scRepertoire submission

ncborcherding commented 4 years ago

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

Repository: https://github.com/ncborcherding/scRepertoire

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bioc-issue-bot commented 4 years ago

Hi @ncborcherding

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: scRepertoire
Title: A toolkit for single-cell immune receptor profiling
Version: 1.2.0
Author: Nick Borcherding
Maintainer: Nick Borcherding <ncborch@gmail.com>
Description: scRepertoire was built to process data derived from the 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with the popular Seurat R package and SingleCellExpression data.
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
biocViews: Software, ImmunoOncology, SingleCell, Classification, Annotation, Sequencing
Depends: dplyr, ggalluvial, ggplot2, reshape2, Seurat, R (>= 3.6)
Imports: Biostrings, RColorBrewer, Startrac, colorRamps, ggdendro, ggfittext, powerTCR, stringr, vegan
Suggests: knitr, rmarkdown
VignetteBuilder: knitr

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bioc-issue-bot commented 4 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 4 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.

mtmorgan commented 4 years ago

Please make sure the your package can interoperate with (i.e., accept as input and return as output, when appropriate) standard Bioconductor data representations, in particular the SingleCellExperiment class. Relevant packages should at least appear in the Suggests: field (if the support is optional) or in the Imports: field (preferred).

ncborcherding commented 4 years ago

Thanks - packages does interoperate with SingleCellExperiment already.

DESCRIPTION changes just committed: Added SingleCellExperiment to Imports Moved Startrac and powerTCR to Suggests to fix error in compiling.

lshep commented 4 years ago

Please set up your webhook. Once this is done please do a version bump in your DESCRIPTION to kick off a new build on the builders. Bioconductor policy is not to allow dependency on packages that are not on either CRAN or Bioconductor.

bioc-issue-bot commented 4 years ago

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

a65eb62 Update DESCRIPTION Suggests startrac and powerTCR d700d89 Merge branch 'master' of https://github.com/ncborc... ab3e19a Version Bump Build for bioconductor

bioc-issue-bot commented 4 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.

lshep commented 4 years ago

Startrac does not appear to be a CRAN or Bioconductor package. Dependencies can only be packages that are actively on CRAN or Bioconductor.

ncborcherding commented 4 years ago

Do I need to remove the function that uses Startrac then? Or how would I allow for the build and keep the function?

Just looked through the startrac code, it looks like I would have to copy all the code into scRepertoire, just for one function to be used in scRepertoire function.

Apologies if that is a dumb question.

lshep commented 4 years ago

I would suggest reaching out to the Startrac package and ask about submitting to CRAN or Bioconductor. But yes, otherwise you will have to remove the Startrac functionality from your package -- either reimplement in your package or find equivalent functionality in a CRAN/Bioconductor package.

bioc-issue-bot commented 4 years ago

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

402611b v1.2.2 Removed startrac functionality for biocond...

bioc-issue-bot commented 4 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 4 years ago

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

5f5ffbd v1.2.3 Added sample data to dowload form github.i...

bioc-issue-bot commented 4 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: "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.

ncborcherding commented 4 years ago

New comit to address errors with version change from 1.2.3 to 0.99.0 per error message. Complete changes:

CHANGES IN VERSION 0.99.0

-Changed DESCRIPTION version to 0.99.0 -Removed file seurat_example.rda, accidentally committed -Deleted git attributes -reduced Seurat object size for alluvialClonotype in vignette -Changed the alluvialClonotype assessment to account for only 1 condition

bioc-issue-bot commented 4 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 4 years ago

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

f6c34b4 Changed R version

bioc-issue-bot commented 4 years ago

Dear Package contributor,

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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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ncborcherding commented 4 years ago

Is the version bump flair an issue with having to revert versions from 1.2.x to 0.99 per instructions from the builds?

lshep commented 4 years ago

It normally appears when you do a push to the repository without a version bump. To indicate that there were code changes that aren't included in the last given build report.

bioc-issue-bot commented 4 years ago

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

2fcc630 dev bump 0.99.2

ncborcherding commented 4 years ago

Ahhh sorry, I'm an idiot, made a minor edit in the readme and didn't even think about version control. Thanks for the clarification.

bioc-issue-bot commented 4 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: "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 4 years ago

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

2a13383 Version bump Change to authors@r

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

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

5b4506e bump 0.99.4 Modified expression2List() to allow f...

bioc-issue-bot commented 4 years ago

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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.

hpages commented 4 years ago

Thanks @ncborcherding for submitting the scRepertoire package.

There are 2 immediate issues that will likely require significant changes to the package:

The vignette and some examples in the man pages use Seurat objects. Bioconductor has a strong preference for SingleCellExperiment objects so please use this instead.
Also the vignette and some examples in the man pages download datasets from GitHub. This is not the Bioconductor way. Please include the datasets in the package if they don't grow its size beyond the allowed limit, or wrap them in a data experiment package. If you choose the latter, and if the data is more than 50Mb, then the data should preferrably be hosted on ExperimentHub but it should still be associated with a data experiment package. Whether the datasets are included in scRepertoire or in a dedicated data experiment package, they should have man pages giving as much details about the data as possible.

Other issues, mostly cosmetic:

Please remove the HTML vignette from the vignettes/ folder. The HTML vignette will be automatically generated by R CMD build and included in the resulting source tarball.
The vignette has no title, no author name, and no introduction. Please add all of these.
Also please add a sessionInfo() section at the end of the vignette.
The section/subsection headers are not rendered properly in the HTML vignette.
Code snippet csv1 <- read.csv(“location/of/file.csv”, stringsAsFactors = FALSE) should be made a real markdown code chunk so it is rendered as such.
The man page for abundanceContig says "This function takes the output of combineContig() or expression2List()" but I don't see any combineContig() defined in the package.

Thanks, H.

bioc-issue-bot commented 4 years ago

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

a22b6d2 99.5 push Addressing Bioconductor concerns: 1) Up...

bioc-issue-bot commented 4 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: "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 git@git.bioconductor.org:packages/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

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

0caabd3 push 99.6 modified import

bioc-issue-bot commented 4 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: "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 git@git.bioconductor.org:packages/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

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

960675b push for 99.7 Fixed colData error.

bioc-issue-bot commented 4 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: "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 git@git.bioconductor.org:packages/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

ncborcherding commented 4 years ago

Seems to be a general issue here with the build:

R CMD check is giving an error for the build, I can replicate it on another system with the following log:
- installing source package ‘scRepertoire’ ... using staged installation R ** data * moving datasets to lazyload DB inst ** byte-compile and prepare package for lazy loading sh: line 1: 47521 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/bt/30h0rxyd2kq_g012_zyq6mjc0000gn/T//RtmparjZoU/fileb99aa5774' ERROR: lazy loading failed for package ‘scRepertoire’
- removing ‘/Users/nick/scRepertoire.Rcheck/scRepertoire’
Statement that Biostrings is not a Bioconductor package
I cannot replicate

Error: package or namespace load failed for scRepertoire in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called Biostrings Execution halted

bioc-issue-bot commented 4 years ago

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

09eed51 Bump 0.99.8 Updated GrabMeta() to produce consist...

bioc-issue-bot commented 4 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: "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 git@git.bioconductor.org:packages/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

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

6809ad6 bump 99.8 Passed check and bioccheck after updati...

bioc-issue-bot commented 4 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: "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 git@git.bioconductor.org:packages/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

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

3694b5e Update 0.99.10

bioc-issue-bot commented 4 years ago

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

2bffd5c compareClonotype Update

bioc-issue-bot commented 4 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: "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 git@git.bioconductor.org:packages/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

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

55ec4e8 Update 0.99.12 Reduced size of screp_example to 1...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

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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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bioc-issue-bot commented 3 years ago

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

edcc0e8 Update 99.13 Updated exportTable for viz function...

bioc-issue-bot commented 3 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. 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/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

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

bdf6c50 0.99.14 removed bracket

bioc-issue-bot commented 3 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. 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/scRepertoire to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

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

bf5a0ea v0.99.15 Fixed numerator in morisita index

Bioconductor / Contributions

scRepertoire submission #1503

CHANGES IN VERSION 0.99.0