220_Das_SingleCellRNASeq.Rmd

Question

220_Das_SingleCellRNASeq.Rmd

Closed this issue 6 years ago · 20 comments

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

aroma.light issue, to be resolved on server side.

LiNk-NY commented 6 years ago

Thanks!

Answer 1 · 2018-07-07T15:27:10.000Z

it looks like for a couple of workshops (including ours) the problem is that aroma.light is failing its checks in bioc-devel and hence biocLite won't be able to install it. Any workaround? Or should we ask @HenrikBengtsson to fix it? :)

The workaround is to install https://cran.r-project.org/src/contrib/Archive/princurve/princurve_1.1-12.tar.gz or GitHub devel branch of princurve. The reason is Issue rcannood/princurve#8.

Answer 2 · 2018-07-09T14:27:49.000Z

Getting a new problem now that aroma.light is installed from HenrikBengtsson/aroma.light:

Quitting from lines 386-390 (220_Das_SingleCellRNASeq.Rmd) 
Error in project_to_curve(X, s, pcurve$ord, stretch = stretch) : 
  unused argument (pcurve$ord)
Calls: <Anonymous> ... getCurves -> .local -> lapply -> FUN -> .shrink_to_avg
In addition: Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
Execution halted

Answer 3 · 2018-07-09T14:46:19.000Z

That:

Error in project_to_curve(X, s, pcurve$ord, stretch = stretch) : 
  unused argument (pcurve$ord)

appears to come from princurve. For troubleshooting purposes, see if it works with https://cran.r-project.org/src/contrib/Archive/princurve/princurve_1.1-12.tar.gz.

BTW, what timeline are you on here? I can try to push for a CRAN update of princurve - they seem to be willing to make a new release quite soon.

Answer 4 · 2018-07-09T18:43:48.000Z

Hi Henrik,
I get a different error:

Quitting from lines 393-397 (220_Das_SingleCellRNASeq.Rmd) 
Error: package 'princurve' 1.1.12 is loaded, but >= 2.0.2 is required by 'slingshot'
Execution halted

Answer 5 · 2018-07-09T18:49:28.000Z

Hey all,
The project_to_curve function was added in princurve version 2.0.2 (it was previously called get.lam), so I think updating that package may solve this issue.

Answer 6 · 2018-07-09T20:49:42.000Z

The problem with aroma.light has been fixed with princurve 2.0.4, which is now available on CRAN. Please use that version, instead of the @devel version on GitHub.

Answer 7 · 2018-07-09T21:45:41.000Z

And the problem with slingshot is being caused by princurve 2.0.4. kstreet13/slingshot#19 should do the trick.

Answer 8 · 2018-07-09T23:13:31.000Z

I can confirm that aroma.light passes R CMD check --as-cran with the princurve 2.0.4 that just hit CRAN. I've/Travis CI/AppVeyor CI verified on Linux and Windows with various R versions - as soon as macOS binaries are rolled out, I'd expect it to also work there too. This means that aroma.light should build and pass all checks on Bioc release & devel at the next round of Bioc builds.

Answer 9 · 2018-07-10T16:31:53.000Z

Quitting from lines 400-404 (220_Das_SingleCellRNASeq.Rmd) 
Error in project_to_curve(X, s, pcurve$ord, stretch = stretch) : 
  unused argument (pcurve$ord)
Calls: local ... getCurves -> .local -> lapply -> FUN -> .shrink_to_avg
In addition: Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
Execution halted
Error in Rscript_render(f, render_args, render_meta) : 
  Failed to compile 220_Das_SingleCellRNASeq.Rmd
Calls: <Anonymous> ... render_new_session -> tryCatch -> tryCatchList -> Rscript_render
Execution halted

Exited with status 1.

Answer 10 · 2018-07-10T17:04:16.000Z

kstreet/slingshot#19 was merged yesterday, but slingshot v 0.99.11 still needs to be published on Bioconductor. Once slingshot v 0.99.11 is out, this error should disappear :)

Answer 11 · 2018-07-10T17:38:01.000Z

Yeah, I pushed the new version yesterday, so it should be available soon!

Answer 12 · 2018-07-17T18:38:38.000Z

Hi @LiNk-NY ,

can you confirm that the new version of slingshot solves the issue above? It works on my local machine with slingshot 0.99.12 and princurve 2.1.0, but not sure which versions you have for the build.

Answer 13 · 2018-07-17T18:55:40.000Z

Hi Davide, @drisso
The builder has these versions:

> packageVersion("slingshot")
[1] ‘0.99.12’
> packageVersion("princurve")
[1] ‘2.1.0’

and it solves the issue. Thanks.

Answer 14 · 2018-07-17T18:56:32.000Z

Awesome! Thanks Marcel!

Answer 15 · 2018-07-18T16:07:16.000Z

Hi Diya, @diyadas
Could you please fix the citations in your workshop? I don't see any entries in the .bib file for:

pandoc-citeproc: reference Peer2017 not found
pandoc-citeproc: reference Pierson2015 not found
pandoc-citeproc: reference Tseng2005 not found

cc: @drisso @kstreet13

Answer 16 · 2018-07-18T16:43:30.000Z

Will do! Have small formatting things I will also address. Thanks Marcel!

Answer 17 · 2018-07-25T13:34:03.000Z

I did fix the citation issue locally - but I'm unable to push commits. Any chance that someone could check the permissions I have? So sorry for the last-minute change.

Answer 18 · 2018-07-25T14:46:09.000Z

@diyadas, could you make a pull request with just that change? We have disabled commits on the repo for everyone, as the workflows are "live" now. Sorry for the inconvenience.

Answer 19 · 2018-07-25T15:31:15.000Z

PR submitted, sorry if you got a lot of notifications as I had an interesting time with GitHub.