Closed kvittingseerup closed 1 year ago
Hi @kvittingseerup
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: pfamAnalyzeR
Type: Package
Title: Identification of domain isotypes in pfam data
Version: 0.99.0
Authors@R: person(given="Kristoffer",family="Vitting-Seerup", role=c("cre","aut"),email="k.vitting.seerup@gmail.com",comment = c(ORCID = "0000-0002-6450-0608"))
Description: Enables the user to read pfam prediction from both webserver and local versions into R. Afterwards it supports the identification of protein domain isotypes.
License: GPL (>= 2)
Depends:
R (>= 4.0.0),
readr,
stringr,
tibble,
dplyr,
magrittr
Imports: utils
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.1
Suggests:
knitr,
rmarkdown
VignetteBuilder: knitr
biocViews:
AlternativeSplicing,
TranscriptomeVariant,
BiomedicalInformatics,
FunctionalGenomics,
SystemsBiology,
Annotation,
FunctionalPrediction,
GenePrediction,
DataImport
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Received a valid push on git.bioconductor.org; starting a build for commit id: 9ec917e4f193440452714f46739b862d2a9a1862
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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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: 70051b2732846f6f0d1e711a1f58a56172dc0d23
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. 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
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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: ce3117beb404c6d93d828fb0ba90b87ad6d37da7
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.
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Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
@kvittingseerup - 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. Also, keep in mind that the deadline for packages to be accepted for the upcoming release is April 19th.
importFrom()
is encouraged over importing the
entire package.exportPattern("^[[:alpha:]]+")
is
strongly discouraged and not allowed. Functions and generics should be
exported individually, for clarity and control.utils::news(package="pfammAnalyzeR")
.inst/extdata/
. The documentation belongs in inst/script/
and can vary.
Most importantly the script must clearly document how the data was generated and
source information. 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.eval = FALSE
code chunk.sessionInfo()
.seq_len()
or seq_along()
instead.Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: 18fded9583a75f1ebdee74805ff799ecfa8d3a05
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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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: 4acd9163f1ca1996fe8d2217fb8098bb441711b0
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/pfamAnalyzeR
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: b8602cef685b1f6b66c385ffb4513ab7f003d37d
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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @Kayla-Morrell
Thank you so much for taking the time to review my package! I really appreciate it 😃 .
In the new version, I have updated pfamAnalyzeR in accordance with your guidelines. All REQUIRED
has been implemented, and most SUGGESTION
as well.
The only exception for the REQUIRED
are the use of suppressWarnings
Due to the strange file format of the Pfam outputs, the suppressWarnings()
are needed (as warnings are expected from some of the things I have to try and would just confuse the user) .
I hope the package is now acceptable, given the upcoming deadline you mention 🤞
Dear @Kayla-Morrell
Do you think we can have pfamAnalyzeR ready before the 19th of April?
@kvittingseerup - Thank you for making the necessary changes. I've looked everything over and have just one requirement that must be met before I accept the package. Please let me know when the change has been made and I'll review the change. I am very confident this can be done by the 19th of April.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: 0aa5a249e82afb74f86400bb5de48e7f2f4db228
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/pfamAnalyzeR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @Kayla-Morrell
Thank you for your prompt action. I have now added the description and the license file.
@kvittingseerup - Great, thanks for making that change! I'm happy to accept the package now.
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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Thanks for all the help @Kayla-Morrell. It really improved the package.
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