Closed richardheery closed 11 months ago
Hi @richardheery
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: TumourMethData
Title: A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples
Version: 0.99.0
Date: 2023-09-29
Authors@R:
person("Richard", "Heery", , "richardheery@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-8067-3114"))
Description: TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments, facilitating easy extraction of methylation data for regions of interest.
License: Artistic-2.0
URL: https://github.com/richardheery/TumourMethData
BugReports: https://support.bioconductor.org/tag/TumourMethData
biocViews: ExperimentData, ExperimentHub, MethylSeqData, Homo_sapiens_Data
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.2
Depends:
R (>= 2.10),
SummarizedExperiment
Imports:
ExperimentHub,
GenomicRanges,
HDF5Array,
rhdf5
Suggests:
ggplot2,
knitr,
rmarkdown
VignetteBuilder: knitr
LazyData: false
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TumourMethData_0.99.0.tar.gz macOS 12.6.5 Monterey: TumourMethData_0.99.0.tar.gz
Links above 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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Received a valid push on git.bioconductor.org; starting a build for commit id: c0fc4bfa73a8da0322b6c10cf6fb7c1519c590ba
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: TumourMethData_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): TumourMethData_0.99.1.tar.gz
Links above 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/TumourMethData
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: 379f4d58917af829277f3c438e0bef0029ad3eb6
I haven't figured out why yet but something changed and is preventing the build report from posting. It is limited to this package.
Should I try bump the package to initiate another build?
On Tue, 10 Oct 2023 at 18:23, lshep @.***> wrote:
I haven't figured out why yet but something changed and is preventing the build report from posting. It is limited to this package.
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3189#issuecomment-1755788914, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMP6CXBK6QD4IVFJMDJK343X6VY67AVCNFSM6AAAAAA5MSGAYKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJVG44DQOJRGQ . You are receiving this because you were mentioned.Message ID: @.***>
If you have updates to the package yes. If there aren't any updates no; I already tried to manually set off a build this morning and it also failed.
In the meantime, here are my review comments:
man
tempdir()
instead of
the users working directory for download_dataset
R code
vignette
[ ] Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope.
[ ] It might be useful in the vignette to describe and demonstate the call to
download the data. Perhaps there is smaller one that won't take quite as long?
Or perhaps this chunk could be in an eval=FALSE
@richardheery were you able to work on the above points at all and push these changes to git.bioconductor.org?
Received a valid push on git.bioconductor.org; starting a build for commit id: 7fb7da99ed6224fab08a5645346bfa7d8dc6a42d
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
On one or more platforms, the build results were: "WARNINGS, 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.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TumourMethData_0.99.3.tar.gz macOS 12.6.5 Monterey: TumourMethData_0.99.3.tar.gz
Links above 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/TumourMethData
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I've updated the download function to keep the files in the cache and use symbolic links to them and also to use tempdir() as the default location to locate these links.
I've also added an example of downloading data in the vignette and expanded the introduction/abstract.
I added a function to download RNA-seq count datasets corresponding to the methylation datasets in the package. Since this data isn't in ExperimentHub yet, I can't add an example for downloading it so now I'm getting an error from BiocCheck saying that less than 80% of functions have examples. Is it okay to leave this as it is for now?
Yes okay to leave for now. When do you expect to have the data uploaded to ExperimentHub? I will review the rest of the changes later today and provide any additional feedback
I will try to get the final datasets uploaded today or else tomorrow. I have some of the RNA-seq data already on Zenodo, but I guess it's easier to let you know once I've everything finalized so you can add all the remaining data at once?
Yes once would be easier.
If a user calls a call again, wouldn't you want to skip the download and load instead of failing?
_wgbs_hg38_chr11")
snapshotDate(): 2023-10-13
see ?TumourMethData and browseVignettes('TumourMethData') for documentation
downloading 2 resources
retrieving 2 resources
|======================================================================| 100%
|======================================================================| 100%
|======================================================================| 100%
|======================================================================| 100%
loading from cache
require("rhdf5")
> mcrpc_wgbs_hg38_chr11 = TumourMethData::download_meth_dataset(dataset = "mcrpc_wgbs_hg38_chr11")
Error in TumourMethData::download_meth_dataset(dataset = "mcrpc_wgbs_hg38_chr11") :
/tmp/RtmpMO0qa0/mcrpc_wgbs_hg38_chr11 already exists
Received a valid push on git.bioconductor.org; starting a build for commit id: 1093599f01e2c309bab18425cb50543dd2c5d978
I just changed the download function to load the dataset if it was already downloaded instead of giving an error
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
On one or more platforms, the build results were: "WARNINGS, 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.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TumourMethData_0.99.4.tar.gz macOS 12.6.5 Monterey: TumourMethData_0.99.4.tar.gz
Links above 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/TumourMethData
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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