Closed kkdey closed 7 years ago
Hi @kkdey
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: Logolas
Type: Package
Title: Flexible and Customized Logo Plots using symbols, alphabets, numbers and alphanumeric strings
Version: 0.0.1
Date: 11.5.2016.
Author: c(
person("Kushal", "Dey", email = "kkdey@uchicago.edu", role = c("aut","cre")),
person("Matthew", "Stephens", email = "stephens999@gmail.com", role ="ctb"))
Maintainer: Kushal Dey <kkdey@uchicago.edu>
Description: Produces logo plots of a variety of symbols and names comprising English alphabets, numerics and punctuations. Can be used for sequence motif generation, mutation pattern generation, protein amino acid geenration and symbol strength representation in any generic context.
License: GPL (>= 2)
LazyData: TRUE
Depends: R (>= 3.3), grid
URL: https://github.com/kkdey/Logolas
Imports:
grid,
graphics
Suggests:
knitr, BiocStyle, Biobase, roxygen2, devtools, xtable, gridExtra, RColorBrewer, aRxiv
VignetteBuilder: knitr
biocViews: SequenceMatching, Alignment, Software, Visualization
RoxygenNote: 5.0.1
Your package has been approved for building. Your package is now submitted to our queue.
IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.
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: "WARNINGS". 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/Logolas_buildreport_20161106083432.html
Received a valid push; starting a build. Commits are:
3614cb5 fixed a citation
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: "WARNINGS". 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/Logolas_buildreport_20161106095008.html
It seems I am getting the warning for the version number
Currently my version number is 0.99.1. I am wondering what should I put as version number?
Thank you
Received a valid push; starting a build. Commits are:
36133a2 updated the desription
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: "WARNINGS". 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/Logolas_buildreport_20161106101843.html
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.
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: "WARNINGS". 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/Logolas_buildreport_20161212083738.html
We updated our builders so I manually reran a build of your package. I will be reviewing shortly and provide any additional feedback.
I'm looking forward to working with you on getting your package submitted to Bioconductor.
Lori
Thank you so much !! Looking forward too
Kushal
On 12 December 2016 at 07:39, lshep notifications@github.com wrote:
We updated our builders so I manually reran a build of your package. I will be reviewing shortly and provide any additional feedback. I'm looking forward to working with you on getting your package submitted to Bioconductor. Lori
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/186#issuecomment-266432937, or mute the thread https://github.com/notifications/unsubscribe-auth/AJFRjEA--hOul1Lm4u9SdMXqILY_Gu8Wks5rHU6GgaJpZM4KqbsW .
-- Kushal K. Dey Graduate Student 4th Year, Department of Statistics University of Chicago Contact: +1 312-709-0680 | kkdey@uchicago.edu
Hello, Thank you for your submission. A few comments:
General:
Vignette:
R code:
if(plot){ }
in all the individual 7letter/Aletter/etc and then just have a call to that function. R/Rd/man files:
@rdname or @describeIn
that will concatenate documentation files together. Any repeated arguments don't need to be repeated but any unique arguments will be added to the appropriate sections. Please respond back here after updates stating what has changed or any clarification/justification for current implementation. I think it is very close to acceptance.
Lori
Great points...I will fix up these issues and get back to you.. Thanks for looking into this
Kushal
On 13 December 2016 at 09:05, lshep notifications@github.com wrote:
Hello, Thank you for your submission. A few comments:
General:
- Please fix the WARNINGS/NOTES in the build report. While they may seem trivial we like to have clean reports upon submission
- Please remove the Logolas.Rproj file from top directory and any other non essential files/hidden files
Vignette:
- Please add the downloading from Biocondcutor information to your README file as well
- Remove the intermediate folders/files from the directory
- I think it might be worth while to show in the first example that the user could also use p@pwm as input from seqLogo [not just m and set the colnames/rownames]. This of course is optional.
R code:
- Clarification question: what is the difference between addlogos_text and addlogos? Could these be different?
- Please use seq_len()/seq_along() rather than 1:n/1:length(x)
- We like to not duplicate code chunks that get used repeatedly. I would suggest having a plotting function that contains the code in if(plot){ } in all the individual 7letter/Aletter/etc and then just have a call to that function.
R/Rd/man files:
- I would also suggest having one man file for all the <>letter.R functions. The arguments are all (or nearly all the same and seems a waste to be repeated. There is a documenting syntax that can be used @rdname or @describeIn that will concatenate documentation files together. Any repeated arguments don't need to be repeated but any unique arguments will be added to the appropriate sections.
Please respond back here after updates stating what has changed or any clarification/justification for current implementation. I think it is very close to acceptance.
Lori
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/186#issuecomment-266761860, or mute the thread https://github.com/notifications/unsubscribe-auth/AJFRjJHsKFUP1mylkvl6t80vF-RHdWGKks5rHrQsgaJpZM4KqbsW .
-- Kushal K. Dey Graduate Student 4th Year, Department of Statistics University of Chicago Contact: +1 312-709-0680 | kkdey@uchicago.edu
@kkdey Just wanted to check in to see how the updates were going. Did you have any questions? When you have committed changes, please bump the version so a new build will generate and please respond back here with what of the above recommendations were addressed.
Hi Ishep,
Sure!!
I got caught up with some work in the middle but now am working on it and also adding a few more updates. I am hoping to be able to submit the updated version by the end of next week. I apologise for not being very responsive in that thread and causing delay on this.
Thanks
Kushal
On Jan 23, 2017 5:51 AM, "lshep" notifications@github.com wrote:
@kkdey https://github.com/kkdey Just wanted to check in to see how the updates were going. Did you have any questions? When you have committed changes, please bump the version so a new build will generate and please respond back here with what of the above recommendations were addressed.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/186#issuecomment-274469291, or mute the thread https://github.com/notifications/unsubscribe-auth/AJFRjEEl96chkS0um09mMs_SK0XLBBadks5rVJQ8gaJpZM4KqbsW .
No apologizes necessary. Just wanted to make sure you weren't waiting on anything from our end and that everything was going smoothly. It looks like an interesting package and is very close to acceptance.
Received a valid push; starting a build. Commits are:
9401f81 updated logolas
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: "WARNINGS". 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/Logolas_buildreport_20170130011109.html
Received a valid push; starting a build. Commits are:
3b1df85 used rdname on the letters functions
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: "WARNINGS". 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/Logolas_buildreport_20170130024711.html
Received a valid push; starting a build. Commits are:
975fc9d bumped up the 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: "WARNINGS". 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/Logolas_buildreport_20170130025215.html
Received a valid push; starting a build. Commits are:
1933702 put .Rproj file under .gitignore
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: "WARNINGS". 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/Logolas_buildreport_20170130025634.html
Hi Lori,
Thanks for the great suggestions. I have addressed your comments.
General:
I have fixed warnings under 'R CMD Check'. It now shows 1 Note which is because I am using Travis CI to track my package build and 'R CMD Check' does not like the .travis.yml file in the folder. May I keep the .travis.yml file in the folder ? I find it useful !! Also the 'BiocCheck' gives me a warning message "y of x.y.z version should be even in release" which I am not sure how to address
I have removed the Logolas.Rproj file.
Vignette:
R code
You asked about the distinction between addlogos_text and addlogos. addlogos allows an user to give a shorthand expression for a new symbol letter that he adds to the library. I have updated the vignette to give an example of how a user may use a shorthand for the actual symbol "Lambda". I found this to be helpful specially when dealing with strings comprising of many symbols that an user would add to her personal library of logos. Shortand for the symbols would keep the strings shorter.
replaced 1:n/1:length(x) by seq_len and seq_along
added a new plotting function get_plot()
and replaced all the codes inside plot(){}
by the get_plot()
function
Rd/Man
Would love to hear what you think of the changes that have been made.
Best
Kushal
Thank you for your changes. I think it makes it much easier to use and has madeyour code more efficient. Last few minor notes and once these are addressed I believe we will be able to accept your package.
travis.yml - If you would like to keep for your own use just please make sure when you upload to bioconductor you do not include this file.
vignettes: It appears there is only one figure that you actually call instead of generate interactively (figures/logolas_arxiv_1.png) . Is there a reason this figure can not be generated by the code and thereby allowing you to remove the figures directory?
The warning in BiocCheck WARNING: Update R version dependency from 3.3 to 3.4. Please update the version dependency in your DESCRIPTION file to be R (>= 3.4)
Thank you for your efforts. Once these changes are implemented please do a version bump. If all is well I'll mark your package as accepted. Once accepted please leave your issue open. You will receive an email (normally within a week) with instructions on how to upload your package to Bioconductor.
Received a valid push; starting a build. Commits are:
406cd4f removed figures, updated vignette
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 following build report for more details:
http://bioconductor.org/spb_reports/Logolas_buildreport_20170131000447.html
Hi Ishep,
I have removed the "figures" folder and running that chunk now. Also removed .travis.yml. R CMD Check is not showing me any NOTE or WARNING. Also updated the R dependency from 3.3 to 3.4.
Thanks for all the great suggestions. Let me know if things look alright.
Best
Kushal
Received a valid push; starting a build. Commits are:
59ad4c1 changed the README slightly
Received a valid push; starting a build. Commits are:
c1c9722 addressing version bump error
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 following build report for more details:
http://bioconductor.org/spb_reports/Logolas_buildreport_20170131002803.html
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 following build report for more details:
http://bioconductor.org/spb_reports/Logolas_buildreport_20170131003034.html
Received a valid push; starting a build. Commits are:
04b08da some minor fizes to the README
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 following build report for more details:
http://bioconductor.org/spb_reports/Logolas_buildreport_20170131003658.html
All set. Again please leave the issue open and you should receive svn instructions within the next week. Thank you!
thanks a lot !!
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