tximeta - Githubissues

mikelove commented 6 years ago

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Repository: https://github.com/mikelove/tximeta

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bioc-issue-bot commented 6 years ago

Hi @mikelove

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: tximeta
Version: 0.0.16
Title: Transcript Quantification Import with Automatic Metadata
Description: Transcript quantification import from Salmon with
    automatic population of transcript metadata and ranges.
Authors@R: c(
    person("Michael", "Love", email="michaelisaiahlove@gmail.com", role = c("aut","cre")),
    person("Rob", "Patro", role = "aut"),
    person("Peter", "Hickey", role = "ctb"),
    person("Charlotte", "Soneson", role = "ctb"))
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
License: GPL-2
VignetteBuilder: knitr
Depends: SummarizedExperiment
Imports:
    tximport,
    jsonlite,
    S4Vectors,
    AnnotationDbi,
    GenomicFeatures,
    ensembldb,
    BiocFileCache,
    tibble,
    GenomeInfoDb,
    rtracklayer,
    rappdirs,
    utils,
    methods
Suggests:
    knitr,
    rmarkdown,
    testthat,
    tximportData,
    org.Dm.eg.db
biocViews: Annotation, DataImport, Preprocessing,
    RNASeq, Transcriptomics, Transcription, GeneExpression
RoxygenNote: 6.0.1

bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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bioc-issue-bot commented 6 years ago

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

da1e70e standardize to 'metadata and transcript ranges'

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

d3f9f45 removing cache from Rmd

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

d219440 i think this solves the non-interactive issue

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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bioc-issue-bot commented 6 years ago

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

7fe8a4e same fix for other vignette

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

99cd942 fix version number

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

cca4cfe subset an example to speed things up

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

9c366dd trying to speed up R CMD check

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

eef23ff try speeding up R CMD check by dropping addIds fro...

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

44ef7e0 move SE from depends to imports, remove rtracklaye...

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

9eb0bc5 vapply induces a bug actually

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

93cb059 fixing language: txome 'version' => 'release'

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

8b49892 rename index seq hash to sha256 internally, change...

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bioc-issue-bot commented 6 years ago

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

8aba0ae add unranged SE support for other quantifiers

bioc-issue-bot commented 6 years ago

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lshep commented 6 years ago

Hi @mikelove did you want me to do an initial review or are you still making updates?

mikelove commented 6 years ago

hi @lshep Good question! :-)

I was doing some rolling updates getting ready for BioC and then after feedback from other developers.

Now is a good time to take a break from any updates for the initial review.

BTW there were two extra slides from BioC that I didn't get to, which might be useful for reviewing the package, and seeing how it's leveraging BiocFileCache. If you go to the last 2 slides here:

http://bit.ly/tximeta

Thanks for your time!

lshep commented 6 years ago

Looking good to me. Some minor points and questions:

inst/ [Optional] I personally like to see an inst/script/ directory that includes information on what is in extdata/ ,why it is included, and code or sudo code of how it was generated. (I realize a lot of this is in the vignette now - I still like a quick view in inst too but this is optional as long as it is somewhere)

VIGNETTE (by sections)

What Happened? See the linkedTxome vignette in this package for a demonstration. Should this be the a section of the current vignette? else there is no other vignette currently included in the package?

Examining SummarizedExperiment output

Here we show the three matrices that were imported. (Note: this part would need updating for un-reduced inferential variance matrices.) (Second note: the downstream packages would need updating of their functions or workflows, e.g. DESeqDataSetFromTximport needs a little update to work with these
SummarizedExperiments instead of simple lists.)

I guess I was confused by the clarification points - was this a note to update in the future or this seemed unclear to me?

Easy summarization to gene-level If the user wanted to regenerate rather than use the stashed version is there an overwrite?

Run a differential expression analysis So is there a plan for a convenience function?

Metadata galore [Optional] I particularly like the syntax of str(metadata(se)[["quantInfo"]]) rather than str(metadata(se)$quantInfo) but this is obviously optional.

R code:

addIds.R: minor point: message(paste0("mapping to new IDs using '", orgpkg.name, "' data package")) I don't think you need the paste0, message does a sep="" to arguments message("mapping to new IDs using '", orgpkg.name, "' data package")

bfcLocation.R more of a note for me - if you think of it can you open an issue on BiocFileCache to possible expose this use of rapp with a default or tempdir - I think we talked at CSAMA about how BiocFileCache does this internally automatically already but a package specific cache will want to expose like you have done - I probably should make some sort of template for this to provide

mikelove commented 6 years ago

Thanks for these notes @lshep! I'll work on these and open the BiocFileCache Issue.

lshep commented 6 years ago

Hey how is this looking? Any updates?

mikelove commented 6 years ago

Sorry for the delay, everything seems straightforward, I just got caught up with the rnaseqDTU workflow revision, but plan to fix up tximeta next week.

lshep commented 6 years ago

sounds good thanks.

bioc-issue-bot commented 6 years ago

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

7940dd7 new version for Bioc submission

bioc-issue-bot commented 6 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.

mikelove commented 6 years ago

@lshep, I've addressed all your points. Mostly removing pieces that were confusing.

For the DESeq2 integration, I added some code to DESeq2 devel branch right now to deal with the hand off. There's one remaining line of code I will delete once the DESeq2 version propagates.

bioc-issue-bot commented 6 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 6 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/mikelove.keys is not empty), then no further steps are required. Otherwise, do the following:

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 biocLite(\"tximeta\"). The package 'landing page' will be created at

https://bioconductor.org/packages/tximeta

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.

Bioconductor / Contributions

tximeta #806