Closed svenbioinf closed 2 years ago
Hi @svenbioinf
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: OGRE
Type: Package
Title: Calculate, visualize and analyse overlap between genomic regions
Version: 0.99.0
Authors@R:c(
person("Sven", "Berres", email="sven.berres@ukmuenster.de", role = c("aut","cre")),
person("Jörg", "Gromoll", role = c("ctb")),
person("Marius", "Wöste", role = c("ctb")),
person("Sarah", "Sandmann", role = c("ctb")),
person("Sandra", "Laurentino", role = c("ctb")))
Description: OGRE calculates overlap between user defined genomic region datasets.
Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments.
Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges
Depends: R (>= 4.0), S4Vectors
Suggests: knitr, rmarkdown
biocViews: Software, WorkflowStep, BiologicalQuestion, Annotation, Metagenomics,
Visualization
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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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/OGRE
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: 45e68a52acce0aec119555c188fad90e619350a0
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/OGRE
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: c6ba03ba2d2c26f33ebc5f25cabe49ae0a0ffc40
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/OGRE
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: 36b9c1ae7df7ab073a0499832583bfe99acdeb7c
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/OGRE
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@svenbioinf - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.
LazyData
to false.importFrom()
over importing the entire package.importFrom("grDevices", "dev.off", "pdf")
and importFrom("stats", "setNames")
to your NAMESPACE file.inst/extdata/
directory to be present in the inst/scripts/
directory. The scripts in this directory can vary. Most importantly the script must clearly document how the data was generated. It should include source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data.BiocStyle
package for formatting.eval = FALSE
.
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("OGRE")
@keywords internal
tag so the function is removed from the documentation index.sapply()
; use vapply()
if possible. Found in files: R/methods.R, lines 158 and 165.1:...
; use seq_len()
or seq_along()
if possible. Found in files: methods.R, lines 221.Best, Kayla
@svenbioinf - Checking in to see if any progress has been made on the review I posted. We like to see changes within 2-3 weeks to be sure the package is actively being worked on. If there are no improvements made in the next few days I will have to close this issue for inactivity.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: 42791c35fbb275302c46bdfffc695183178065e6
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, skipped". 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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/OGRE
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@svenbioinf - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.
DESCRIPTION
- [x] SUGGESTION: Set
LazyData
to false.- [ ] REQUIRED: Update R version dependency from 4.0 to 4.2.0.
- [x] SUGGESTION: Consider adding these automatically suggested biocViews: Sequencing.
- [x] SUGGESTION: We strongly encourage the use of the 'BugReports:' field which includes a relevant link to GitHub for reporting Issues.
NAMESPACE
- [ ] SUGGESTION: We strongly encourage the use of
importFrom()
over importing the entire package.- [x] SUGGESTION: Consider adding
importFrom("grDevices", "dev.off", "pdf")
andimportFrom("stats", "setNames")
to your NAMESPACE file.NEWS
- [x] SUGGESTION: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.
Data
- [x] REQUIRED: We require documentation of data in the
inst/extdata/
directory to be present in theinst/scripts/
directory. The scripts in this directory can vary. Most importantly the script must clearly document how the data was generated. It should include source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data.Vignette
- [ ] SUGGESTION: We recommend using the
BiocStyle
package for formatting.- [x] REQUIRED: There should be an 'Installation' section that demonstrates to the user how to install and load the package from Bioconductor. The code should look like the following and include
eval = FALSE
.if(!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("OGRE")
- [x] REQUIRED: 'sessionInfo' not found in vignette(s).
- [x] SUGGESTION: We encourage the use of a package man page with an overview of the package and links to the main functions.
- [x] SUGGESTION: For any function that is documented but not exported I would suggest adding the
@keywords internal
tag so the function is removed from the documentation index.Unit testing
- [x] SUGGESTION: Consider adding unit tests. We strongly encourage them.
R code
- [x] SUGGESTION: Partial argument match of 'chr' to 'chromosome' (this came from R CMD check).
- [x] SUGGESTION: Consider clarifying how 8 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within().
- [x] REQUIRED: Avoid
sapply()
; usevapply()
if possible. Found in files: R/methods.R, lines 158 and 165.- [x] REQUIRED: Avoid
1:...
; useseq_len()
orseq_along()
if possible. Found in files: methods.R, lines 221.- [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 93 lines that are > 80 characters long.
- [ ] SUGGESTION: For formatting reasons, consider 4 spaces instead of tabs. There is 1 line that contains tabs.
- [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 153 lines that are not.
Best, Kayla
Hi Kayla, I managed to address various points during the christmas holidays, however there are a couple of issues I would appreciate your input:
Thank you for your support!
Best and Happy new year, Sven
Received a valid push on git.bioconductor.org; starting a build for commit id: 6e61a78a59f181b8b23adb271c692fd2334b9d98
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, skipped". 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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/OGRE
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear Kayla, could you please comment on the note I wrote to you responding to your suggestion/requirements list? Here it is again: "Your internal MacOS buildcheck stops with "Graphics API version mismatch" It seems to be fine on Linux though are you able to do anything from your side?"
So I updated all my R packages, do you need to do the same for your MacOS testing system maybe? (Just guessing) Best, Sven
@svenbioinf - I will bring this to the attention of our team. I was able to build it locally on my mac so I'm assuming it's something on our end. In the mean time I will re-review the package based on the other builders. I will have the rereview posted here in the next few days.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: d86561e048be64f6bd81237a4413847aad10c8e3
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, skipped". 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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/OGRE
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@svenbioinf - I will bring this to the attention of our team. I was able to build it locally on my mac so I'm assuming it's something on our end. In the mean time I will re-review the package based on the other builders. I will have the rereview posted here in the next few days.
Best, Kayla
@Kayla-Morrell Just to keep you updated: I added more of your suggested points, however the Error from your builder system still pops up. Best, Sven
@svenbioinf - Thank you for making the necessary changes. I've looked them over and everything looks good, I'm more than happy to accept the package. In regards to the Mac ERROR - this can be ignored for now. Our team did some digging and found that ggsave()
uses packages ragg
and textshaping
which CRAN has not provided Mac binaries yet for R 4.2. Until this happens the ERROR will persist. If there are further changes that need to be made we will notify you.
Best, Kayla
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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Thank you Kayla & the Bioconductor Team! This is good news and I am happy to have OGRE accepted here at Bioconductor. Have a nice day, Sven
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