bioc-issue-bot
commented
6 years ago Received a valid push; starting a build. Commits are:
be7d411 Updated the package based on review comments.
Closed divy-kangeyan closed 6 years ago
bioc-issue-bot
commented
6 years ago Received a valid push; starting a build. Commits are:
be7d411 Updated the package based on review comments.
bioc-issue-bot
commented
6 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: "skipped, 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.
Liubuntu
commented
6 years ago HI @Divyagash ,
The cpgDensity function has these arguments of organism, and passed to the other 2 functions of GenomeInfoDb::seqlevelsStyle() and Repitools::cpgDensityCalc, which has required different format for the input. If the values to organism are fixed, it would be suggested to use the match.arg for an automatic check of input. Is there a way that you could pass the character input and evaluate as a BSgenome after the match.arg()?
For your other question about genome argument, you should at least specify the input values as in your example code in the @parameter documentation. Because it only takes Hsapiens for Homo Sapiens, or Mmusculus which could confuse the users for what to type in for other species.
In general, you could figure out some other solution for these kind of problems, and make sure to document them appropriately.
Please comment back if you are ready for a 2nd review.
Best, Qian
bioc-issue-bot
commented
6 years ago Received a valid push; starting a build. Commits are:
020c2ad version bump
bioc-issue-bot
commented
6 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: "skipped, 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.
divy-kangeyan
commented
6 years ago Hi @Liubuntu, I think I have addressed the comments that you pointed in the first review. Please take a look at the package for the 2nd review.
Thank you, Divy
Liubuntu
commented
6 years ago Hi,
Please check out the following comments and seek to address them. Comment back with any question and when you have fixed all and bumped the version.
scmeth.R is not generated in this repo. (try add a white space after #' for those don't).repMask and cpgDensity, the argument organism used Hsapiens or Mmusculus in the example, but mentioned in documentation with full name, which is not clear to users by only seeing the documentation. You can make it clearer by adding the abbreviated name in documentation: @parameter organism scientific name of the organism of interest, e.g. Mus musculus(Mmusculus) or Homo sapiens(Hsapiens).vignettes/my-vignette_files/figure-html/unnamed-chunk-6-1.png here? Seems it is not used inside your vignette. You should remove all unnecessary files here.library(scmeth) into new section 2, e.g., 2. Installation and package loading. Remove the library(scmeth) in following codes.library(scmeth) in your vignette, you don't need to add scmeth:: before calling any function.
-typo: "1. Introduction... scmeth package offers a few functions to asseess the quality of the methylation data."3. Input files: ... can be read via loadHDF5SummarizedExperiment function in SummarizedExperiment package.. This function is now in HDF5Array package. Please be consistent throughout.Cheers! Qian
bioc-issue-bot
commented
6 years ago Received a valid push; starting a build. Commits are:
1e49b4b Updated according to second review
bioc-issue-bot
commented
6 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: "skipped, 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.
divy-kangeyan
commented
6 years ago Hi @Liubuntu, I have updated the package according to the comments. Please take a look. Thank you, Divy
Liubuntu
commented
6 years ago Hi @Divyagash ,
Thanks for your efforts in contributing to Bioconductor. You package is accepted. Wish you success in your career, and Happy Chinese New Year!
Cheer, Qian
bioc-issue-bot
commented
6 years ago Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.
Thank you for contributing to Bioconductor!
mtmorgan
commented
6 years 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/Divyagash.keys is not empty), then no further steps are required. Otherwise, do the following:
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 biocLite(\"scmeth\"). The package 'landing page' will be created at
https://bioconductor.org/packages/scmeth
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.
divy-kangeyan
commented
6 years ago Hi @Liubuntu, Thank you for your time and suggestions for improving the package. Happy Chinese New Year to you as well.
Divy
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