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broadSeq resubmission
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/dasroy/broadSeq
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[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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Hi @vondoRishi
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: broadSeq
Title: broadSeq : for streamlined exploration of RNA-seq data
Version: 0.99.0
Authors@R:
person("Rishi", "Das Roy", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-3276-7279"))
Description: This package helps user to do easily RNA-seq data analysis with multiple
methods (usually which needs many different input formats). Here the user will
provid the expression data as a SummarizedExperiment object and will get results
from different methods. It will help user to quickly evaluate different methods.
License: MIT + file LICENSE
URL: https://github.com/dasroy/broadSeq
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: GeneExpression, DifferentialExpression, RNASeq,
Transcriptomics
Suggests:
knitr,
limma (>= 3.54.0),
rmarkdown,
stats (>= 4.2.2),
samr
Depends:
dplyr,
ggpubr,
SummarizedExperiment
Imports:
DELocal,
EBSeq (>= 1.38.0),
DESeq2 (>= 1.38.2),
NOISeq,
forcats (>= 1.0.0),
genefilter,
ggplot2,
ggplotify,
plyr,
clusterProfiler (>= 4.8.2),
pheatmap,
sechm (>= 1.6.0),
stringr,
purrr (>= 0.3.5),
edgeR (>= 3.40.1)
VignetteBuilder: knitr
Please include an inst/scripts that has a file that describes how the data in inst/extdata was generated. It can be text, psuedo-code, or code but should contain any relevant source and licensing information.
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): broadSeq_0.99.0.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/broadSeq to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2e5b3fb93f877359baac323374bf72b0c0ebd6fe
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): broadSeq_0.99.1.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/broadSeq to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
I'm so sorry for the long delay; I have been extremely backed up with post release tasks. I will have a review for you within the next day.
README
- [ ] Include Bioconductor installation instructions
man
- [ ] Please have a package level man page so that if a naive user does
?broadSeqthey are directed appropriately how to get started.
DESCRIPTION
- [ ] When doing R CMD build the following occurs
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
'broadSeq/inst/extdata/rat_vole_mouseSE_salmon.rds'
We would appreciate a manual entry of R (>= 4.4.0) as this is the R value tested against on our builders
BiocCheck
- [ ] Plesae correct coding NOTES
general
- [ ] We like to see endomorphism whenever possible. Curious your reasoning for taking in a SummarizedExperiment but then not returning it?
vignette broadSeq.rmd
-
[ ] Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope.
-
[ ] This vignette shows no evaluated code. If I were a user I would not know where to start. Please include either references to the other vignettes or show/reference the main functions that can be used.
test
- [ ] We really strongly encourage tests to ensure functions are working correctly
NEWS
- [ ] We strongly advise a NEWS file. NEWS file not only make changes visible to end users, we collate the NEWS file for the Bioconductor relesae announcements. See example release announcement
For the most part yes. You could justify why something shouldn't be implemented and if reasonable I could potentially make an exception.
Received a valid push on git.bioconductor.org; starting a build for commit id: 16391d5cb1aa374eb2a9339c83a18ee56b031e4d
README
- [x] Include Bioconductor installation instructions
man
- [x] Please have a package level man page so that if a naive user does
?broadSeqthey are directed appropriately how to get started.DESCRIPTION
- [x] When doing R CMD build the following occurs
Fixed the serialized object
NB: this package now depends on R (>= 3.5.0) WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'broadSeq/inst/extdata/rat_vole_mouseSE_salmon.rds'We would appreciate a manual entry of R (>= 4.4.0) as this is the R value tested against on our builders
BiocCheck
- [ ] Plesae correct coding NOTES
There is no preprint or publication for this package yet
general
- [x] We like to see endomorphism whenever possible. Curious your reasoning for taking in a SummarizedExperiment but then not returning it?
There are many functions which return SummarizedExperiment object , like broadSeq::transformDESeq2 or broadSeq::normalizeEdgerCPM
vignette broadSeq.rmd
- [x] Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope.
- [x] This vignette shows no evaluated code. If I were a user I would not know where to start. Please include either references to the other vignettes or show/reference the main functions that can be used.
test
- [ ] We really strongly encourage tests to ensure functions are working correctly
At this moment, there is no manpower to write tests.
NEWS
- [ ] We strongly advise a NEWS file. NEWS file not only make changes visible to end users, we collate the NEWS file for the Bioconductor relesae announcements. See example release announcement
In future releases, news will be included.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): broadSeq_0.99.2.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/broadSeq to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Could you please fix the NOTES in BiocCheck. Some may be ignored but the coding practices and BugReports field in the description should minimally be fixed.
There is still no package level page. Nothing appears with a ?broadSeq call
> ?broadSeq
No documentation for 'broadSeq' in specified packages and libraries:
you could try '??broadSeq'
How can I add package-level documentation? Though I have added R/broadSeq-package.Rd
See something like the following txdbmaker example. You want to actually have values not be internal so that something displays with ?broadSeq
Received a valid push on git.bioconductor.org; starting a build for commit id: 788035bc21a8fdad93a762c7d26e85c32d7141b1
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): broadSeq_0.99.3.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/broadSeq to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
With this new build, there should be displays with ?broadSeq. Can you please confirm?
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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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
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(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 BiocManager::install("broadSeq"). The package 'landing page' will be created at
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