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FuseSOM
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/ecool50/FuseSOM
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Hi @ecool50
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: FuseSOM
Title: A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets
Version: 0.99.0
Authors@R:
person("Elijah", "Willie", , "[email protected]", role = c("aut", "cre"))
Description: A correlation based multiview self organizing map for the characterization of cell types (`FuseSOM`)
is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by
combining a `Self Organizing Map` architecture and a `Multiview` integration of
correlation based metrics to cluster highly multiplexed in situ imaging cytometry assays.
License: `use_mit_license()`, `use_gpl3_license()`
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
Imports:
yasomi,
psych,
FCPS,
analogue,
coop,
pheatmap,
ggplotify,
fastcluster,
fpc,
ggplot2,
stringr,
ggpubr,
LazyData: true
Depends:
R (>= 2.10)
Suggests:
knitr,
rmarkdown
VignetteBuilder: knitr
LinkingTo: Rcpp
biocViews:
SingleCell, CellBasedAssays
Thanks for your contribution, it looks very interesting. However, yasomi is not in CRAN. At this time, Bioconductor packages can depend only on other Bioconductor packages, or packages distributed by CRAN. Consider using the som package at CRAN. Let us know if we should close out this submission.
As a less important change that will also need to be addressed at some point:
I also see this line in the DESCRIPTION file above:
License: `use_mit_license()`, `use_gpl3_license()`
Those are functions of the usethis package.
The authors will need to either:
- Call
usethis::use_mit_license()orusethis::use_gpl3_license()from the R console to fill this field automatically. - Choose a valid license name (see here) and manually edit this field, e.g.
License: Artistic-2.0
Amazing! Thanks for the feedback. I am currently working on the changes and will update when it is ready for reevaluation.
Hey @vjcitn and @kevinrue, I have made updates to the FuseSOM package to remove the dependence on yasomi and also fixed the licensing issue. Would it be possible to reevaluate?
Thanks
-- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 66-68 (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
"batch_som_optim_continuous" not available for .C() for package "FuseSOM"
--- failed re-building ‘Introduction.Rmd’
SUMMARY: processing the following file failed:
‘Introduction.Rmd’
Error: Vignette re-building failed.
BTW it is much preferred to use .Call instead of .C -- please see Writing R Extensions.
FYI this is the commit behind the source I used to generate error above:
commit b3921fba5a13e0233abf08a78ab1cbe815256d58
Author: Elijah Willie <[email protected]>
Date: Sat Aug 27 00:06:45 2022 -0700
Update Introduction.Rmd
Hi @vjcitn, I will fix the introduction compilation issue and remove the .so and .o files. However, for the C-code, is it essential to have using the .Call format? I did not write the source code and it will take me some time to rewrite everything to use the .Call format. Can it be assessed and accepted using the .C format and I will update it in the next iteration? Please let me know.
Thanks
HI @vjcitn, I have made the necessary updates. Please have look and let me know your thoughts.
Sorry for delay. My latest attempt led to:
Quitting from lines 66-68 (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
"batch_som_optim_continuous" not available for .C() for package "FuseSOM"
--- failed re-building ‘Introduction.Rmd’
But I was able to run the vignette code, so pre-check is passed. Now the build system.... after it is ingested ... gets to have a try.
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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/FuseSOM to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @ecool50, please address the issues reported by the automated single package builder (SPB) above, so I can start the review. Thanks!
I have addressed all the errors and warnings apart from ERROR: Maintainer must subscribe to the bioc-devel mailing list. in version 0.99.1 which is now on the repository.
Received a valid push on git.bioconductor.org; starting a build for commit id: 6a45134f3097ba889de4f98b4362779ae95c6862
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
[email protected]:packages/FuseSOM 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: 542d409b24b9c3de85e19b6f748cab117b95931b
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/FuseSOM 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: e3e1c1025b3d9bb3fd428fd540eaad487ca375cf
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
[email protected]:packages/FuseSOM 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: f529d0f76ce027d51d8d7e2679743a5c27274ed4
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
[email protected]:packages/FuseSOM 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: 7be5389c7a3b355cdebe1de3515e4c685495a724
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/FuseSOM to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @ecool50,
Please address the import issues (various "no visible global function definition for" NOTES by R CMD check). For the methods, stats, and S4Vectors imports, full imports (e.g. import(stats)) are preferred over selective imports (e.g. importFrom("stats", "aggregate", "cor", "cov.wt", "kmeans", "prcomp", "princomp", "quantile", "sd")).
Also please try to reduce the number of NOTES reported by BiocCheck(). 13 NOTES is a lot and some of them should be easy to avoid.
I'm not sure what this NOTE is about:
NOTE: License 'GPL (>=2)' unknown; licenses cannot restrict use
The GPL licenses (version 2 or 3) are fine and plenty of Bioconductor packages use them. Maybe BiocCheck() fails to parse your License: field properly. Maybe try with GPL (>= 2) (note the space between >= and 2). If that doesn't help we'll just ignore that note.
Thanks, H.
Received a valid push on git.bioconductor.org; starting a build for commit id: 400f75acce6a5f5769b61f04e1bed239a39dfd56