Re: [Bioc-devel] Participating in the development of Bioconductor
Hi Franck, thanks for writing. I think it would be great to hear from
users about performance
concerns. We would like to do more profiling and instrumentation of key
worksteps to help
increase throughput and ensure available compute resources are used. In
the cuda/gpu
space we don't have anything touching
https://github.com/NVIDIA-Genomics-Research/rapids-single-cell-examples
as far as I know and it would be interesting if you would have a look at
this and see whether
the is a clear path to some development integrating these approaches.
You might want to join our community slack for more interaction.
slack.bioconductor.org
Best regards
Vince Carey
On Wed, May 3, 2023 at 12:12 PM Franck RICHARD
wrote:
> Hello community!
>
> I am the author of several software programs including this astronomy
> program: https://winstars.net/en I recently had the opportunity to
> participate in the activities of a neuroscience laboratory in Madrid. I
> learned how to use Bioconductor and I would like to participate in the
> development of new features (if possible). The researchers in the lab
> complain about the slowness of these tools when used on simple PCs. So I
> wonder if it would not be interesting to integrate Cuda in some indexing
> packages, I think of Bowtie2 or Salmon for example... (there is a
> version of bowtie2 that works with cuda, but it seems old). But the task
> would be very complex I guess. There are simpler things to do, like
> creating a wrapper for Salmon or something like that. What do you think
> would be useful to do at this moment for Bioconductor users?
>
> With my thanks,
>
> Franck
>
> [[alternative HTML version deleted]]
>
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> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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[Bioc-devel] Participating in the development of Bioconductor
Hello community! I am the author of several software programs including this astronomy program: https://winstars.net/en I recently had the opportunity to participate in the activities of a neuroscience laboratory in Madrid. I learned how to use Bioconductor and I would like to participate in the development of new features (if possible). The researchers in the lab complain about the slowness of these tools when used on simple PCs. So I wonder if it would not be interesting to integrate Cuda in some indexing packages, I think of Bowtie2 or Salmon for example... (there is a version of bowtie2 that works with cuda, but it seems old). But the task would be very complex I guess. There are simpler things to do, like creating a wrapper for Salmon or something like that. What do you think would be useful to do at this moment for Bioconductor users? With my thanks, Franck [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error pushing changes to upstream
I will reply off list and help you resolve this. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Gaurav Sharma Sent: Wednesday, May 3, 2023 9:49 AM To: Kern, Lori ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Error pushing changes to upstream Hi, Thanks for your reply. Yes, that's what I did. Here are the commands before `git push`: ``` > git rm DESCRIPTION~ rm 'DESCRIPTION~' > git commit -m 'remove additional description file' [devel 69c5a8b] remove additional description file 1 file changed, 45 deletions(-) delete mode 100644 DESCRIPTION~ ``` After this when I tried to push these changes upstream, I got the error I shared in the previous email. It is a `pre-receive hook declined` error, so it is possible that the server-side hook has an issue. Perhaps, it is based on the assumption that merge conflict markers are not checked in already, but in this case, they are already in the repo. Let me know if you need any other information. Best, Gaurav From: Kern, Lori Sent: Wednesday, May 3, 2023 9:33 AM To: bioc-devel@r-project.org ; Gaurav Sharma Subject: Re: [Bioc-devel] Error pushing changes to upstream Are you able to do a git rm DESCRIPTION~ and git commit those changes? Removing l ocally if it is already checked in means you have to do a git rm to remove from git repo. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Gaurav Sharma via Bioc-devel Sent: Wednesday, May 3, 2023 12:33 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Error pushing changes to upstream Hi, I am a developer of the package proejctR. Following the FAQ, I have checked that I have R W access to projectR and my upstream is configured correctly. I get the following error on git push: ``` Counting objects: 2, done. Delta compression using up to 12 threads. Compressing objects: 100% (2/2), done. Writing objects: 100% (2/2), 235 bytes | 5.00 KiB/s, done. Total 2 (delta 1), reused 0 (delta 0) remote: Error: You cannot push without resolving merge conflicts. remote: remote: Please check the files in the commit pushed to the git-server remote: for merge conflict markers like '<<<', '', '>>>'. remote: To git.bioconductor.org:packages/projectR.git ! [remote rejected] devel -> devel (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org:packages/projectR.git' ``` I believe this is due to a file named DESCRIPTION~ in the repo upstream (on Bioconductor). The file does have merge conflict markers. However, I removed the file locally, performed a commit, and got the error while git push. That's the only change I did and I didn't do any merge. So, the error is a bit misleading. I am unable to push the removal of DESCRIPTION~ upstream from my end, and I think this is causing the error. If someone could remove the file and help with this issue, I'll appreciate it. Thank you. Best, Gaurav [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1pchIcqFTrYIP6xoiFuAdN5qp1escj-BLtj5KULR7drSyzv8aISDzs7ifW3hQCZHJenGHbobHDSoUd_4WFAztFLiLc8lLHGas-IKPqzCeTWAyVJI2bZBSbZ6RL6MVlfeWpMnJn_XckjMpABioTAdZB7qv7xjS8bpq55uxWN7YHRMT1QVlEowJ7KrbBxrhCQ-ksXUQkRwkXu4hQ-Apxia2FlQlyGM2ZjCuTTUjaguuTPYhRFINX24ZhQREruJ7ul-EPZeeqAVyZXtyzM5Wf6dfTVXB2uTMOa4BOo2oDBG5js_qhqfbVZohbM3cp66YLkkE/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list
Re: [Bioc-devel] Error pushing changes to upstream
Hi, Thanks for your reply. Yes, that's what I did. Here are the commands before `git push`: ``` > git rm DESCRIPTION~ rm 'DESCRIPTION~' > git commit -m 'remove additional description file' [devel 69c5a8b] remove additional description file 1 file changed, 45 deletions(-) delete mode 100644 DESCRIPTION~ ``` After this when I tried to push these changes upstream, I got the error I shared in the previous email. It is a `pre-receive hook declined` error, so it is possible that the server-side hook has an issue. Perhaps, it is based on the assumption that merge conflict markers are not checked in already, but in this case, they are already in the repo. Let me know if you need any other information. Best, Gaurav From: Kern, Lori Sent: Wednesday, May 3, 2023 9:33 AM To: bioc-devel@r-project.org ; Gaurav Sharma Subject: Re: [Bioc-devel] Error pushing changes to upstream Are you able to do a git rm DESCRIPTION~ and git commit those changes? Removing l ocally if it is already checked in means you have to do a git rm to remove from git repo. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Gaurav Sharma via Bioc-devel Sent: Wednesday, May 3, 2023 12:33 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Error pushing changes to upstream Hi, I am a developer of the package proejctR. Following the FAQ, I have checked that I have R W access to projectR and my upstream is configured correctly. I get the following error on git push: ``` Counting objects: 2, done. Delta compression using up to 12 threads. Compressing objects: 100% (2/2), done. Writing objects: 100% (2/2), 235 bytes | 5.00 KiB/s, done. Total 2 (delta 1), reused 0 (delta 0) remote: Error: You cannot push without resolving merge conflicts. remote: remote: Please check the files in the commit pushed to the git-server remote: for merge conflict markers like '<<<', '', '>>>'. remote: To git.bioconductor.org:packages/projectR.git ! [remote rejected] devel -> devel (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org:packages/projectR.git' ``` I believe this is due to a file named DESCRIPTION~ in the repo upstream (on Bioconductor). The file does have merge conflict markers. However, I removed the file locally, performed a commit, and got the error while git push. That's the only change I did and I didn't do any merge. So, the error is a bit misleading. I am unable to push the removal of DESCRIPTION~ upstream from my end, and I think this is causing the error. If someone could remove the file and help with this issue, I'll appreciate it. Thank you. Best, Gaurav [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1pchIcqFTrYIP6xoiFuAdN5qp1escj-BLtj5KULR7drSyzv8aISDzs7ifW3hQCZHJenGHbobHDSoUd_4WFAztFLiLc8lLHGas-IKPqzCeTWAyVJI2bZBSbZ6RL6MVlfeWpMnJn_XckjMpABioTAdZB7qv7xjS8bpq55uxWN7YHRMT1QVlEowJ7KrbBxrhCQ-ksXUQkRwkXu4hQ-Apxia2FlQlyGM2ZjCuTTUjaguuTPYhRFINX24ZhQREruJ7ul-EPZeeqAVyZXtyzM5Wf6dfTVXB2uTMOa4BOo2oDBG5js_qhqfbVZohbM3cp66YLkkE/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel 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
Re: [Bioc-devel] Error pushing changes to upstream
Are you able to do a git rm DESCRIPTION~ and git commit those changes? Removing l ocally if it is already checked in means you have to do a git rm to remove from git repo. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Gaurav Sharma via Bioc-devel Sent: Wednesday, May 3, 2023 12:33 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Error pushing changes to upstream Hi, I am a developer of the package proejctR. Following the FAQ, I have checked that I have R W access to projectR and my upstream is configured correctly. I get the following error on git push: ``` Counting objects: 2, done. Delta compression using up to 12 threads. Compressing objects: 100% (2/2), done. Writing objects: 100% (2/2), 235 bytes | 5.00 KiB/s, done. Total 2 (delta 1), reused 0 (delta 0) remote: Error: You cannot push without resolving merge conflicts. remote: remote: Please check the files in the commit pushed to the git-server remote: for merge conflict markers like '<<<', '', '>>>'. remote: To git.bioconductor.org:packages/projectR.git ! [remote rejected] devel -> devel (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org:packages/projectR.git' ``` I believe this is due to a file named DESCRIPTION~ in the repo upstream (on Bioconductor). The file does have merge conflict markers. However, I removed the file locally, performed a commit, and got the error while git push. That's the only change I did and I didn't do any merge. So, the error is a bit misleading. I am unable to push the removal of DESCRIPTION~ upstream from my end, and I think this is causing the error. If someone could remove the file and help with this issue, I'll appreciate it. Thank you. Best, Gaurav [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1pchIcqFTrYIP6xoiFuAdN5qp1escj-BLtj5KULR7drSyzv8aISDzs7ifW3hQCZHJenGHbobHDSoUd_4WFAztFLiLc8lLHGas-IKPqzCeTWAyVJI2bZBSbZ6RL6MVlfeWpMnJn_XckjMpABioTAdZB7qv7xjS8bpq55uxWN7YHRMT1QVlEowJ7KrbBxrhCQ-ksXUQkRwkXu4hQ-Apxia2FlQlyGM2ZjCuTTUjaguuTPYhRFINX24ZhQREruJ7ul-EPZeeqAVyZXtyzM5Wf6dfTVXB2uTMOa4BOo2oDBG5js_qhqfbVZohbM3cp66YLkkE/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel 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
[Bioc-devel] Error pushing changes to upstream
Hi, I am a developer of the package proejctR. Following the FAQ, I have checked that I have R W access to projectR and my upstream is configured correctly. I get the following error on git push: ``` Counting objects: 2, done. Delta compression using up to 12 threads. Compressing objects: 100% (2/2), done. Writing objects: 100% (2/2), 235 bytes | 5.00 KiB/s, done. Total 2 (delta 1), reused 0 (delta 0) remote: Error: You cannot push without resolving merge conflicts. remote: remote: Please check the files in the commit pushed to the git-server remote: for merge conflict markers like '<<<', '', '>>>'. remote: To git.bioconductor.org:packages/projectR.git ! [remote rejected] devel -> devel (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org:packages/projectR.git' ``` I believe this is due to a file named DESCRIPTION~ in the repo upstream (on Bioconductor). The file does have merge conflict markers. However, I removed the file locally, performed a commit, and got the error while git push. That's the only change I did and I didn't do any merge. So, the error is a bit misleading. I am unable to push the removal of DESCRIPTION~ upstream from my end, and I think this is causing the error. If someone could remove the file and help with this issue, I'll appreciate it. Thank you. Best, Gaurav [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
