[Bioc-devel] Please bump the docker build for bioconductor/devel_core2

On Apr 17, 2020, at 1:20 PM, Pariksheet Nanda <pariksheet.nanda at uconn.edu> wrote:

Hi Nitesh,

Can you confirm if the bioconductor/bioconductor_docker:devel is the
functional equivalent of bioconductor/devel_core2 docker image?

That wasn't clear to me, but maybe that was explained and I messed it.

Thanks,

Pariksheet


On 4/17/20 1:10 PM, Turaga, Nitesh wrote:

*Message sent from a system outside of UConn.*


Hi Pariksheet,

Yes, we have deprecated our previous docker images. Please use bioconductor/bioconductor_docker instead.

http://secure-web.cisco.com/15S73a43-piuVcdLwX5xHbVuzjGy7MFnAoiOXTai9804jfdlqOUPjaWJ6xvzdhowiofT-BdKIDwU3tbCbafZ0QNroDomBS9dGAfsP6Cg_VRmfhVu_ei7z6kIfSrR-lTXUWmMtBznXRhe7xBcJpKKaF082y8LXzgQpJpA7GTBu0Mtgu76HcTihxdV6t3ecA4zUj7AMUhzaxyHHdEGftxwA8oE8eAhaO0zP9lduyNN7-hwSf96GVH3M1Yq6xBnNtRgc8lzyoFL-W8CFaQ1J-9UuVyQjs_nNPhaK1srB_wznTPxKAubJ6-PtjEVZxPpLYLf5FRrL3kVRsghfvA0lIzLfQzeRvpPfI_O8Je8nhHj3OMs/http%3A%2F%2Fbioconductor.org%2Fhelp%2Fdocker%2F%23deprecation

Best,

Nitesh

On Apr 17, 2020, at 1:03 PM, Pariksheet Nanda <pariksheet.nanda at uconn.edu> wrote:

Hi folks,



TL;DR: I just noticed the deprecation notice at the top of the docker hub page[1] to use one of the images suggested bioconductor_docker[4] instead.  Do you recommend that I use bioconductor/bioconductor_docker:devel instead of bioconductor/devel_core2?



I'm writing to this e-mail address because it is the maintenance contact for the devel_core2 docker image listed in the docker hub page[1].

I use your the devel_core2 docker image extensively for my GitLab CI builds, and at the minute it looks like due to this change introduced by Herve Pages[2], installing any number of packages is throwing this error:

   Functions found when exporting methods from the namespace ?IRanges? which are not S4 generic: ?parallelSlotNames?
And after updating that, it complains about exactly the same error with XVector, GenomicRanges, Biostrings, IRanges, GenomicAlignments, etc.

I get the error when a package I'm trying to install / update fails to install it's dependency GenomicFeatures[3].

I would prefer not to waste CI time by globally updating outdated packages with:

   BiocManager::install(ask ="FALSE")

... the value of having a container is not to need to do globally update to install Bioconductor packages.



Pariksheet

[1] https://secure-web.cisco.com/1cjYBx58qnoy2Yql1wjg4eG_qjdPoNkFLzkrOVbXyMYjpf3VDH9u7DB31_8TuU6Am3ZEGky8ECDzJaNDy_9C5nnZXvsU3-xtW2klQOO_LoikS8SX5V424chfXqBsEpvReK6ECjiqwmiQpHtkYnrymN9-5U6As6Xd32nv-mOsvvApByN-XbyzWihD3_gChe-ktxE1Yr5nEdc2805fpB7lKWZhWR3QtQHqpp-q9tJRpc42TkKtokXkMWmV5hlPRiIyYZ9bwduIATYNGUGhMln9-ChCsDlNm4vMh8PXei9edmkezQoc6M0j40MGbfq6ni0R2o4xuBKraj6kSC_oMq4JnMJcQ43Ok8Se0soWqxdn2eLc/https%3A%2F%2Fhub.docker.com%2Fr%2Fbioconductor%2Fdevel_core2

[2] https://secure-web.cisco.com/1eNvn0BLOoWQ5mUrAOQNcjYKAHPbsZ0isv-9urGW4ZSVS4fEp4V2cUirZ242fCkB68w8Pt3hJMRXhl6NHX-of4hZpgaJ8fmSFL7QznFSEKOno8PTsfeobmO4HtdZdJ3wPjrP2bVsS-qGIKiYPvG0FIqbRLGNy9v-k5cHCMjo68w8SbiQlYPKIcroAsC-qNCy661NyB-FMwm7OgwM3bSjY4_qElugZxhxIFE1rL1NhIYRf5yV0ymJjXupFNwP1jyTC7ZWiPN9OO1fy3G1LF0fmLuSlaSvLQ35LwauZCT5up9VhIVTlLwmK4Cgh2rr4mhlGlZPlJz06cIsAJBTg8OoZmg/https%3A%2F%2Fgithub.com%2FBioconductor%2FS4Vectors%2Fcommit%2F95fd9c39de54b840f87779b3692ba6b599afa5bc

[3] https://secure-web.cisco.com/1lYSRAieQakiuf6JkOHUwEwVwRC4kIiRL5oKBXi1bgnqV6B-zdjtYlX8TIc6BLBi4RtBL_eJBH3Nf8eJdslWINB2VCQkoX8sesOSshetyHC1P2ClQF7T6HV_FEDyPnYIBSzzx1TRndxKIj796UcrjmaaF3pVdIiu-Qz7fQjhtPfksiC4BCHDVknC0l2P_zgYtuXR8wj1oRVkRk_88P0B8ZPQYeaoMZ4j4GSAmYayd9LzPJxmbNoORcvyCg8xVRXwmO4j2SAm6B6Xo0B4KrHryzu5hXL_V6MejDAwRXPlaTX0DfbMh0Hj4CxpBcJdQEgrvhGTxrKQ_AVwIgMyhwG7szw/https%3A%2F%2Fgitlab.com%2Fcoregenomics%2Fevolength%2F-%2Fjobs%2F516336886

[4] https://secure-web.cisco.com/1R6bZhtIwSc0I-G0m1Q5x_ETpVUwX334QqUxPXwdPy4QNxhOVTbY9mdmOG0rRlmdkTrMbwEmujygvEDOF-T9Pp8p2UTbEqSZIg97bX-c3rdXiGHjwfFOLb5rgxWlqZ0i9nEH0kgnF0lpMN8I2kr9d-JE-0jM27A-Oc4Zrmmzfu3Q-W99vk2Q95I5g1PQ6rgTE7hWUmaFb1gDyu85agNo49nJlMs2DFfDum-dTctrgddPthQT5kuBnYBj8Y9_qSqSU9qwMdE5ZtNpU9lJY2qzZBFB7R4Y08svbFsqTAqVuTgYWtEOKiZz13ZpEzWALUY0uzmPMv2yAZB72lXuLZlpsNw/https%3A%2F%2Fgithub.com%2FBioconductor%2Fbioconductor_docker

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