Closed fuerzhou closed 2 years ago
Hi @fuerzhou
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: spaSim
Title: Spatial point data simulator for tissue images
Version: 0.99.0
Date: 2022-02-16
Authors@R:
c(person("Yuzhou", "Feng", email = "yuzhou.feng@petermac.org", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-2955-4053")),
person("Anna", "Trigos", email = "anna.trigos@petermac.org", role = c("aut"),
comment = c(ORCID = "xxxx-xxxx-xxxx-xxxx")))
Description: A suite of functions for simulating spatial patterns of cells in
tissue images. Output imagesare multitype point data in SingleCellExperiment
format. Each point represents a cell, with its 2D locations and cell type.
Potential cell patterns include background cells, tumour/immune cell clusters,
immune rings, and blood/lymphatic vessels.
License: Artistic-2.0
URL: https://trigosteam.github.io/spaSim/
BugReports: https://support.bioconductor.org/t/spaSim
biocViews: StatisticalMethod, Spatial, BiomedicalInformatics
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Imports:
ggplot2,
methods,
stats,
dplyr,
spatstat.geom,
SummarizedExperiment,
spatstat.random,
SingleCellExperiment
Depends:
R (>= 4.1.0)
LazyData: true
Suggests:
RefManageR,
BiocStyle,
knitr,
testthat (>= 3.0.0),
sessioninfo,
rmarkdown,
markdown
Config/testthat/edition: 3
VignetteBuilder: knitr
Please remove or qualify carefully
# install from GitHub
install.packages("devtools")
devtools::install_github("TrigosTeam/spaSim", ref = "dev")
Thank you for the reminder. I have fixed it.
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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.
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/spaSim
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
ok
ok
ok - make sure it can be parsed by utils::news()
.
Indent your R code by 4 spaces. https://bioconductor.org/developers/how-to/coding-style/ - follow this.
Explain the default arguments: https://github.com/TrigosTeam/spaSim/blob/09b9ff57000e54161cfbb9201177edd778a18c5a/R/multiple_images_with_immune_rings.R#L59 , not just in this function but throughout your codebase.
Lines 50, 51 are not needed, https://github.com/TrigosTeam/spaSim/blob/09b9ff57000e54161cfbb9201177edd778a18c5a/R/simulate_background_cells.R#L50. Please make sure there is 'space' efficiency in your code, don't assign variables for no reason.
Is the goal of a function like this to have the user run it without any user parameters given as input? The number of parameters in this function is not very helpful. There are also no validity checks for the parameters. It is very likely to break unless they know exactly what to input.
There is a risk of failure if there are no validity checks for the parameters, please include them. And this risk increases as the number of parameters increase.
sysdata.rda
file in the R/
folder? Whatever you want to install with the package should go in the inst/extdata
section.R/
directoryok, try to include more details on the parameters.
ok
ok
Thank you @nturaga for the comments. Much appreciated.
utils::news()
after installation. On the number of parameters and the default arguments:
We note that this package generates simulated data based on user parameters, rather than analysing external datasets. Hence, most functions require more parameters than functions from a regular package. For functions where there is a larger number of parameters, we set the default arguments to generate a typical simulation, giving users an example of what can be obtained with the function. We also have@examples
in the manual which include the code to generate the same results as that with the default parameters. We believe this set up will improve user experience. We have added clarifications in the @description
of those functions - "The default values for the arguments give an example which enables an automatic simulation without the specification of any argument."
On the internal data:
The sysdata.rda
file is the internal data that is not visible to the users. I followed the guidance in this book data. The function I used to generate the data is usethis::use_data()
which automatically generates the data in R/
folder. Could you please give more instructions on why and how the internal data should be stored in inst/extdata
?
I tried pushing the updated version 0.99.1 to Bioconductor. However, I encountered an error:
$ git push upstream main
The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be established.
ED25519 key fingerprint is SHA256:h60zj69etEaWmD4S9vpI3KFRBvPlodTMxZjYpGh4ZjQ.
This key is not known by any other names
Are you sure you want to continue connecting (yes/no/[fingerprint])? yes
Warning: Permanently added 'git.bioconductor.org' (ED25519) to the list of known hosts.
Enumerating objects: 88, done.
Counting objects: 100% (88/88), done.
Delta compression using up to 8 threads
Compressing objects: 100% (57/57), done.
Writing objects: 100% (57/57), 22.82 KiB | 417.00 KiB/s, done.
Total 57 (delta 45), reused 0 (delta 0), pack-reused 0
remote: FATAL: W refs/heads/main packages/spaSim fuerzhou DENIED by fallthru
remote: error: hook declined to update refs/heads/main
To git.bioconductor.org:packages/spaSim.git
! [remote rejected] main -> main (hook declined)
error: failed to push some refs to 'git.bioconductor.org:packages/spaSim.git'
Looks like the issue was not the SSH. It might have something to do with hooks on remote. Could you please help me with this? Thank you!
Multiple issues:
#5
of the given new package workflow git . Received a valid push on git.bioconductor.org; starting a build for commit id: d556f4b95bfcc5cf1861f520f2a647109f662fe7
@lshep Thank you very much for the advice. I have now pushed the new version to Bioconductor.
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/spaSim
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: 3afc583d5d41cfb3e25202cc4fff7114a54ab957
Remove ORCID id if not available, https://github.com/TrigosTeam/spaSim/blob/3afc583d5d41cfb3e25202cc4fff7114a54ab957/DESCRIPTION#L9
Please check the latest build report https://bioconductor.org/spb_reports/spaSim_buildreport_20220603124633.html and fix as many of the simple "NOTE" issues as possible.
Otherwise, it looks good to me. As soon as the build finishes, I'll accept it. Please make the change above.
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/spaSim
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@nturaga Thank you for the update! I have added the ORCID id.
Meanwhile, we are thinking about updating the main data object from SingleCellExperiment
to SpatialExperiment
as SpatialExperiment
is the standard class for spatial data on Bioconductor. The other package that we have submitted, SPIAT
, was suggested to do the same update. This will not take long, as SpatialExperiment
is an extension of SingleCellExperiment
. We would appreciate your comments on this!
SpatialExperiment is probably appropriate modification.
Hi @fuerzhou
Let me know when you have switched the object class, and i'll take a look again (please issue a new build report).
Received a valid push on git.bioconductor.org; starting a build for commit id: 4475b1a6f47a9663b3246e89947307f8e0d77fd2
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/spaSim
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@nturaga We have updated the package and the builds are successful. There are several notes that we could not resolve.
Please let me know if we should do any further changes. Thank you!
Received a valid push on git.bioconductor.org; starting a build for commit id: ef39bdf99b0e1ab95101d4587d80461b6a9d21b8
Received a valid push on git.bioconductor.org; starting a build for commit id: bd78b5207647f6053f7c2fc452a051a7a3b11615
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/spaSim
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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/spaSim
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@nturaga We have updated the package and the builds are successful. There are several notes that we could not resolve.
- Could not set LazyData to false - if set to false, our external data can not be accessed by the user.
- NOTE: Consider multiples of 4 spaces for line indents; 465 lines (13%) are not. I have tried my best to change the indentation generated from Roxygen2, but they can not be changed manually.
- NOTE: Consider shorter lines; NOTE: The recommended function length is 50 lines or less. These two notes are related to each other and I have tried to reduce them.
- NOTE: Avoid using '=' for assignment and use '<-' instead. - I checked all the files and there shouldn't be any. Do you have any suggestions on how to find out where the issue is?
Please let me know if we should do any further changes. Thank you!
I have deleted the workflow file from the repo.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
Thank you @nturaga @vjcitn @lshep for all your help!
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