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(inactive) MMAPPR2 #902

Closed kjohnsen closed 5 years ago

kjohnsen commented 5 years ago

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

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

kjohnsen commented 5 years ago

Ok. I have a couple ideas to handle the reference genome. Maybe you can spare me some of the trial and error if you know one of these is preferable, or if there's a better way.

  1. Include the raw fasta file in the data package and build a GmapGenome
  2. Get Ensembl's most recent version of the zebrafish genome (which I need for this project) on Bioconductor as a BSgenome, to then use a small piece of it in examples like gmapR does with TP53genome()
lshep commented 5 years ago

We generally prefer using existing data so 2 would be preferred.

lshep commented 5 years ago

Can we expect some updates soon?

kjohnsen commented 5 years ago

Yes. I've been working on the artificial dataset and should have that updated data package ready within a few weeks. Then it shouldn't be too much work to integrate it into the main package vignette and examples. If all goes well, we should no longer need the ExperimentHub data.

bioc-issue-bot commented 5 years ago

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

13e0fb7 Another docs link fix; bump to v0.99.8

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.

lshep commented 5 years ago

Please continue to fix the ERROR/Warnings/NOTES in the build report and since I know you have been actively updating - please comment back here when you are ready for a re-review of the packages

kjohnsen commented 5 years ago

Will do. The synthetic data is almost done.

bioc-issue-bot commented 5 years ago

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

f5c2c84 Toy data (#2) * DESCRIPTION update

bioc-issue-bot commented 5 years ago

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

1234d2b Bump version to 0.99.10

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

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:

3b1443c Rename script to make-data.R 96c07f0 Update vignette 643f261 Bump to version 0.99.11

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: "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.

kjohnsen commented 5 years ago

@lshep I've run into problems setting up my synthetic data for use with the vignette, that is, making a small reference genome with a single gene. I figure the best way to solve the problem is to create a BSgenome package for the GRCz11 zebrafish genome. I don't see in the vignette much in the way of submitting a BSgenome package to Bioconductor after creating it--is that something I need to talk with Herve Pages about?

lshep commented 5 years ago

Is there a reason why one of the current BSGenome's could not be used?

http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Drerio.UCSC.danRer10.html

kjohnsen commented 5 years ago

The biggest reason is that names for the UCSC version don't match with Ensembl, which they need to for VEP. Also, we would need to figure out how to use a previous version of Ensembl/VEP (with GRCz10) on the Bioconductor pipeline for it to work right.

lshep commented 5 years ago

I would check in with Herve Pages @hpages on when/if a new version of the package will be created before submitting a new one.
If he doesn't plan on making it and you would like to submit one it would follow the guidelines of ExperimentHub like packages but for AnnotationHub.

kjohnsen commented 5 years ago

I thought of an easier way: instead of relying on the standard zebrafish VEP cache, I can just run VEP using the small fasta file and a GTF file for just this gene. It seems like all I'll have to do is configure the VEPFlags object. Let me know if this wouldn't work--I'll try it out.

lshep commented 5 years ago

I'm not that familiar with using VEP but that sounds reasonable if you can get it to work.

bioc-issue-bot commented 5 years ago

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

230d7db Change coordinates to 1-based, document files d8111d5 Add slc24a5.gtf 6e57af8 Bump to v0.99.12

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: "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:

3e7c365 Add scripts for annotation data; bump to v0.99.13

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: "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:

92f1c98 Add scripts for annotation data; bump to v0.99.13 8dd0781 Merge branch 'master' of https://github.com/kjohns... 3aec042 Change annotations to gz, cut gff ef12c96 Change BAM reference name to 18 6f554d4 Update accessors and docs 3076448 Update BAMs to reflect reference name change 0216f7f Bump to v0.99.14

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: "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 5 years ago

I just wanted to check it on progess as the deadline for accepting packages for this release has been announced as Wed April 24.

kjohnsen commented 5 years ago

I think I'll be able to make it. The toy dataset is now working on the vignette, so soon I'll be able to merge the branch and keep polishing things up.

lshep commented 5 years ago

Keep in mind the last day to be accepted is April 24th. Once you push changes I will still have to review the packages and accept by this date to be included in the release

kjohnsen commented 5 years ago

Ok, thanks. Hopefully I can get it done in time.

bioc-issue-bot commented 5 years ago

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

628fe5d Toydata (#99) * Suppress loess warnings

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, UNSUPPORTED, 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.

kjohnsen commented 5 years ago

I'm not quite sure why the build failed...I looked through R source code to see it's a result of a zero-length conditional statement, but I don't know where that code would be called from. If you happen to have seen this error before I'd appreciate the help.

lshep commented 5 years ago

R CMD Stangle MMAPPR2.Rmd will give you an MMAPPR2.R command with all the executed R in your vignette to run. Doing this and running the code in the vignette 

> md <- new('MmapprData', param=param) ## calculateDistance() takes a MmapprData object
> postCalcDistMD <- calculateDistance(md)
  |======================================================================| 100%
Error in if (cuid %in% names(env)) rm(list = cuid, envir = env) : 
  argument is of length zero
> traceback()
6: .ClusterManager$drop(x$.uid)
5: .bpstop_impl(x)
4: BiocParallel::bpstop(bpParam)
3: BiocParallel::bpstop(bpParam)
2: .runFunctionInParallel(chrList, .calcDistForChr, param = mmapprData@param)
1: calculateDistance(md)
lshep commented 5 years ago

Am i also correct that you still have an ExperimentData package but that it no longer uses the ExperimentHub? May I remove the resources from the ExperimentHub?

kjohnsen commented 5 years ago

Ok, thanks. I'll look into that. And yes, go ahead and remove the ExperimentHub resources.

kjohnsen commented 5 years ago

The vignette was running fine on my machine until I updated to the latest version of BiocParallel (from 1.16.6 to 1.17.18), when I was able to reproduce the error from the Bioconductor build. I'll try and figure out what's happening, but could I get some help from the BiocParallel developers?

lshep commented 5 years ago

Sure, I recommend reaching out either by opening an issue on the BiocParallel github or on the bioc-devel@r-project.org

bioc-issue-bot commented 5 years ago

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

dfe367c v0.99.4, try MulticoreParam

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, UNSUPPORTED, 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 5 years ago

The deadline for acceptance in the 3.9 release is tomorrow; packages accepted after this date will remain in bioc devel and be released under 3.10 in the fall.

kjohnsen commented 5 years ago

Yeah, we'll have to do the next release. Sorry I've been so slow; I've had very limited time to work on this.

bioc-issue-bot commented 5 years ago

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

7118284 Replace .runFunctionInParallel (#100) * Replace ....

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, UNSUPPORTED, 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.

kjohnsen commented 5 years ago

It looks like there's a problem on the server: There is no package called rtracklayer

bioc-issue-bot commented 5 years ago

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

fc22217 Bump to v0.99.6

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, UNSUPPORTED, 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:

382f958 Depend R 3.5, bump to v0.99.7

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, UNSUPPORTED". 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.

kjohnsen commented 5 years ago

All right @lshep, it's passing! I updated the R dependency, which should fix the last warning. As for the notes, there's line length--all of those are boilerplate lines like setGeneric or strings in logging messages and such which would be awkward to break up. Indentation: I only depart from the 4-space rule to match with parentheses when splitting a line. There are 3 long functions, the most egregious of which I'm working on fixing. Let me know what you want me to change.