Closed hillarykoch closed 6 years ago
Hello,
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BUILD REPORT
README
VIGNETTE/CODING:
NOTE I'm not going to insist on this, given that a class designed for this seems slightly overkill and its reuse would be unlikely, but for future reference you may consider designing packages with a designated class structure (S4 class) for output and input to other functions/methods (reusing any Bioconductor infastructure is most ideal). This is a more formalized way to define output/input and we strongly suggest it. This also allows for easier customized accessor methods, show methods, etc .... Given that the output is more list like and variable with statistical output, again I won't insist on it but just something to keep in mind for future Bioconductor submissions.
Please address the above issues and/or comment with clarification or justification. When you are ready for another review ensure that a new build is generated with a version bump and comment back here in some way addressing the above concerns for a second review. Thank you.
Cheers.
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Thank you @lshep for your helpful comments. I have made several changes to the package in response to your recommendations.
Build Report
README I took the Bioconductor installation instructions out because I thought maybe I was being a little bit premature. I put it back, however.
Vignette/Coding
NOTE I thought about S4 classes much after I started this project, but decided against it because I thought it might be a lot of trouble for such simple data types. Definitely for future development I need to (and am) familiarize myself with the selection of classes out there and make sure that code is in line with relevant S4 classes for given assays.
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4789b2a Add reference to desponds in vignete
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30559c2 add external data to parse.Rd man file
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Received a valid push; starting a build. Commits are:
fa9a6d4 adjust unicode error
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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Dear Package contributor,
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push; starting a build. Commits are:
579697e revert to old version
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86a2ee4 revert to old version
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.
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.
Received a valid push; starting a build. Commits are:
470f5b0 revert to old version
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.
Received a valid push; starting a build. Commits are:
eff32e7 revert to old version
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Thank you for your updates a few more comments below:
Vignette
Cheers
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61a319e change 1:n to seq_len in vignette
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Hi @lshep
Thanks, I changed the vignette. The my paper thing was just a placeholder for me so that I could go back and drop the paper reference in there, when available. Our paper is in its final stages before submitting to a journal, and we wanted to be able to point to a package available when submitting. Currently there is no pre-print as one of the data sets we analyzed is unpublished and the data generators are not ready to publish it yet. However, we could possibly have a preprint in the near future. Of course I am happy to change the "my paper " to whatever you think is appropriate.
Cheers-
Maybe add a my paper(pending) or something similar like a coming soon... so that users aren't confused
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829db50 mark my paper as pending
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