[Bioc-devel] MultiAssayExperiment not found in docker devel image

[Joseph Gerrein]

Great, thanks, Nitesh!

On Mon, Aug 3, 2020 at 11:51 AM Nitesh Turaga <nturaga.bioc using gmail.com>
wrote:

> Development work should be done usually on the devel version of
> Bioconductor (3.12), which is in the bioconductor_docker:devel image.
>
> The stable release, has the latest Bioconductor stable release version
> 3.11 on the image bioconductor_docker:RELEASE_3_11.
>
> Hope that answers your question.
>
> Best,
>
> Nitesh
>
>
> On Aug 3, 2020, at 11:46 AM, Joseph Gerrein <gerrein.joseph using gene.com>
> wrote:
>
> Hi Nitesh,
>
> Thank you so much for that detailed explanation! I have just one
> follow-up question – we are internally developing A wrapper for
> MultiAssayExperiment. Do you recommend using the devel version or the
> stable release version?
>
> Thanks,
>
> Joe
>
> On Mon, Aug 3, 2020 at 8:11 AM Nitesh Turaga <nturaga.bioc using gmail.com>
> wrote:
>
>
> 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/. 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.
>
> Best,
>
> Nitesh
>
> On Aug 3, 2020, at 11:03 AM, Shepherd, Lori <Lori.Shepherd using 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.joseph using gene.com>
> Sent: Tuesday, July 28, 2020 11:03 AM
> To: bioc-issue-bot using bioconductor.org <bioc-issue-bot using bioconductor.org>
> Cc: Jerry (Zhijun) Tang <jtang using gene.com>; Lala Motlhabi <motlhabl using 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>
> <https://hub.docker.com/r/bioconductor/bioconductor_docker/tags%3Chttps://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%3E>)
> 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>
> <https://hub.docker.com/r/mr148/multiassayworkshop%3Chttps://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%3E>
> - Is this container reliable and good to use in general for working with
> SummarizedExperiment and MultiAssayExperiment in bioconductor?
>
>
> Thanks!
>
> Joe
>
>
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