Yes it is. It's better and comes with system dependencies to install most Bioconductor packages.
The details about the image are given in the https://bioconductor.org/help/docker/. Best, Nitesh > On Apr 17, 2020, at 1:20 PM, Pariksheet Nanda <pariksheet.na...@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.na...@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 >>> >> >> >> 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. > 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. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
