Closed divy-kangeyan closed 6 years ago
Received a valid push; starting a build. Commits are:
be7d411 Updated the package based on review comments.
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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
Received a valid push; starting a build. Commits are:
020c2ad version bump
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.
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
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
Received a valid push; starting a build. Commits are:
1e49b4b Updated according to second review
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.
Hi @Liubuntu, I have updated the package according to the comments. Please take a look. Thank you, Divy
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
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.
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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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