the stable version, the devel version will keep changing every week based on updates in R and any fixes Bioconductor issues. 3. The bioconductor_docker:bioc2020 image is based on the ‘devel’ image, but a frozen tag during the conference. The docker images used for workshops come with pre-installed packages, and they are derived from the bioconductor/bioconductor_docker:devel image. I would recommend using the bioconductor/bioconductor_docker:RELEASE_3_11 (stable) image for analysis work. All images provided by Bioconductor are reliable. If you need to report any issues, please use the https://github.com/Bioconductor/bioconductor_docker/issues <https://github.com/Bioconductor/bioconductor_docker/issues>. Best, Nitesh > On Aug 3, 2020, at 11:03 AM, Shepherd, Lori <lori.sheph...@roswellpark.org> > wrote: > > Marcel or Nitesh? This was sent to the issue bot. > > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Joseph Gerrein <gerrein.jos...@gene.com> > Sent: Tuesday, July 28, 2020 11:03 AM > To: bioc-issue-...@bioconductor.org <bioc-issue-...@bioconductor.org> > Cc: Jerry (Zhijun) Tang <jt...@gene.com>; Lala Motlhabi <motlh...@gene.com> > Subject: MultiAssayExperiment not found in docker devel image > > Dear bioconductor team, > > Hello! I would like to use MultiAssayExperiment in a preloaded bioconductor > Docker container that does not require any package installations. I loaded > the docker devel image and also the Docker release 3_11 image (from > https://hub.docker.com/r/bioconductor/bioconductor_docker/tags<https://secure-web.cisco.com/1CBV0e1ECW2oH221MZYDrB6ZGZnORfj8i0E9oO6_S0_SuOZu0RxuZrxoZW9vYhbr2tTlHVmXyKmcJ2WgF1J7h4raEyxj58wLe_inCrFX8GSAHS5ffkFppkFmgSUCPTs5LcxpjWSv_mte_V7N06JxxOoJUv5Pud1y9hdtxZESlOdfd1B_VXICfy1Q3I8_82FpVSfJui4CzuCYP49JynqpFLfB01cW6zEwv4Eog3D95hVXysXypD8GZJ4oxWykkGJ-9HtsYnLf01P6EtvTPcNaOur8hADTTJdvz6vJFIi0GES24GSiGjpYgIjRkYOsVcHQPTDx_94vh0mCcsOoa4zQ6EQ/https%3A%2F%2Fhub.docker.com%2Fr%2Fbioconductor%2Fbioconductor_docker%2Ftags>) > into Docker desktop on my Windows machine. I wanted to use the > MultiAssayExperiment and also SummarizedExperiment, but when I tried to load > them using the library function they were not found. Are these docker images > preloaded with MultiAssayExperiment? Do you have any Docker images preloaded > with MultiAssayExperiment that are well maintained and/or supported? > > I loaded the docker image from the MultiAssayExperiment's/TCGA bioconductor > 2020 workshop and I was able to load MultiAssayExperiment using the library > function � > https://hub.docker.com/r/mr148/multiassayworkshop<https://secure-web.cisco.com/13jSFAuYhSC2URJ4K7zjh4ouo3I63T-6Hw8z5s-Wr2qDEf5SxOaf6kXJP4pWIKe0noQlGgA_GF6LSHHKyxFSt_LM1tgF5_GxjeTCvWXAEtKc2CjiWbaWTzsGBmRYcDqguPf6o52KE_BuYnnGxWJ9_c0WMKjztdEXwZJvZU_cQqn1moo8yPoLpvkf3LXpcDYETRkPKUo6bEpeo3dXxR4sBarXMsI3Rbm9TP30eQM9M2XzFV6-eLG_otc5kS0QZA-wNooTaDtQMDLIouLRkIF1YUHDVDdO9S4MOMaIqNVd-cOLYzpSykcoMr4an7S0DWjLiXoRdO8b1AaEz5PxkLiApiw/https%3A%2F%2Fhub.docker.com%2Fr%2Fmr148%2Fmultiassayworkshop> > - Is this container reliable and good to use in general for working with > SummarizedExperiment and MultiAssayExperiment in bioconductor? > > > Thanks! > > Joe > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
