Closed lambdamoses closed 2 years ago
Hi @lambdamoses
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: SFEData
Title: Example SpatialFeatureExperiment datasets
Version: 0.99.0
Authors@R:
c(person("Lambda", "Moses", email = "dlu2@caltech.edu",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7092-9427")),
person("Lior", "Pachter", email = "lpachter@caltech.edu",
role = c("aut", "ths"),
comment = c(ORCID = "0000-0002-9164-6231")))
Description:
Example spatial transcriptomics datasets with Simple Feature annotations
as SpatialFeatureExperiment objects. In the first version, the only full
dataset is a mouse skeletal muscle Visium dataset 2 days after notexin
injury from 'Large-scale integration of single-cell transcriptomic data
captures transitional progenitor states in mouse skeletal muscle
regeneration'. More datasets will be added in later versions.
Imports:
AnnotationHub,
ExperimentHub
Suggests:
knitr,
rmarkdown,
SpatialFeatureExperiment,
testthat (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
biocViews:
ExperimentHub,
ExpressionData,
Mus_musculus_Data,
SpatialData,
Tissue,
SingleCellData
VignetteBuilder: knitr
Config/testthat/edition: 3
Will you be following the https://github.com/Bioconductor/Contributions#submitting-related-packages so that SpatialFeatureExperiment is in place for checking SFEData?
I installed SpatialFeatureExperiment from pachterlab repo to check this package and it seemed fine. You will need to submit SpatialFeatureExperiment too, as a related package.
@vjcitn to have the interface for submitting related packages work correctly they can't submit it until the data package is already in review with a 'review in progress' tag (and therefore already initialized in the review process). If it is good please proceed with the 'pre-check passed'
A reviewer has been assigned to your package. Learn what to expect during the review process.
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AdditionalPackage: https://github.com/pachterlab/SpatialFeatureExperiment
Hi @lambdamoses, Thanks for submitting your additional package: https://github.com/pachterlab/SpatialFeatureExperiment. We are taking a quick look at it and you will hear back from us soon.
AdditionalPackage: https://github.com/pachterlab/Voyager
Hi @lambdamoses, Thanks for submitting your additional package: https://github.com/pachterlab/Voyager. We are taking a quick look at it and you will hear back from us soon.
Hi, bump your version numbers/commit/push to get a new build.
Additional Package has been approved for building.
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Additional Package has been approved for building.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
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Dear Package contributor,
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Received a valid push on git.bioconductor.org; starting a build for commit id: 11579860423af00cea4cf7f2f36a5298c659b02d
Received a valid push on git.bioconductor.org; starting a build for commit id: 624514c3976d27cf38c903dd2410d2bbae47f9a3
Received a valid push on git.bioconductor.org; starting a build for commit id: d13cd4cf79d885c6304769e0fd66ae9e55367b00
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Received a valid push on git.bioconductor.org; starting a build for commit id: bc10e766faa0573951752cf498c6b1329ecac666
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Hello @lambdamoses - I'm working through the initial reviews of these packages. I wanted to check in and see how you wanted to handle the review process. Would you prefer working through one package at a time or would you rather I post all three reviews at the same time?
Best, Kayla
I suppose one package at a time.
@lambdamoses - Great, then below is the initial review of SFEData. 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.
BiocStyle
for formatting. eval = FALSE
code chunk.Best, Kayla
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DESCRIPTION
- [x] SUGGESTION: We encourage using the 'BugReports' field and including the relevant link to GitHub for reporting issues. (I also added URL in the DESCRIPTION file.)
Vignette
- [x] SUGGESTION: We encourage the use of
BiocStyle
for formatting.- [x] REQUIRED: Add an 'Installation' section that demonstrates to the user how to download and load the package from Bioconductor. This code can be included in an
eval = FALSE
code chunk.R code
- [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 2 lines that are > 80 characters long. (I can't locate those lines in the R code files. It's probably referring to the plain text in the vignette, which I think is fine since RStudio wraps the plain text.)
- [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 14 lines that are not. (I'm accustomed to indenting by 2 spaces.)
@lambdamoses - Great, thank you for making those changes. I've looked them over and SFEData
now looks good. Below is the initial review of SpatialFeatureExperiment. Again, 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.
Title
field.BugReports
field with
relevant links to GitHub for reporting issues.system.file()
instead of
readRDS()
.eval = FALSE
code chunk.1:...
; use seq_len()
or seq_along()
instead.paste
in condition signals.supressWarnings
/*Messages
if possible (found 1 times)Best, Kayla
Question about using :::
: I used S4Vectors:::disableValidity
because I found SingleCellExperiment
and SpatialExperiment
using it, so I thought it's allowed. I also used some internal functions of SingleCellExperiment
that I find useful. If it's not allowed, then what alternative do you suggest? Like copying and pasting the code for the internal functions?
I'd say it's ok to ignore the R CMD check
NOTE about S4Vectors:::disableValidity
. In some rare situations one actually needs to temporarily disable validation of S4 objects but unfortunately the methods package doesn't provide a mechanism for that. A few Bioconductor packages use S4Vectors:::disableValidity
already: InteractionSet, miloR, NxtIRFcore, PhosR, SingleCellExperiment, SpatialExperiment, SpliceWiz, and TreeSummarizedExperiment. Of course S4Vectors:::disableValidity
should be exported and documented but that's on me.
I also used some internal functions of SingleCellExperiment
though, like SingleCellExperiment:::.get_internal_character
, which is used in the implementation of reducedDims
in SingleCellExperiment
, because the new field colGeometries
in int_colData
is implemented in a similar way as reducedDims
. I just don't want to reinvent the wheel. But then if the internals of SingleCellExperiment
change, my package will break. Then I suppose I'd better copy and paste the code from SingleCellExperiment
? Suggestions?
Voyager
uses some internal functions in SpatialFeatureExperiment
; I suppose I can export them even though they're not meant for users.
Hervé @hpages
I could move it and document it in BiocBaseUtils
as we did with replaceSlots
> setSlots
.
Best,
Marcel
@lambdamoses,
But then if the internals of SingleCellExperiment change, my package will break.
You can also look at it the other way around: if they improve SingleCellExperiment:::.get_internal_character
, or fix a bug in it, then your package will immediately benefit. Also note that if they break your package, it'll be in Bioc devel only, so it won't affect regular users and you'll have time to fix. That being said, SingleCellExperiment:::.get_internal_character
is such a simple/small function that maybe it's not a big deal to just have your own copy in your package? It's a trade-off.
@LiNk-NY Sounds good. Almost everything in S4Vectors/R/S4-utils.R
should probably make it to BiocBaseUtils. Plus all the stuff in S4Vectors/R/show-utils.R
and most of the stuff in S4Vectors/vector-utils.R
, S4Vectors/integer-utils.R
, S4Vectors/character-utils.R
, S4Vectors/raw-utils.R
, and S4Vectors/eval-utils.R
. But let's not discuss this here.
Received a valid push on git.bioconductor.org; starting a build for commit id: c17d21b1286925ebd914784f8642cefab9b0f2eb
General package development
- [x] REQUIRED: In the README file the installation instructions should also include Bioconductor installation instructions.
DESCRIPTION
- [x] SUGGESTION: 'SpatialExperiment' is misspelled in the
Title
field.- [x] SUGGESTION: It is encouraged to include the
BugReports
field with relevant links to GitHub for reporting issues.Data
- [x] REQUIRED: Raw data files should be included in the 'inst/extdata' directory. We also require documentation on these files in an 'inst/script/' directory.
- [x] REQUIRED: Documentation of the raw data is needed in the 'inst/script/' directory. The scripts in this directory vary. It's most important to include 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.
- [x] REQUIRED: The 'data-raw' and 'inst/testdata' are not acceptable locations for data. I believe that the 'inst/testdata' belongs in the 'inst/extdata' directory and the 'data-raw' belongs in the 'inst/script' directory. When moving data to 'inst/extdata' you will access it using
system.file()
instead ofreadRDS()
.Vignette
- [x] REQUIRED: Add an 'Installation' section that show to users how to download and load the package from Bioconductor. The instructions should be in an
eval = FALSE
code chunk.Man pages
- [x] SUGGESTION: The use of dontrun{} / donttest{} is discouraged and generally not allowed. However, if this is necessary than we prefer donttest{} over dontrun{} since donttest{} requires valid R code while dontrun{} does not.
R code
- [ ] REQUIRED: Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity'. See the note in ?':::' about the use of this operator.
- [x] REQUIRED: Avoid
1:...
; useseq_len()
orseq_along()
instead.
Question: I did get rid of 1:...
and replaced them with seq_len
. While I understand that 1:n
and 1:length(x)
may be dangerous as n
and length(x)
may be 0, all cases when I used 1:...
did not involve variables, only fixed numbers, for subsetting, like 1:3
. So is something like 1:3
still discouraged?
- [ ] REQUIRED: Avoid the use of
paste
in condition signals.
All cases when I used paste
in warning
or stop
is to collapse multiple items to show, which is allowed per https://contributions.bioconductor.org/r-code.html?q=paste#end-user-messages
- [ ] REQUIRED: Avoid
supressWarnings
/*Messages
if possible (found 1 times)
suppressWarnings
is used in the [
method for SpatialFeatureExperiment
: suppressWarnings(x <- callNextMethod())
, which calls the [
method for SpatialExperiment
. I need to suppress the warning here because the SFE method uses the drop
argument in its unique way that does not apply to SpatialExperiment
and SingleCellExperiment
. I get this warning if the drop
argument is used. The warning comes from callNextMethod
, and the drop
argument is used in the code after callNextMethod
.
sfe_subset <- sfe[1:10, 1:10, drop = TRUE]
Node indices in the graphs are no longer valid after subsetting. Dropping all row and col graphs.
Warning message:
In .nextMethod(x = x, i = i, j = j, drop = drop) :
'drop' ignored '[,SpatialFeatureExperiment,ANY,ANY-method'
- [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 312 lines that are > 80 characters long.
I did some reformatting to shorten some lines, and the remaining ones over 80 characters long aren't that much longer than 80 characters.
- [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 1240 lines that are not.
I usually and consistently indent by 2 spaces as in RStudio's default.
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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,
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