Closed diogo-branco closed 6 years ago
Hi @diogo-branco
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: allenpvc
Title: GEO accession data GSE71585 as a SingleCellExperiment
Version: 0.99.0
Authors@R: person("Diogo", "P. P. Branco", email =
"diogo.pp.branco@gmail.com", role = c("aut", "cre"))
Author: Diogo P. P. Branco
Maintainer: Diogo P. P. Branco <diogo.pp.branco@gmail.com>
Description: Celular taxonomy of the primary visual cortex in adult mice based
on single cell RNA-sequencing from a study performed by the Allen Institute
for Brain Science. In said study 49 transcriptomic cell types are
identified.
License: CC0
NeedsCompilation: no
Depends: R (>= 3.5.0), GEOquery, SingleCellExperiment
Suggests: BiocStyle, ExperimentHub, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
biocViews: ExperimentData, ExpressionData, SingleCellData, RNASeqData
A reviewer has been assigned to your package Learn what to expect during the review process.
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@Liubuntu will review this package. I think it would be a useful convenience to have a single function allenpvc()
that simply returns eh[["EH..."]]
.
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.
@Liubuntu @mtmorgan Thank you, I will create the allenpvc()
function.
Regarding the error on the building: the Package Builder seems to be using BiocVersion 3.7 and not 3.8. This package will only work on version >= 3.8. Is there anything to be fixed on my side in that regard?
the build system should heal itself; @lshep might post here when it is updated.
I apologize for the delay. We are working on the updates - I will post back here when they are complete.
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.
Hi @diogo-branco ,
Thank you for your contribution to Bioconductor. Please refer to the following technical review and address any issue. This is my first time reviewing an experiment data package. I will talk to Bioconductor core team about any potential points to add possibly. Please let me know for any questions or concerns. Thanks!
query()
on line 34 is not needed.Installation
after Introduction
, and show to users how to download and library this package as it is already available in Bioconductor. E.g., to use BiocInstaller
function for downloading. BiocInstaller::biocLite("allenpvc")
sessionInfo()
to show users your working environment.metadata.csv
is not consistent with make-metadata.R
, in the BiocVersion
filed (3.6 versus 3.8).Cheers, Qian
Hello @Liubuntu,
Thank you for you review. I will address all the points you have made, but I am unsure about the following:
Please add a section called
Installation
afterIntroduction
, and show to users how to download and library this package as it is already available in Bioconductor. E.g., to useBiocInstaller
function for downloading.BiocInstaller::biocLite("allenpvc")
The package was only submitted to ExperimentHub (by myself) but, from what I could understand from the documentation, that does not mean it is available on Bioconductor, as it needs to load the associated package which is the one being submitted in this issue. Furthermore, running BiocInstaller::biocLite("allenpvc")
just returns a warning stating that said package is not available.
Reiterating: I will comply with all the other points but I am confused regarding the one mentioned above.
Best, Branco
I would say as if it is already available in Bioconductor
. Because when users are exposed to the vignette, the package should already be available on Bioconductor. Be sure to make the code trunk eval=FALSE
for this Installation
section.
Thank you for clarifying, I will include the Installation
section after Introduction
. Is a version bump required for this push to be built by the SPB? I have already added a web hook to the repository.
Yes. Be sure to bump the version whenever you are ready for a new build.
Received a valid push; starting a build. Commits are:
40ca492 Minor fixes to comply with reviews from Bioconduct...
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.
@Liubuntu I believe I have complied with all the review points in this latest build. Please let me know in case I have overlooked something.
HI @diogo-branco ,
Sorry for the delay. I will look into the updates and get back to you very soon!
Cheers, Qian
Hi @diogo-branco ,
You experiment data package is accepted. Please expect some follow up emails about how to maintain your package. Thanks for your contribution to Bioconductor.
Cheers, Qian
Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.
Thank you for contributing to Bioconductor!
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See further instructions 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 biocLite(\"allenpvc\")
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If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.
Since you have remained unresponsive to emails - this is our last attempt to contact you - Your software package condcomp has been failing in Bioconductor since before the last release. We have tried to contact you to fix the ERRORs but you have remained unresponsive and the repository has been unchanged. If your package is not fixed in the next week we will be deprecating condcomp and allenpvc do to being an unresponsive maintainer.
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