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Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation #2275

Closed Danis102 closed 1 year ago

Danis102 commented 3 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

Submitter: There are very few specific warnings/errors: for example that we don't have enough run-able examples, using too much of \donttest{}. But since our package depend on user provided references for best function, we cannot provide good examples with fully functional code all the time. We have, however, tried to provide as many self-sustained examples as possible. We hope that this is something reviewers may test and comment on during the review process, but we have tried to fix all R CMD checks and BioChecks as far as we can without disturbing package examples and fuctions

I am familiar with the essential aspects of Bioconductor software management, including:

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.

jianhong commented 2 years ago

Package 'seqpac' Review

The package passed check and build. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review.

The DESCRIPTION file

The CITATION file

R code

Documentation

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d17dc4d11799ac1b69214d7e7dc0c5e697038bb2

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3d55cfbb7c521325643242bde30d98f15468f4f8

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 51bf8715a86980e6a5e23786149ab26b1baa8faa

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0942651c661e693ea1944d1ee4b319e6efdeb9d1

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Danis102 commented 2 years ago

Dear Jianhong (please forgive me if I got the name wrong),

We have now completed the revision of our package following the recommendations in your review comments to the best of our ability. It seems, our package has passed on the Linux, Mac and Window servers. While most of the issues have been resolved there are a few that remain. Those issues, however, we are unable to resolve further without your feedback. All is explained in the attached pdf where we respond to all comments, issue by issue, “line” by “line”. Please tell us if you have any more requests. And please receive our gratitude and thanks for the feedback on our package.

Yours sincerely, Professor Daniel Nätt (chief developer of Seqpac)

From: JIANHONG OU @.> Sent: Tuesday, 25 October 2022 15:15 To: Bioconductor/Contributions @.> Cc: Daniel Nätt @.>; Mention @.> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Package 'seqpac' Review

The package passed check and build. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review.

The DESCRIPTION file

The CITATION file

R code

Documentation

— Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-1290533275&data=05%7C01%7Cdaniel.natt%40liu.se%7C4c4f41472ec64c43b56c08dab68adf18%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638023004839769053%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1B51YdlLS6Ymg%2F5FUfM2cNwndJaMQwu7JrQFpt5M858%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUX3QKFZGOSYL6SJTJOTWE7ML3ANCNFSM5DZM52BA&data=05%7C01%7Cdaniel.natt%40liu.se%7C4c4f41472ec64c43b56c08dab68adf18%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638023004839925736%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e%2BZDZR36vrhXA5rYBRhQYOFTTDy661OHlt5y22pkh7M%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.**@.>>

Danis102 commented 2 years ago

Dear Jianhong, This is a gentle reminder of the resubmission of our package, Seqpac. A few weeks ago, we bumped a new version of Seqpac that we believe would meet all remaining issues. The few notes that still remains are commented in the attached pdf. We are currently in revision with a manuscript in Bioinformatics (journal), that will present Seqpac for a wider audience. Several reviewers request that Seqpac is published on Bioconducter prior of getting published in Bioinformatics. Since the time given for the revision is about to run out, we are keen to hear about the progress of our submission to Bioconductor. Would we expect a decision shortly? And when it is accepted in Bioconductor, what is the timeline until it will appear in Bioconductor – development? Weeks? Months?

Yours sincerely, Professor Daniel Nätt (chief developer of Seqpac)

From: Daniel Nätt Sent: Wednesday, November 2, 2022 6:23 PM To: Bioconductor/Contributions @.***> Subject: RE: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Dear Jianhong (please forgive me if I got the name wrong),

We have now completed the revision of our package following the recommendations in your review comments to the best of our ability. It seems, our package has passed on the Linux, Mac and Window servers. While most of the issues have been resolved there are a few that remain. Those issues, however, we are unable to resolve further without your feedback. All is explained in the attached pdf where we respond to all comments, issue by issue, “line” by “line”. Please tell us if you have any more requests. And please receive our gratitude and thanks for the feedback on our package.

Yours sincerely,

From: JIANHONG OU @.**@.>> Sent: Tuesday, 25 October 2022 15:15 To: Bioconductor/Contributions @.**@.>> Cc: Daniel Nätt @.**@.>>; Mention @.**@.>> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Package 'seqpac' Review

The package passed check and build. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review.

The DESCRIPTION file

The CITATION file

R code

Documentation

— Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-1290533275&data=05%7C01%7Cdaniel.natt%40liu.se%7C4c4f41472ec64c43b56c08dab68adf18%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638023004839769053%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1B51YdlLS6Ymg%2F5FUfM2cNwndJaMQwu7JrQFpt5M858%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUX3QKFZGOSYL6SJTJOTWE7ML3ANCNFSM5DZM52BA&data=05%7C01%7Cdaniel.natt%40liu.se%7C4c4f41472ec64c43b56c08dab68adf18%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638023004839925736%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e%2BZDZR36vrhXA5rYBRhQYOFTTDy661OHlt5y22pkh7M%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.**@.>>

jianhong commented 2 years ago

Package 'seqpac' Review

The package passed check and build. However the package still need to be improved. Please try to answer the comments line by line when you are ready for a second review. Please make sure cover all the review comments. Otherwise it will take another round of review. And I did not see any attachment of pdf for last revise. Maybe I missed something.

General package development

R code

Danis102 commented 2 years ago

Dear Jianhong, That is very strange, that you cannot find an attached pdf. I double ckecked and it was included in the original email that was sent immediately following our latest bumb, as well as in the our gentle request for a an update that was sent yesterday. Maybe your email server removes certain kind of attachments or you search the wrong email. Nonetheless, to this email I have attached both a pdf and doc version of the responses. It is important that our responses reaches you. Some of the remaining issues we are discussing in our responses. Of particular importance, is our response to the use of “Message” instead of “cat” and the discussion about text color options that is very limited in “Message”. Changing “cat” to “Message” will disrupt the very intention with our color scheme. We are happy to improve our package, and are very grateful for your comments, but if you wants us to change to “Message”, you must provide us with an alternative that doesn’t destroy the integrity of our package.

Yours sincerely, Daniel

From: Daniel Nätt Sent: Monday, November 21, 2022 4:15 PM To: Bioconductor/Contributions @.***> Subject: RE: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Dear Jianhong, This is a gentle reminder of the resubmission of our package, Seqpac. A few weeks ago, we bumped a new version of Seqpac that we believe would meet all remaining issues. The few notes that still remains are commented in the attached pdf. We are currently in revision with a manuscript in Bioinformatics (journal), that will present Seqpac for a wider audience. Several reviewers request that Seqpac is published on Bioconducter prior of getting published in Bioinformatics. Since the time given for the revision is about to run out, we are keen to hear about the progress of our submission to Bioconductor. Would we expect a decision shortly? And when it is accepted in Bioconductor, what is the timeline until it will appear in Bioconductor – development? Weeks? Months?

Yours sincerely, Professor Daniel Nätt (chief developer of Seqpac)

From: Daniel Nätt Sent: Wednesday, November 2, 2022 6:23 PM To: Bioconductor/Contributions @.**@.>> Subject: RE: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Dear Jianhong (please forgive me if I got the name wrong),

We have now completed the revision of our package following the recommendations in your review comments to the best of our ability. It seems, our package has passed on the Linux, Mac and Window servers. While most of the issues have been resolved there are a few that remain. Those issues, however, we are unable to resolve further without your feedback. All is explained in the attached pdf where we respond to all comments, issue by issue, “line” by “line”. Please tell us if you have any more requests. And please receive our gratitude and thanks for the feedback on our package.

Yours sincerely,

From: JIANHONG OU @.**@.>> Sent: Tuesday, 25 October 2022 15:15 To: Bioconductor/Contributions @.**@.>> Cc: Daniel Nätt @.**@.>>; Mention @.**@.>> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Package 'seqpac' Review

The package passed check and build. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review.

The DESCRIPTION file

The CITATION file

R code

Documentation

— Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-1290533275&data=05%7C01%7Cdaniel.natt%40liu.se%7C4c4f41472ec64c43b56c08dab68adf18%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638023004839769053%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1B51YdlLS6Ymg%2F5FUfM2cNwndJaMQwu7JrQFpt5M858%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUX3QKFZGOSYL6SJTJOTWE7ML3ANCNFSM5DZM52BA&data=05%7C01%7Cdaniel.natt%40liu.se%7C4c4f41472ec64c43b56c08dab68adf18%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638023004839925736%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e%2BZDZR36vrhXA5rYBRhQYOFTTDy661OHlt5y22pkh7M%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.**@.>>

jianhong commented 2 years ago

This review process will not receive attachment as normal email. You can insert hyperlink of online resources. Forget the cat issue and please go ahead to address the other issues.

Jianhong.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2d49ca6a42534c2a581af073bd3feaa3354446e6

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2ee20ceb33ac40a1915f6eeefafdef4ac96c622a

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d70699171a9d440d5123d7dc654c173fd3e91ec7

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 70233391894c4c165e4c866864afdcceda747ad6

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Danis102 commented 2 years ago

Dear Jianhong, Our package was successfully built and tested on all three platforms. We hope that all remaining issues has now been fixed, and Seqpac can proceed in becoming a full member of Bioconductor. Please indicate as soon as possible if this is not the case. As we indicated before, we are currently in review with an article in Bioinformatics in which several reviewers demand that Seqpac is being accepted in Bioconductor prior of publishing the paper. The deadline for submitting a revised manuscript is quickly approaching. Below are our responses to your last review comments. Thank you! Yours sincerely, Daniel Nätt (Associate professor and chief developer of Seqpac)

Package 'seqpac' Review

The package passed check and build. However the package still need to be improved. Please try to answer the comments line by line when you are ready for a second review. Please make sure cover all the review comments. Otherwise it will take another round of review. And I did not see any attachment of pdf for last revise. Maybe I missed something.

General package development

Response: Fixed!

Response: This is a result of the package failing to complete in time on your Mac server. For testing internally, by our own group members, we have two additional test files. These tests are more extensive and will take time, which will probably result in the Mac server time limit problem again (mark well that Linux and Windows don't fail). However, all functions now have self running examples. Thanks to this Bioconductor review, no function are excluded using dontrun(). Eventhough the additional testthat tests are a little bit more extensive and time consuming, much of the package are tested in the examples. However, if you insist and provide more time for completing the tests on your servers, we can easily provide a more complete pack of unit tests.

R code

Response: This was responded to in our previous reviews. In recent discussion with the reviewer, he/she told us to disregard this issue (see below email). For a reminder we post our original argument here: "Warning() and message() will produce red text. We use these functions when we like to draw the attention of the user to a specific important issue. Cat() is used to give the user feedback on the progress. You must understand that many of our functions are used on very large file that may take hours to process. Not given any feedback might indicate to the user that something is wrong even if it isn't. Progress messages must not be in red. If it is in red, according to our color convention, it would indicate that something is wrong. When a warning is finally given, this will be "drowned" in the regular progression messages. Thus, users will likely miss an important issue with their analysis. Unless you can suggest how to turn message() into black text, we hope you may allow us to use cat() instead of message(). When proper warnings are at place then we always use warning()."

Response: We believe this is fixed now. We cannot replace paste with file.path completely. File names cannot be constructed using file.path only (results in path/Full_reanno/.Rdata in the example above when it should be path/Full_reanno.Rdata). However, we have limited paste0 to be used only to construct the file name and not path.

Response: Tank you. We finally understand the problem with "/". Sorry for being so slow minded. No function was mentioned here, though. Found the above mentioned code in PAC_mapper and have changed it accordingly. Corrected a few more in for example make_counts.

Response: All fixed!

Response: Fixed!

opt_sci <- options(scipen=999)

on.exit(options(scipen=opt_sci))

....

options(scipen=opt_sci)

on.exit()

return(plots)

Response: Found a few places where option() were used and changed them accordingly. We have tried to avoid changing the options as far as possible. Didn't think Seqpac had any left. Thank you for making us aware. Fixed!

- Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-1322416407&data=05%7C01%7Cdaniel.natt%40liu.se%7C326c887bad3a43694ace08dacbe62b48%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638046486677837161%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UKXxAZ6rhaZoSDZ9r0x5bGtHgDyRT1w5eFcfueOGBmE%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUX3K5QGRUNVKXSCY3BTWJOWVRANCNFSM5DZM52BA&data=05%7C01%7Cdaniel.natt%40liu.se%7C326c887bad3a43694ace08dacbe62b48%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638046486677837161%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2KTWjohPly7CTaTd8Aiu%2BWWx%2B6nqsZtn5vAuvBE6Wzw%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

From: JIANHONG OU @.> Sent: Tuesday, November 22, 2022 2:41 PM To: Bioconductor/Contributions @.> Cc: Daniel Nätt @.>; Mention @.> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

This review process will not receive attachment as normal email. You can insert hyperlink of online resources. Forget the cat issue and please go ahead to address the other issues.

Jianhong.

- Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-1323696019&data=05%7C01%7Cdaniel.natt%40liu.se%7Cef367ca6a674441bca0808dacc8f2e33%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638047212569141825%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OP9g7nh9czI%2BDX%2BBZdC4jP6EjRNqqB8HfmNhscCraCs%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUX6X27EBS2W24D6MYVTWJTEONANCNFSM5DZM52BA&data=05%7C01%7Cdaniel.natt%40liu.se%7Cef367ca6a674441bca0808dacc8f2e33%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C638047212569141825%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2LzothnMX4sIw40m4W9TyLgTX%2FEaTYm9W18uqNxezo0%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.**@.>>

bioc-issue-bot commented 1 year ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

lshep commented 1 year ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/Danis102.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("seqpac"). The package 'landing page' will be created at

https://bioconductor.org/packages/seqpac

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.