Closed js2264 closed 1 year ago
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Received a valid push on git.bioconductor.org; starting a build for commit id: 6c1943eb35532ac3660a5cde0dc188b9ff8f1371
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.
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Received a valid push on git.bioconductor.org; starting a build for commit id: 8caa5d336a258131c823830d69d7863b654e3e77
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.
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Remember: if you submitted your package after July 7th, 2020,
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@lshep,
Thanks for letting my 2 extra packages run on the builder. I have now fixed things and:
Also, should @DarioS review these packages, or someone else take over? Cheers, J
I will continue the review process. One of the Bioconductor employees might know how to solve the Python-related timeout.
With every version bump, all python infrastructure is re-downloaded and installed. I think there is no desirable workaround at the basilisk/client end. However if @lshep would manually trigger a rebuild, the installed python infrastructure should be available -- it goes to .cache/R, as long as that is not purged with every build it should be reusable.
I'll try a manual trigger now to see how it changes --
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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@DarioS gentle ping: is there anything you would need for the review of HiCool and fourDNData? Cheers, J
Just more free time. I have got seven packages to review and university administrative work, too. I should do it next week.
AdditionalPackage: https://github.com/js2264/DNAZooData
Hi @js2264, Thanks for submitting your additional package: https://github.com/js2264/DNAZooData. We are taking a quick look at it and you will hear back from us soon.
Hi @DarioS @lshep 👋,
Just to let you know I have added (yet) another AdditionalPackage (DNAZooData
). It is also a ExperimentData package, providing programmatic access to HiC and genome references generated by the DNA Zoo consortium. It operates the same way than the fourDNData
package, by fetching metadata from the consortium database, caching the HiC contact matrix file and creating a HicFile
(BiocFile
variant) to be imported in R with HiCExperiment::import()
. Sorry for the extra burden, and please let me know if I should rather submit it as a separate issue.
Cheers, J
Additional Packages Review
HiCool
The parameter descriptions are good and not single words like previously in HiCExperiment. Checks don't have any warnings or errors. Parameters could use more explanation. For example
#' @param balancing_args Balancing arguments for cooler (Default: " --cis-only --min-nnz 3 --mad-max 7 ")
What are all of the valid parameter names? Are there more than just --cis-only
, --min-nnz
, --mad-max
acceptable? A link to some list of valid options somehere would be desirable.
The package now has a vignette but it only has one code chunk and it is a template rather than executable code. Although this package does some intensive processing, I think it could be demonstrated on real data, perhaps subset to chr22, a small chromosome.
One of the outputs produced is "several diagnostic plots". What quality control does each one show and how should the package user interpret the graphs?
fourDNDdata
R CMD check ERROR on all operating systems. Vignette is well-written and shows how to programatically download a data set from the consortium.
DNAZooData
Not yet accepted for review, but it looks similar in spirit to fourDNDdata. The parameters are not similar, however, but I wonder if downloading from both consortiums could be merged into a single package. Currently, both packages consist of just three R files, so even after merging, the package would not be big.
Received a valid push on git.bioconductor.org; starting a build for commit id: 8d7f8de30136b40d34faf6a83033ad1b9e774cc6
Dear Package contributor,
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Your package has been built on Linux, Mac, and Windows.
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Please see the build report for more details. This link will be active for 21 days.
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Received a valid push on git.bioconductor.org; starting a build for commit id: b492acdec1af80b2f5500620fedb8e3058500b3d
Received a valid push on git.bioconductor.org; starting a build for commit id: 386d05faf8e982266c5e611741ff04d8f3b54f19
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,
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Thanks for this extra round of reviews @DarioS.
I have made some internal changes and contribution changes in HiCExperiment
package and forgot to push it to Bioc, so perhaps the fourDNData-related CHECK errors you are seeing are due to a mismatch in versions. I have now bumped HiCExperiment
to 0.99.10 and pushed it to Bioc and build/check was ok (except for the previously reported check > 10min only in mac builder). I have also bumped fourDNData to 0.99.3, pushed it to Bioc and build/check is ok. I have also bumped HiCool to 0.99.4 and pushed it to Bioc and build/check was ok (except for time limit due to building the basilisk env. only in mac builder as previously reported).
Regarding documentation changes:
I have now clarified this in HiCool
doc and in the vignette.
I have added an executable chunk in the vignette, to demonstrate real use (on a subset of yeast fastq files)
I have added a paragraph re: this in the vignette.
Regarding fourDNData:
Could you please provide the check results? Bioc SPB builds/checks fourDNData without errors, perhaps yours are due to a mismatch in versions. I've bumped all packages up, would be worth updating all of them.
Regarding DNAZoo:
This is because the two consortia have very different strategies to label data, different associated metadata and different types of files. E.g. 4DN consortium can provide contact matrices (.cool
files), but also automatically processed .bigwig
files, or .bed
files, ... matching a single dataset. One may wish to recover all of these files together or only a subset of them, hence the added type
argument in fourDNData
. On the other hand, DNA Zoo only provides a contact map per species.
It is feasible, but I don't think it would be a valuable improvement. The 2 consortia do provide contact matrices, but processing workflows are vastly different. 4DN processes data from published experiments (from a 20+ different labs) on known genome references (90% human or mouse). DNA Zoo is a project led by a single lab (working in collaboration with others of course), and aims to correct/improve genome assemblies of non-model organisms. So the contact map is the result of a large amount of upstream work to re-assemble an original genome reference into an improved reference. IMO, providing a gateway to the two types of contact matrices in the same package would feel unnatural. Let me know what you think based on this answer.
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
git@git.bioconductor.org:packages/HiCool
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @DarioS @lshep 👋,
Just to let you know I have added (yet) another AdditionalPackage (
DNAZooData
). It is also a ExperimentData package, providing programmatic access to HiC and genome references generated by the DNA Zoo consortium. It operates the same way than thefourDNData
package, by fetching metadata from the consortium database, caching the HiC contact matrix file and creating aHicFile
(BiocFile
variant) to be imported in R withHiCExperiment::import()
. Sorry for the extra burden, and please let me know if I should rather submit it as a separate issue.
Gentle nudge following my replies to @DarioS review, to ask whether the AdditionalPackage DNAZooData
could be added to the the build report? As @DarioS said, it follows the exact same structure than fourDNData
which has already be added to the builds.
Thanks! J
Hi @lshep, sorry for being pushy, but would it be possible to add DNAZooData
to the build system? Many thanks for your help,
J
Additional Package has been approved for building.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
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/DNAZooData
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @DarioS 👋 Sorry for coming back to it, I know this has been a heavy reviewing assignment, but would it be possible to wrap this up soonish? Let me know if I can provide any help. May thanks! J
I have no further requests and the packages seem to be building well together. Thanks for your comprehensive infrastructure.
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