samexplorer RNA-seq depth analysis

shaileshtripathi commented 8 years ago

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mtmorgan commented 8 years ago

@shaileshtripathi Have you contacted the Rsubread authors with a (pull?) request to expose the API you are interested in?

shaileshtripathi commented 8 years ago

@mtmorgan No, I did not , we used their code available from bioconductor because our approach is related to the "sequence depth analysis" which is related with the random sample of sequence depth and did not find any function in Rsubread which allows to do so, therefore we made some modification inside the code.

mtmorgan commented 8 years ago

@shaileshtripathi you'll have to help me see what you've done by cleaning up the code to include essential functionality and a clear 'diff' between the source files in Rsubread and your own source files. I'm very reluctant for you to simply copy Rsubread's source code, because this means that bug fixes and improvements in Rsubread are not propagated to your package. Rather than 'Have you contacted...' I should have said 'Contact the Rsubread authors with a pull request to expose the API you are interested in'.

shaileshtripathi commented 8 years ago

@mtmorgan Ok, thanks ya sure I will contact them regarding to use API according to my need.

bioc-issue-bot commented 8 years ago

Received a valid push; starting a build. Commits are:

0a72b9f minor correction 1

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bioc-issue-bot commented 8 years ago

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bioc-issue-bot commented 8 years ago

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bioc-issue-bot commented 8 years ago

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bioc-issue-bot commented 8 years ago

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bioc-issue-bot commented 8 years ago

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bioc-issue-bot commented 8 years ago

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bioc-issue-bot commented 8 years ago

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mtmorgan commented 8 years ago

It looks like your package is almost ready for review. Can you clean up the missing imports and other notes and warnings from the build report, and subscribe to the Bioconductor 'devel' mailing list to remove the remaining ERROR flag? I will then review this package.

Alternatively, if you'd like to continue to develop your package before review, please remove the web hook and close this issue, develop it on your own system, and when ready open a new issue?

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mtmorgan commented 8 years ago

It looks like your package still includes Rsubread code rather than using functionality exposed by the Rsubread package or other Bioconductor tools. Also, it looks like there are additional easily corrected errors or warnings. I suggest either that the package be updated to avoid using Rsubread code directly and that the R code be updated to address the minor remaining issues, or that we close the issue and you can resubmit when you've had a chance to revise your package in line with these requirements.

From what I understand, you have been in touch with the Rsubread author and they have given you guidance on how to avoid using Rsubread C code directly. Please let me know promptly how you would like to proceed.

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bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

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If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

Dear Package contributor,

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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.

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http://bioconductor.org/spb_reports/samExploreR_buildreport_20160913095904.html

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

de5cdd4 new data added

bioc-issue-bot commented 7 years ago

Dear Package contributor,

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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 following build report for more details:

http://bioconductor.org/spb_reports/samExploreR_buildreport_20160913100549.html

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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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.

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http://bioconductor.org/spb_reports/samExploreR_buildreport_20160913101708.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

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bioc-issue-bot commented 7 years ago

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shaileshtripathi commented 7 years ago

Hi Martin,

We have removed the dependencies of samExploreR on Rsubread I updated it long ago but it is not accepted yet, can you please take a look on that.

Best, Shailesh

On Tue, Aug 2, 2016 at 1:36 PM, Martin Morgan notifications@github.com wrote:

@shaileshtripathi https://github.com/shaileshtripathi you'll have to help me see what you've done by cleaning up the code to include essential functionality and a clear 'diff' between the source files in Rsubread and your own source files. I'm very reluctant for you to simply copy Rsubread's source code, because this means that bug fixes and improvements in Rsubread are not propagated to your package. Rather than 'Have you contacted...' I should have said 'Contact the Rsubread authors with a pull request to expose the API you are interested in'.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/62#issuecomment-236890798, or mute the thread https://github.com/notifications/unsubscribe-auth/ATkbzHL81-9w1axpv7TTTb9SOx5FokURks5qbznGgaJpZM4JO7QV .

mtmorgan commented 7 years ago

I asked for clarification on the status of your package on August 23, and when you did not respond declined the package on September 7. I take it you would now like your package to be considered for review. I will re-open the issue, and will proceed with a review when the remaining warnings and errors are addressed; see the most recent build report.

bioc-issue-bot commented 7 years ago

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Bioconductor / Contributions

samexplorer RNA-seq depth analysis #62