Closed TrinhNguyenP closed 3 months ago
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: <tinh.nguyen@nih.gov>
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
You need a VignetteBuilder entry in DESCRIPTION
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:
Also saw ``` -- re-building ‘Vineggeteanalyses.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 'Vineggeteanalyses.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
git@git.bioconductor.org: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
git@git.bioconductor.org: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 git@github.com:CBIIT-CGBB/DeepTarget.git (fetch)
origin git@github.com:CBIIT-CGBB/DeepTarget.git (push)
upstream git@git.bioconductor.org:packages/DeepTarget.git (fetch)
upstream git@git.bioconductor.org: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
?
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
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 git@git.bioconductor.org: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 <50640811+TrinhNguyenP@users.noreply.github.com>
Date: Wed Jun 28 16:25:30 2023 -0400
Delete .DS_Store
commit cc601d81e168b6498baec7d095d98c3950e0312f
Merge: c841774 d8879a3
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
Date: Wed Jun 28 16:22:59 2023 -0400
Merge branch 'master' of https://github.com/CBIIT-CGBB/DeepTarget
commit c841774a6db03fad3cf61b22f7dbef45c0f68998
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
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 <50640811+TrinhNguyenP@users.noreply.github.com>
Date: Fri Jun 16 16:25:12 2023 -0400
Update README.md
commit b455bb9e0e25676c9e183c38dcf8b0e9286af2d2
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
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 git@git.bioconductor.org: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 <50640811+TrinhNguyenP@users.noreply.github.com> Date: Wed Jun 28 16:25:30 2023 -0400 Delete .DS_Store commit cc601d81e168b6498baec7d095d98c3950e0312f Merge: c841774 d8879a3 Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com> Date: Wed Jun 28 16:22:59 2023 -0400 Merge branch 'master' of https://github.com/CBIIT-CGBB/DeepTarget commit c841774a6db03fad3cf61b22f7dbef45c0f68998 Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com> 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 <50640811+TrinhNguyenP@users.noreply.github.com> Date: Fri Jun 16 16:25:12 2023 -0400 Update README.md commit b455bb9e0e25676c9e183c38dcf8b0e9286af2d2 Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com> 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.
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 git@git.bioconductor.org: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 <50640811+TrinhNguyenP@users.noreply.github.com>
Date: Wed Aug 9 15:08:17 2023 -0500
Fix the name
commit 1a0aa2b1b872f7118d3d2fc8de2d1b9a32d795ae
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
Date: Wed Aug 9 14:56:35 2023 -0500
Registration for maintainer.
commit f5889a02b09bdb0c3fa3bb94f2ddeb0bf5decca1
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
Date: Wed Aug 9 10:48:54 2023 -0500
addressing error from V_analyses.Rmd
commit a8ec76460eaef37d181bcd11261f7e76ecde7ef0
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
Date: Wed Jun 28 16:25:30 2023 -0400
Delete .DS_Store
commit cc601d81e168b6498baec7d095d98c3950e0312f
Merge: c841774 d8879a3
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
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
git@git.bioconductor.org: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 git@git.bioconductor.org: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
git@git.bioconductor.org: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
Did you remove them with a git rm
and then git commit
?
Received a valid push on git.bioconductor.org; starting a build for commit id: 393fae3105753cafdb97c381a4d99b2cde7e227f
Hi @lshep, I missed git commit. I just updated and re-submitted. Thanks, Trinh
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: Linux (Ubuntu 22.04.2 LTS): DeepTarget_0.99.3.tar.gz macOS 12.6.5 Monterey: DeepTarget_0.99.3.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
git@git.bioconductor.org:packages/DeepTarget
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: dbb96cf4b1f94150e5419d78badaf85de0df7121
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: Linux (Ubuntu 22.04.2 LTS): DeepTarget_0.99.4.tar.gz macOS 12.6.5 Monterey: DeepTarget_0.99.4.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
git@git.bioconductor.org:packages/DeepTarget
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @lshep,
Based on the latest build report, I have added my email to the list of bioc-devel.
Can you please suggest me how to fix the error of LaTeX errors and to resolve the warnings?
Thanks,
Trinh
@TrinhNguyenP I believe the LaTeX error is caused by the ạ
(U+1EA1
) character in Sạnju
in the DESCRIPTION
, but I cannot verify on my machine.
The build report also has a number of NOTES
that should be addressed as part of the package review.
Many are self-explanatory but I've provided some guidance for some raised by R CMD check
.
Most, if not all, dependencies should be in Imports
rather than Depends
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'rlang', 'tictoc', 'fgsea', 'ggplot2', 'ggpubr', 'statar',
'interactions', 'reshape2', 'parallel', 'pROC', 'ggrepel', 'grid',
'gridExtra', 'stringb', 'DEGreport', 'readxl', 'stringr'
Many of your functions specify default values for all arguments.
This is not usually done and is I think causing the large number of 'no visible binding for global variable
* checking R code for possible problems ... [26s/26s] NOTE
DMB: no visible binding for global variable Drugname
<many more such cases>
Your documentation seems to use some sort of template but then leaves lots of sections blank. Either fill in these sections or, if they are not relevant, remove them from the documentation.
* checking Rd files ... [0s/0s] NOTE
prepare_Rd: DMB.Rd:37-39: Dropping empty section \details
<many more such cases>
The formatting of the code, both in the documentation and in the source files, makes reviewing and understanding the code much trickier than it needs to be.
R CMD check
and BiocCheck::BiocCheck()
are highlighting specific examples, but it would help the review if you tidy up the formatting of all the code and documentation in the package.
Bioconductor has a style guide (https://contributions.bioconductor.org/r-code.html#coding-style).
The formatR package, by Yihui Xie, makes it easier to clean up poorly formatted code. It can’t do everything, but it can quickly get your code from terrible to pretty good. Make sure to read the introduction before using it.
* checking Rd line widths ... NOTE
Rd file 'DMB.Rd':
\usage lines wider than 90 characters:
DMB(DN = Drugname, GN= GOI, Pred = Pred, Mutant = Mutant, DRS = DRS, GES = GES, plot = TRUE)
<more such examples>
Received a valid push on git.bioconductor.org; starting a build for commit id: 5e94d4334fae76b0832f0a13857b769005ac801a
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: Linux (Ubuntu 22.04.2 LTS): DeepTarget_0.99.5.tar.gz macOS 12.6.5 Monterey: DeepTarget_0.99.5.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
git@git.bioconductor.org:packages/DeepTarget
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7607da805668f5b64285863685d67ae4116a4aff
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: Linux (Ubuntu 22.04.2 LTS): DeepTarget_0.99.6.tar.gz macOS 12.6.5 Monterey: DeepTarget_0.99.6.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
git@git.bioconductor.org:packages/DeepTarget
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 4e54a3995ee7a2685e927a0728f856acc4a1a7a5
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". 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: Linux (Ubuntu 22.04.2 LTS): DeepTarget_0.99.7.tar.gz macOS 12.6.5 Monterey: DeepTarget_0.99.7.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
git@git.bioconductor.org:packages/DeepTarget
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 063f9e2f24120a4c4fd5205e0fe8d9c7cfcb19f4
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". 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: Linux (Ubuntu 22.04.2 LTS): DeepTarget_0.99.8.tar.gz macOS 12.6.5 Monterey: DeepTarget_0.99.8.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
git@git.bioconductor.org:packages/DeepTarget
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@TrinhNguyenP I believe the LaTeX error is caused by the
ạ
(U+1EA1
) character inSạnju
in theDESCRIPTION
, but I cannot verify on my machine.The build report also has a number of
NOTES
that should be addressed as part of the package review. Many are self-explanatory but I've provided some guidance for some raised byR CMD check
.Most, if not all, dependencies should be in
Imports
rather thanDepends
* checking package dependencies ... NOTE Depends: includes the non-default packages: 'rlang', 'tictoc', 'fgsea', 'ggplot2', 'ggpubr', 'statar', 'interactions', 'reshape2', 'parallel', 'pROC', 'ggrepel', 'grid', 'gridExtra', 'stringb', 'DEGreport', 'readxl', 'stringr'
Many of your functions specify default values for all arguments. This is not usually done and is I think causing the large number of 'no visible binding for global variable ` notes.
* checking R code for possible problems ... [26s/26s] NOTE DMB: no visible binding for global variable Drugname <many more such cases>
Your documentation seems to use some sort of template but then leaves lots of sections blank. Either fill in these sections or, if they are not relevant, remove them from the documentation.
* checking Rd files ... [0s/0s] NOTE prepare_Rd: DMB.Rd:37-39: Dropping empty section \details <many more such cases>
The formatting of the code, both in the documentation and in the source files, makes reviewing and understanding the code much trickier than it needs to be.
R CMD check
andBiocCheck::BiocCheck()
are highlighting specific examples, but it would help the review if you tidy up the formatting of all the code and documentation in the package. Bioconductor has a style guide (https://contributions.bioconductor.org/r-code.html#coding-style).The formatR package, by Yihui Xie, makes it easier to clean up poorly formatted code. It can’t do everything, but it can quickly get your code from terrible to pretty good. Make sure to read the introduction before using it.
* checking Rd line widths ... NOTE Rd file 'DMB.Rd': \usage lines wider than 90 characters: DMB(DN = Drugname, GN= GOI, Pred = Pred, Mutant = Mutant, DRS = DRS, GES = GES, plot = TRUE) <more such examples>
Dear @PeteHaitch, Based on the last update, there is an" ERROR: At least 80% of man pages documenting exported objects must have runnable examples.". When I test locally by installing and then run example under Examples in R without problems. Can you please give me some suggestions?
Thanks, Trinh
"ERROR: At least 80% of man pages documenting exported objects must have runnable examples" this means that you have man pages without examples. You need to find which these are, and add an example(s) or explain why there isn't one.
Received a valid push on git.bioconductor.org; starting a build for commit id: 900376fd6fa949b4287b48e8363db4ac9a9f5e98
Thanks @PeteHaitch, Trinh
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Received a valid push on git.bioconductor.org; starting a build for commit id: 677748316e7dbf411787c077c908d16b463375af
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