Contributions
Contributions copied to clipboard
Bioconductor
Deep characterization of cancer drugs mechanism of action
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/CBIIT-CGBB/DeepTarget
Confirm the following by editing each check box to '[x]'
-
[x ] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
-
[x ] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
-
[x ] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
-
[x ] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
-
[x ] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
-
[ x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
-
[x ] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
- [x ] The 'devel' branch for new packages and features.
- [ x] The stable 'release' branch, made available every six months, for bug fixes.
- [x ] Bioconductor version control using Git (optionally via GitHub).
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.
Hi @TrinhNguyenP
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: DeepTarget
Type: Package
Title: Deep characterization of cancer drugs
Version: 0.99.0
Author: sanjusinha7, tinh.nguyen, yhu
Maintainer: <[email protected]>
Description: Deep characterization of cancer drugs mechanism of action by integrating large-scale genetic and drug screens.
License: GPL-2
Encoding: UTF-8
LazyData: true
biocViews: GeneTarget, GenePrediction
RoxygenNote: 7.2.3
LazyDataCompression:xz
Depends: R (>= 3.5.0),rlang,tictoc, fgsea, ggplot2, ggpubr, statar, interactions, reshape2, base, parallel, pROC, ggrepel, grid, gridExtra, stringb, DEGreport, readxl,stringr
Thank you for this interesting submission. There are various tasks that need to be executed before review. First, .Rproj and renv and other material inessential to package installation and use should be removed from the main repo branch. Place them in a different branch. Second, a vignette is obligatory. I see the user guide in PDF. Please make the source code available in vignettes folder. See contributions.bioconductor.org for full guidelines.
Thank you for this interesting submission. There are various tasks that need to be executed before review. First, .Rproj and renv and other material inessential to package installation and use should be removed from the main repo branch. Place them in a different branch. Second, a vignette is obligatory. I see the user guide in PDF. Please make the source code available in vignettes folder. See contributions.bioconductor.org for full guidelines.
Hi @vjcitn , I have updated the requirements as you pointed out. These changes have been committed and pushed again to github. Please let me know if I miss anything else. Thanks, Trinh
Also saw ```
-- re-building ‘Vineggete_analyses.Rmd’ using rmarkdown
() NOTE: I saw chunk options "Finding a drug's primary target(s)"
please go to https://yihui.org/knitr/options
(it is likely that you forgot to quote "character" options)
Error: processing vignette 'Vineggete_analyses.Rmd' failed with diagnostics:
SUMMARY: processing the following files failed: ‘Vineggete_analyses.Rmd’ ‘Vineggete_analyses.Rmd’
Error: Vignette re-building failed. Execution halted
Also saw ``` -- re-building ‘Vineggete_analyses.Rmd’ using rmarkdown () NOTE: I saw chunk options "Finding a drug's primary target(s)" please go to https://yihui.org/knitr/options (it is likely that you forgot to quote "character" options) Error: processing vignette 'Vineggete_analyses.Rmd' failed with diagnostics: :1:24: unexpected symbol 1: alist( 'Finding a drug's ^ () NOTE: I saw chunk options "Finding a drug's primary target(s)" please go to https://yihui.org/knitr/options (it is likely that you forgot to quote "character" options) Error: tangling vignette 'Vineggete_analyses.Rmd' failed with diagnostics: :1:24: unexpected symbol 1: alist( 'Finding a drug's ^ --- failed re-building ‘Vineggete_analyses.Rmd’
SUMMARY: processing the following files failed: ‘Vineggete_analyses.Rmd’ ‘Vineggete_analyses.Rmd’
Error: Vignette re-building failed. Execution halted
Hi @vjcitn, I have added VignetteBuilder entry in DESCRIPTION file. Also,I have fixed the errors. In addition to that, I have run R CMD check and R CMD build to make sure that there was no error. These changes have been committed and pushed again to github. Thanks a lot.
Best, Trinh
Hi @vjcitn, It has been 3 weeks since updated the github directory according to your suggestions. I am wondering whether you have any update for this package.
Thanks,
Trinh
You need a VignetteBuilder entry in DESCRIPTION
Dear @vjcitn, I have updated the package as you mentioned about a month but I didn't hear any feedback. Can you please give me some update? Thanks, Trinh
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: DeepTarget_0.99.0.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/DeepTarget to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @TrinhNguyenP ,
Can you please try to address the errors in the build report and then submit a new version. Once we have that then I can begin my review.
Thanks, Pete
Hi @PeteHaitch, Yes, I will fix the error and will let you know ASAP. Thanks, Trinh
Hi @PeteHaitch,
I have pushed an updated version to Github repo, which I have fixed the errors that I could see from my side by using BiocCheck.
Best, Trinh
Please follow the instructions and when making changes to your repository push to
[email protected]:packages/DeepTarget to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @PeteHaitch , I think I have sucessfully pushed it to bioconductor upstream.
git remote -v
origin [email protected]:CBIIT-CGBB/DeepTarget.git (fetch)
origin [email protected]:CBIIT-CGBB/DeepTarget.git (push)
upstream [email protected]:packages/DeepTarget.git (fetch)
upstream [email protected]:packages/DeepTarget.git (push)
git fetch --all
Fetching upstream
From git.bioconductor.org:packages/DeepTarget
* [new branch] devel -> upstream/devel
Fetching origin
Could you please check?
Thanks, Trinh
Have you run
git push upstream devel?
I just checked. Actually I didn't.
I ran git merge upstream/devel.
I just ran git push upstream devel, it has error as below:
error: src refspec devel does not match any
error: failed to push some refs to 'git.bioconductor.org:packages/DeepTarget.git'
Best, Trinh
Have you run
git push upstream devel?
Hi @PeteHaitch, I ran git push upstream main:master
Enumerating objects: 62, done. Counting objects: 100% (62/62), done. Delta compression using up to 16 threads Compressing objects: 100% (51/51), done. Writing objects: 100% (62/62), 1.46 MiB | 78.61 MiB/s, done. Total 62 (delta 1), reused 62 (delta 1), pack-reused 0 To git.bioconductor.org:packages/DeepTarget.git
- [new branch] main -> master It runs without errors. Please check. Thanks, Trinh
It looks to me that your git isn't set up as expected by the Bioconductor build system or that you're not doing something quite right. Here is what I see when I clone your repository from Bioconductor's git server.
$git clone [email protected]:packages/DeepTarget
Cloning into 'DeepTarget'...
remote: Enumerating objects: 309, done.
remote: Counting objects: 100% (309/309), done.
remote: Compressing objects: 100% (193/193), done.
remote: Total 309 (delta 96), reused 245 (delta 93), pack-reused 0
Receiving objects: 100% (309/309), 86.65 MiB | 1.24 MiB/s, done.
Resolving deltas: 100% (96/96), done.
$cd DeepTarget/
$ git branch
* devel
$ git log -n 5
commit a8ec76460eaef37d181bcd11261f7e76ecde7ef0 (HEAD -> devel, origin/devel, origin/HEAD)
Author: Trinh Nguyen <[email protected]>
Date: Wed Jun 28 16:25:30 2023 -0400
Delete .DS_Store
commit cc601d81e168b6498baec7d095d98c3950e0312f
Merge: c841774 d8879a3
Author: Trinh Nguyen <[email protected]>
Date: Wed Jun 28 16:22:59 2023 -0400
Merge branch 'master' of https://github.com/CBIIT-CGBB/DeepTarget
commit c841774a6db03fad3cf61b22f7dbef45c0f68998
Author: Trinh Nguyen <[email protected]>
Date: Wed Jun 28 16:22:41 2023 -0400
adding VigneetteBuilder in the desccription; fix the errors;R CMD build; R CMD check
commit d8879a3bf7171156b2bdf02aef7619854063c2a7
Author: Trinh Nguyen <[email protected]>
Date: Fri Jun 16 16:25:12 2023 -0400
Update README.md
commit b455bb9e0e25676c9e183c38dcf8b0e9286af2d2
Author: Trinh Nguyen <[email protected]>
Date: Fri Jun 16 16:25:00 2023 -0400
Update README.md
From the above output we can see that the most recent commit to the devel branch on Bioconductor's git server is from nearly 2 months ago (2023-06-28). This means that any changes you've made since then (e.g., those on your GitHub repository) have not been properly pushed to the Bioconductor git server.
I can't tell from the output you've provided what you're doing wrong or what might be wrong with your setup. Perhaps @vjcitn or @lshep from the Bioconductor core team will be able to assist.
Hi
It looks to me that your git isn't set up as expected by the Bioconductor build system or that you're not doing something quite right. Here is what I see when I clone your repository from Bioconductor's git server.
$git clone [email protected]:packages/DeepTarget Cloning into 'DeepTarget'... remote: Enumerating objects: 309, done. remote: Counting objects: 100% (309/309), done. remote: Compressing objects: 100% (193/193), done. remote: Total 309 (delta 96), reused 245 (delta 93), pack-reused 0 Receiving objects: 100% (309/309), 86.65 MiB | 1.24 MiB/s, done. Resolving deltas: 100% (96/96), done. $cd DeepTarget/ $ git branch * devel $ git log -n 5 commit a8ec76460eaef37d181bcd11261f7e76ecde7ef0 (HEAD -> devel, origin/devel, origin/HEAD) Author: Trinh Nguyen <[email protected]> Date: Wed Jun 28 16:25:30 2023 -0400 Delete .DS_Store commit cc601d81e168b6498baec7d095d98c3950e0312f Merge: c841774 d8879a3 Author: Trinh Nguyen <[email protected]> Date: Wed Jun 28 16:22:59 2023 -0400 Merge branch 'master' of https://github.com/CBIIT-CGBB/DeepTarget commit c841774a6db03fad3cf61b22f7dbef45c0f68998 Author: Trinh Nguyen <[email protected]> Date: Wed Jun 28 16:22:41 2023 -0400 adding VigneetteBuilder in the desccription; fix the errors;R CMD build; R CMD check commit d8879a3bf7171156b2bdf02aef7619854063c2a7 Author: Trinh Nguyen <[email protected]> Date: Fri Jun 16 16:25:12 2023 -0400 Update README.md commit b455bb9e0e25676c9e183c38dcf8b0e9286af2d2 Author: Trinh Nguyen <[email protected]> Date: Fri Jun 16 16:25:00 2023 -0400 Update README.mdFrom the above output we can see that the most recent commit to the devel branch on Bioconductor's git server is from nearly 2 months ago (2023-06-28). This means that any changes you've made since then (e.g., those on your GitHub repository) have not been properly pushed to the Bioconductor git server.
I can't tell from the output you've provided what you're doing wrong or what might be wrong with your setup. Perhaps @vjcitn or @lshep from the Bioconductor core team will be able to assist.
Good morning @PeteHaitch, I am not sure. I just ran command:
git push upstream master:devel
Enumerating objects: 30, done.
Counting objects: 100% (30/30), done.
Delta compression using up to 16 threads
Compressing objects: 100% (18/18), done.
Writing objects: 100% (25/25), 3.14 KiB | 804.00 KiB/s, done.
Total 25 (delta 7), reused 0 (delta 0), pack-reused 0
To git.bioconductor.org:packages/DeepTarget.git
a8ec764..d10a232 master -> devel
Can you please check once more time? We expect to see there are some update such as an update on vignettes Aug 9.
Thanks very much, Trinh
Good morning @PeteHaitch, I used your commands to see whether I can check by myself. Please see below:
NCI-02225639-ML:testing_bio_github nguyentt6$ git clone [email protected]:packages/DeepTarget
Cloning into 'DeepTarget'...
remote: Enumerating objects: 334, done.
remote: Counting objects: 100% (334/334), done.
remote: Compressing objects: 100% (211/211), done.
remote: Total 334 (delta 105), reused 242 (delta 93), pack-reused 0
Receiving objects: 100% (334/334), 86.65 MiB | 5.81 MiB/s, done.
Resolving deltas: 100% (105/105), done.
NCI-02225639-ML:DeepTarget nguyentt6$ git branch
* devel
*
NCI-02225639-ML:DeepTarget nguyentt6$ git log -n 5
commit d10a232fbbb0b5e75579019f4786de8e4551c855 (HEAD -> devel, origin/devel, origin/HEAD)
Author: Trinh Nguyen <[email protected]>
Date: Wed Aug 9 15:08:17 2023 -0500
Fix the name
commit 1a0aa2b1b872f7118d3d2fc8de2d1b9a32d795ae
Author: Trinh Nguyen <[email protected]>
Date: Wed Aug 9 14:56:35 2023 -0500
Registration for maintainer.
commit f5889a02b09bdb0c3fa3bb94f2ddeb0bf5decca1
Author: Trinh Nguyen <[email protected]>
Date: Wed Aug 9 10:48:54 2023 -0500
addressing error from V_analyses.Rmd
commit a8ec76460eaef37d181bcd11261f7e76ecde7ef0
Author: Trinh Nguyen <[email protected]>
Date: Wed Jun 28 16:25:30 2023 -0400
Delete .DS_Store
commit cc601d81e168b6498baec7d095d98c3950e0312f
Merge: c841774 d8879a3
Author: Trinh Nguyen <[email protected]>
Date: Wed Jun 28 16:22:59 2023 -0400
Merge branch 'master' of https://github.com/CBIIT-CGBB/DeepTarget
It seems that it has been resolved. Please check.
Thanks,
Trinh
Thanks @TrinhNguyenP. I can confirm that your recent changes have now been pushed to Bioconductor's git server.
Please remember that you need to bump the version number when making changes to trigger a new build. This is explained in https://github.com/Bioconductor/Contributions#what-to-expect:
To trigger a new build, include a version bump in your commit, e.g., from Version: 0.99.0 to Version: 0.99.1. Push the changes including version bump to your repository on git.bioconductor.org.
Received a valid push on git.bioconductor.org; starting a build for commit id: 58b0cf3382caae9825623040162df7af3038543b
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Bioconductor Build System: ERROR before build products produced.
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/DeepTarget to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @TrinhNguyenP,
The build report shows there are errors you need to fix. In particular, in these lines
dir.create('./result/')
# <Removed some lines for brevity>
saveRDS(List.sim,file = 'Result/similarity_KO_DrugTreatment.RDS')
you create a directory results and then try to save into a directory named Results; this will only work on a case-insensitive filesystem like Windows (e.g., it doesn't work on Ubuntu that the Single Package Builder uses).
Moreover, the vignettes/ and top-level folders are contaminated with .RData, .Rhistory, .DS_Store, .Rproj.user files and directories.
These files need to be removed from git.
Please make these changes and then push an updated version to [email protected]:packages/DeepTarget to trigger a new build.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
On one or more platforms, the build results were: "WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: DeepTarget_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): DeepTarget_0.99.2.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/DeepTarget to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @PeteHaitch, I have pushed changes to Bioconductor's git server and I have checked on my side to see whether these changes have made sucessfully. I still saw the hidden files though I have deleted them before pushing. :-( Can you please give me some suggestions for the next updated version?
Thanks,
Trinh
Received a valid push on git.bioconductor.org; starting a build for commit id: 393fae3105753cafdb97c381a4d99b2cde7e227f