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

5 messages · Shepherd, Lori, Joseph Gerrein, Nitesh Turaga

Original

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Mon, Aug 3, 2020 8:03 AM #

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

Mon, Aug 3, 2020 8:10 AM #

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

________________________________
From: Joseph Gerrein <gerrein.joseph at gene.com>
Sent: Tuesday, July 28, 2020 11:03 AM
To: bioc-issue-bot at bioconductor.org <bioc-issue-bot at bioconductor.org>
Cc: Jerry (Zhijun) Tang <jtang at gene.com>; Lala Motlhabi <motlhabl at 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

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Mon, Aug 3, 2020 8:46 AM #

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 at gmail.com> wrote:

________________________________
From: Joseph Gerrein <gerrein.joseph at gene.com>
Sent: Tuesday, July 28, 2020 11:03 AM
To: bioc-issue-bot at bioconductor.org <bioc-issue-bot at bioconductor.org>
Cc: Jerry (Zhijun) Tang <jtang at gene.com>; Lala Motlhabi <motlhabl at 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.
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Mon, Aug 3, 2020 8:51 AM #

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

________________________________
From: Joseph Gerrein <gerrein.joseph at gene.com>
Sent: Tuesday, July 28, 2020 11:03 AM
To: bioc-issue-bot at bioconductor.org <bioc-issue-bot at bioconductor.org>
Cc: Jerry (Zhijun) Tang <jtang at gene.com>; Lala Motlhabi <motlhabl at 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.
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Mon, Aug 3, 2020 10:18 AM #

Great, thanks, Nitesh!

On Mon, Aug 3, 2020 at 11:51 AM Nitesh Turaga <nturaga.bioc at 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 at 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 at 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 at 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 at gene.com>
Sent: Tuesday, July 28, 2020 11:03 AM
To: bioc-issue-bot at bioconductor.org <bioc-issue-bot at bioconductor.org>
Cc: Jerry (Zhijun) Tang <jtang at gene.com>; Lala Motlhabi <motlhabl at 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

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 at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel