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BioMartGOGeneSets
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- Repository: https://github.com/jokergoo/BioMartGOGeneSets
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Hi @jokergoo
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: BioMartGOGeneSets
Type: Package
Title: Gene Ontology Gene Sets from BioMart
Version: 0.99.0
Date: 2022-09-20
Authors@R: person("Zuguang", "Gu", email = "[email protected]", role = c("aut", "cre"),
comment = c('ORCID'="0000-0002-7395-8709"))
Depends: R (>= 4.2.0)
Imports: utils, S4Vectors
Suggests: biomaRt, GO.db, GenomicRanges, knitr, testthat
biocViews: AnnotationData, Organism
Description: It contains pre-compiled Gene Ontology gene sets for all organisms
available on the Ensembl database. It also includes GO gene sets for organisms
on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists.
The data was collected with the biomaRt package.
VignetteBuilder: knitr
URL: https://github.com/jokergoo/BioMartGOGeneSets
License: MIT + file LICENSE
NeedsCompilation: no
This package provides pre-compiled GO gene sets for more than 600 organisms from BioMart. Manually creating such gene sets is not difficult (as we have demonstrated in https://jokergoo.github.io/BioMartGOGeneSets/articles/biomart.html), but it would still be nice if the gene sets are already compiled and especially good for the users who are not experienced with Bioconductor or studying non-model organisms.
The script for generating the gene sets is also included in the package (https://github.com/jokergoo/BioMartGOGeneSets/blob/master/inst/scripts/biomart_genesets.R). Currently all the gene set data are stored on github.io (https://github.com/jokergoo/BioMartGOGeneSets_data). We will update the data regularly.
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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.
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
[email protected]:packages/BioMartGOGeneSets 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: 49e01e9fd22f5d82a8acabcfb98032f9d74eb21e
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
[email protected]:packages/BioMartGOGeneSets 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: 03e002eee362c1f487994ac5ae38d2bd581cdc3d
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
[email protected]:packages/BioMartGOGeneSets to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Trying to review, hitting
--- re-building ‘biomart.Rmd’ using rmarkdown
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying asia mirror
Quitting from lines 83-86 (biomart.Rmd)
Error: processing vignette 'biomart.Rmd' failed with diagnostics:
I think this should be an internet issue when connecting to the BioMart web service (using biomaRt package). There might be one of the following two reasons:
- Currently you cannot connect to Ensembl BioMart service? Maybe you can try it later.
- These lines retrieve GO-gene relations for all GO terms. The data is relatively huge. The downloading might be interrupted? (This is unlikely because I guess if so it will give a different error message)
Now I save the intermediate results (GO-gene relations in lines 83-86) to an object, and these lines are not executed in the vignette while I directly read the cached object. Hope this problem will be solved.
Received a valid push on git.bioconductor.org; starting a build for commit id: 140a24be82a3a031405d5759ba7cb087b1c04a73
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
[email protected]:packages/BioMartGOGeneSets to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Every time I try to review, it fails. Can you introduce some fault tolerance so that the value of the package is illustrated even if the networking fails? Messages to the user about what happens in the ideal case?
--- re-building ‘biomart.Rmd’ using rmarkdown
Quitting from lines 63-65 (biomart.Rmd)
Error: processing vignette 'biomart.Rmd' failed with diagnostics:
Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 294464 bytes received
--- failed re-building ‘biomart.Rmd’
Received a valid push on git.bioconductor.org; starting a build for commit id: 366cafe8220f370e7d9bf907db6715dac6ed9029
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, 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,
when making changes to your repository push to
[email protected]:packages/BioMartGOGeneSets to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
--- re-building ‘biomart.Rmd’ using rmarkdown
Quitting from lines 63-65 (biomart.Rmd)
Error: processing vignette 'biomart.Rmd' failed with diagnostics:
Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 294464 bytes received
--- failed re-building ‘biomart.Rmd’ ~~~~~~~~~~~~~~~~~~
I can see the timeout limit on your machine is only 10 seconds. I guess it relates to which biomart mirror to use. As far as I have checked, the useast mirror has a timeout limit of 10 seconds and uswest mirror has a timeout limit of 5min.
The vignette "biomart.Rmd" has nothing related to the functionalities of the BioMartGOGeneSets package. It is just a demonstration of how the data is gathered. Now in the new version, I directly generated the corresponding .md file for this vignette.
Also in the vignette, I additionally inform users to change the biomart mirrors when they see the "timeout" error.
Received a valid push on git.bioconductor.org; starting a build for commit id: 714bf41ca60637d489362122930c784664daad9b
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
[email protected]:packages/BioMartGOGeneSets to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The error was a false positive:
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
I've already subscribed the bioc-devel mailing list.
Received a valid push on git.bioconductor.org; starting a build for commit id: 666f772b3b8905f667d55593e1e3504c26e3ef40
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
[email protected]:packages/BioMartGOGeneSets 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: 26fc2dc0d279b30d9b958e907f96236c5620d9b9
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
[email protected]:packages/BioMartGOGeneSets to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.