Closed VilainLab closed 5 years ago
Hi @VilainLab
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: nanotatoR
Title: nanotatoR: next generation structural variant annotation and classification
Version: 0.99.0
Author: Surajit Bhattacharya,Hayk Barsheghyan, Emmanuele C Delot and Eric Vilain
Maintainer: Surajit Bhattacharya <sbhattach2@childrensnational.org>
Description: Whole genome sequencing (WGS) has successfully been used to identify single-nucleotide variants (SNV), small insertions and deletions and, more recently, small copy number variants. However, due to utilization of short reads, it is not well suited for identification of structural variants (SV) and the majority of SV calling tools having high false positive and negative rates.Optical next-generation mapping (NGM) utilizes long fluorescently labeled native-state DNA molecules for de novo genome assembly to overcome the limitations of WGS. NGM allows for a significant increase in SV detection capability. However, accuracy of SV annotation is highly important for variant classification and filtration to determine pathogenicity.Here we create a new tool in R, for SV annotation, including population frequency and gene function and expression, using publicly available datasets. We use DGV (Database of Genomic Variants), which contains SVs from 7965 individuals, to calculate the population frequency of the SVs identified by the Bionano SVCaller in the NGM dataset of a cohort of 50 undiagnosed patients with a variety of phenotypes. The new annotation tool, nanotatoR, also calculates the internal frequency of SVs, which could be beneficial in identification of potential false positive or common calls. The software creates a primary gene list (PG) from NCBI databases based on patient phenotype and compares the list to the set of genes overlapping the patient’s SVs generated by SVCaller, providing analysts with an easy way to identify variants affecting genes in the PG. The output is given in an Excel file format, which is subdivided into multiple sheets based on SV type. Users then have a choice to filter SVs using the provided annotation for identification of inherited, de novo or rare variants. nanotatoR provides integrated annotation and the expression patterns to enable users to identify potential pathogenic SVs with greater precision and faster turnaround times.
Depends:
R (>= 3.4.3)
Imports:
hash(>= 2.2.6),
openxlsx(>= 4.0.17),
biomaRt(>= 2.34.2),
rentrez(>= 1.1.0),
stats,
grDevices,
graphics,
grDevices,
stringr,
graphics,
knitr,
utils
Suggests:
rmarkdown,
testthat,
yaml
VignetteBuilder:
knitr
License: GPL-2
biocViews: Software, WorkflowStep, Annotation
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
URL: https://github.com/VilainLab/Nanotator
BugReports: https://github.com/VilainLab/Nanotator/issues
Please update your vignette (lower-case directory name, please) to have evaluated code chunks, so that the user is confident that the code actually works.
A reviewer has been assigned to your package. Learn what to expect during the review process.
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: "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.
Please fix the ERROR on the build report before a technical review will take place.
A reminder - There is only a week until the deadline for the 3.8 release - if the package does not undergo review and be accepted by this date it will remain in Bioconductor devel and be in release 3.9.
Please fix all ERROR on the builder report before a technical review will take place.
Hello, Thanks for the reply. I have made the appropriate changes and also done a version bump, but it seems like it still is not been built again. Am I doing anything wrong? Thanks again for the help.
Thanks, Surajit
Please ensure that your webhook is initialized. Once this is initialized a version bump will trigger a new build. https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook
Please do another version bump to kick off a new build. Thank you
Received a valid push; starting a build. Commits are:
8c59f54 Bumped 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: "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.
Received a valid push; starting a build. Commits are:
317e58c Removed unintended inputs Due to version change
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:
293a891 Updated description.
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.
Received a valid push; starting a build. Commits are:
b62b9ab Updated description.
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:
22d5a7e Updated Description.
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.
Hi,
I have cleared all the errors excepting 1. This is happening because the System File nanotatoR.Rproj is tracked by git (ERROR: System Files found that should not be git tracked:nanotatoR.Rproj). I have kept the file on gitignore and also used git rm --cache *.Rproj to remove the file. Then also this error occurs. Can you please help.
Thanks, Surajit
After you do a git rm *.Rproj , did you do a git commit to commit the change to your repository?
Also please consider cleaning up the coding practice notes, the runnable example note, and adding a NEWS file. I will do a technical review of this package shortly.
Received a valid push; starting a build. Commits are:
660899c Updated the changes
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 build report for more details.
Received a valid push; starting a build. Commits are:
fc10d74 Updated the version of R
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 build report for more details.
Thank you for your submission to Bioconductor. Please see the following initial review.
General
Build Report
NEWS
?news
helper. Remove the title section and format accordingly. DESCRIPTION
Vignette
2: In if (returnMethod_bedcomp == "Text") { :
the condition has length > 1 and only the first element will be used. Fix this
conditional to account for length > 1.
## Warning in biomaRt::useMart("ensembl", host = "www.ensembl.org",
## ensemblRedirect = FALSE, : The argument "ensemblRedirect" has been
## deprecated and will be removed in the next biomaRt release.
> run_bionano_filter(SVFile=smappath,fileName,input_fmt_geneList="dataFrame",
> nanotatoR_main(smap, bed, inputfmtBed = c("BNBED"),
Inst
R code
Have not done an indepth look into the R code until the section General
is considered. There should be a re-write making the functions compatible and consistent with existing Bioconductor infastructure. See also:
http://bioconductor.org/developers/how-to/commonMethodsAndClasses/
Please comment back here with changes and updates. Let me know when you would like me to re-review your package.
Cheers
Thanks...will reply back with all the changes.
Hello, Just checking in - have you made any progress or have any questions about updates? We normally like to see some progress within 2-4 weeks of sending feedback to know the issue is still open and active.
Switching reviewer to Valerie.
@VilainLab Are you planning to submit a new version?
Thanks for the reply. Yes we are planning to add a new version. We are adding some new functionalities to the program, which would also take care of some of the reviewer comments. Sorry again for the late reply.
Thanks, Surajit
Closing this issue due to inactivity. We can re-open it when you have a new version ready. Valerie
Hi Valerie,
I have updated my functions, which answers most of the questions related to the coding standards. This tool is built for variants identified using optical mapping methods developed by Bionano Genomics. This is one of the techniques to identify structural variants (SV; variants which have size more than 50 bp), accurately. The data used as example are toy data sets constructed from real data sets deposited in Genome in a bottle consortium.
The question I have is do I submit my tool as a new submission, or is it part of the old submission?
Please let me know if you have further questions.
Thanks, Surajit
Received a valid push; starting a build. Commits are:
53a3af0 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: "skipped, WARNINGS, 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.
@VilainLab , I'm no longer with the Bioconductor project and won't be continuing the review. I'm ccing @lshep and @mtmorgan so the package can be reassigned. Valerie
Is this 'the same' package, or a new package? It is unclear from your description.
Hi Martin,
It is a new version of the earlier submitted package, which takes care of most of the review comments from bioconductor reviewers and also have some additional functionalities to facilitate better variant annotation and classification. Would we treat this as a complete new package submission or a old submission?
Thanks, Surajit
From: Martin Morgan [notifications@github.com] Sent: Thursday, April 04, 2019 5:14 PM To: Bioconductor/Contributions Cc: Bhattacharya, Surajit; Mention Subject: [EXT] Re: [Bioconductor/Contributions] nanotatoR: next generation structural variant annotation and classification (#913)
ATTENTION: External Email! Do not click attachments/links unless sender is known.
Is this 'the same' package, or a new package? It is unclear from your description.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_913-23issuecomment-2D480066388&d=DwMCaQ&c=Zoipt4Nmcnjorr_6TBHi1A&r=A7ikyxJ6NjfZXZkHJSAEEDOxGh2fq1RXLJXrVyw-TI4&m=YmoaaZEcCbgL6seb1Ro7zyH6_zMquUGQMWESprrL2jw&s=xiuJ97RiE6bfvtpyko0n1NaR451MdPWfIn2KliRZjrg&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AlqeLmraXAIbXgf6Xk1TJ4ZnXIItRs2wks5vdmtLgaJpZM4XLHWQ&d=DwMCaQ&c=Zoipt4Nmcnjorr_6TBHi1A&r=A7ikyxJ6NjfZXZkHJSAEEDOxGh2fq1RXLJXrVyw-TI4&m=YmoaaZEcCbgL6seb1Ro7zyH6_zMquUGQMWESprrL2jw&s=d69-QPZ8XqFOyyw9x5sYyllTDGXRVTOuXpQmKr6JKO8&e=.
I'll pick up the review process from here, no need to create a new submission.
Received a valid push; starting a build. Commits are:
f0ca92b Bumped 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: "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.
Received a valid push; starting a build. Commits are:
b928e35 Bumped 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, 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.
Received a valid push; starting a build. Commits are:
2b70e15 Bumped 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: "skipped, ERROR, 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 build report for more details.
Received a valid push; starting a build. Commits are:
ce33948 Bumped 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: "skipped, ERROR, 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 build report for more details.
Received a valid push; starting a build. Commits are:
cf414d2 Bumped 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: "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.
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