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ViSEAGO #1061

Closed ghost closed 5 years ago

ghost commented 5 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

2366579 NAMESPACE update

bioc-issue-bot commented 5 years ago

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.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

29c3280 GOclusters show method mean size clusters bug coor...

bioc-issue-bot commented 5 years ago

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.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

d652688 create_topGOdata requireNamespace adds

bioc-issue-bot commented 5 years ago

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.

nturaga commented 5 years ago

Update

annotate,character-genomic_ressource: warning in getBM(attributes =
  c("ensembl_gene_id", "go_id", "go_linkage_type", "namespace_1003"),
  filters = unlist(go_filter[grep("with GO ID", ignore.case = TRUE,
  go_filter$description), "name", with = FALSE]), value = TRUE, mart =
  myspecies): partial argument match of 'value' to 'values'

compute_SS_distances,ANY-character: warning in select(GO.db, keys =
  onto$values, column = "TERM"): partial argument match of 'column' to
  'columns'

merge_enrich_terms,list : <anonymous>: warning in getBM(attributes =
  c("ensembl_gene_id", "external_gene_name"), value = TRUE, mart =
  myspecies): partial argument match of 'value' to 'values'
  * Checking package NEWS...
      * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.

Give it another build report and version bump with these changes.

Best,

Nitesh

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

df0d14f ViSEAGO 0.99.26

bioc-issue-bot commented 5 years ago

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.

ghost commented 5 years ago

Thank you Nitesh for your comments, I have added responses to your comments.

Update

  • I'd still like to see you remove your calls to base:: in your functions. This doesn't add anything. But if you are getting errors, it means there are other paste methods which are overriding your base::paste method. Same with base::match.arg as well.
  • Check the NOTE in your build report and fix some of these issues,

forgotten "base::" have been removed.


annotate,character-genomic_ressource: warning in getBM(attributes =
  c("ensembl_gene_id", "go_id", "go_linkage_type", "namespace_1003"),
  filters = unlist(go_filter[grep("with GO ID", ignore.case = TRUE,
  go_filter$description), "name", with = FALSE]), value = TRUE, mart =
  myspecies): partial argument match of 'value' to 'values'

this message come from "myspecies" internal object from ViSEAGO::annotate (mart object from biomaRt) and only appears in the check report without error in ViSEAGO::annotate method execution. This message seems come from the existence of several colomns named "ensembl_gene_id" in Ensembl (throught biomaRt) but without code error when executed.

columns(myspecies)[columns(myspecies)%in%"ensembl_gene_id"] [1] "ensembl_gene_id" "ensembl_gene_id" "ensembl_gene_id" "ensembl_gene_id" "ensembl_gene_id"

compute_SS_distances,ANY-character: warning in select(GO.db, keys = onto$values, column = "TERM"): partial argument match of 'column' to 'columns'

the called column "TERM" is real, and I don't understand the origin of this check note. columns(GO.db) [1] "DEFINITION" "GOID" "ONTOLOGY" "TERM"

merge_enrich_terms,list : : warning in getBM(attributes = c("ensembl_gene_id", "external_gene_name"), value = TRUE, mart = myspecies): partial argument match of 'value' to 'values'

same than annotate (seems due to "ensembl_gene_id" column call)

  • Add a NEWS file added

  * Checking package NEWS...
      * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.

NEWS file added

  • You should just depend on methods package and add it to your DESCRIPTION file and see if you can get rid of those NOTEs. Your package looks fairly complete and can be accepted. But every build report will have those NOTE issues which you need to fix.

I added "methods" in DESCRIPTION and also in NAMESPACE for several functions in order to prevents theses NOTES. The last notes can't be removed (come from data.table columns calls)

I have also added a custom2GO method for local GO annotations (species not in EntrezGene, Ensembl, or Uniprot database) in the last version bump.

Thank you Nitesh for your comments that improve this package

Aurélien,

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

6cb0bbe description update

bioc-issue-bot commented 5 years ago

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: "skipped, 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.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

5037eb3 add comma in description

bioc-issue-bot commented 5 years ago

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.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

edf2e7b add utils in description

bioc-issue-bot commented 5 years ago

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.

bioc-issue-bot commented 5 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/abrionne.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("ViSEAGO"). The package 'landing page' will be created at

https://bioconductor.org/packages/ViSEAGO

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Monod79 commented 5 years ago

Hi!

Thanks for the package. Although the package seems to address the redundancy problem from GO terms, the GOterms_heatmap visual output could be greatly improved. Is there a way to display the terms name on the heatmap? Also, how do we change the heatmap colors?

Thanks !

mtmorgan commented 5 years ago

@Monod79 please post issues to the developer of this package on the package github repository https://github.com/abrionne/ViSEAGO

Monod79 commented 5 years ago

The github repository is down...

Monod79 commented 5 years ago

The github repository is down...

mtmorgan commented 5 years ago

Contact maintainer("ViSEAGO") or ask on the support site https://support.bioconductor.org with the tag ViSEAGO; this issue was used exclusively for initial package submission.

ghost commented 5 years ago

Hi @Monod79 ,

For display GO names on GOterms_heatmap, simply set showGOlabels = TRUE (default parameter). You cannot ,for the moment, modifiy heatmap colors. I will add this option in the next release. For bug report go to https://forgemia.inra.fr/UMR-BOA/ViSEAGO/issues Thanks,

Monod79 commented 5 years ago

Hi Aurélien,

Thanks for the quick reply. The default display parameter requires to hover over each clustered terms, in an interactive manner, which is incompatible with results publications, but really great in a live presentation. I would rather like to publish the results in a figure where readers can read the names of the GO terms.

The package has great potential !!! It addresses the inconvenient redundancies of GO terms, and resumes perfectly how biologist would like to display and understand their omics data.

Thanks for the good work !

Jonathan

Jonathan Boulais, PhD

Analyste en bio-informatique & protéomique Computational analyst in proteomics

Institut de recherches cliniques de Montreal (IRCM) Montreal Clinical Research Institute 110 avenue des Pins Ouest Montreal (Qc) H2W 1R7 Canada

Phone: 514 987-3245 Fax: 514 987-5624 [cid:AAECBC98-01EE-4DD5-ABEF-7A30D9A3C997@ircm.priv]

De : Aurélien BRIONNE notifications@github.com Envoyé : Tuesday, November 12, 2019 2:26 AM À : Bioconductor/Contributions Contributions@noreply.github.com Cc : BOULAIS Jonathan Jonathan.Boulais@ircm.qc.ca; Mention mention@noreply.github.com Objet : Re: [Bioconductor/Contributions] ViSEAGO (#1061)

Hi @Monod79https://github.com/Monod79 ,

For display GO names on GOterms_heatmap, simply set showGOlabels = TRUE (default parameter). You cannot ,for the moment, modifiy heatmap colors. I will add this option in the next release. For bug report go to https://forgemia.inra.fr/UMR-BOA/ViSEAGO/issues Thanks,

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ghost commented 5 years ago

Dear @Monod79,

A new version of ViSEAGO (1.1.0) will be available in few hours on bioconducor, where you could modify heatmap colors on GOterms_heatmap.