Cooley_DECIPHER.Rmd

Question

Cooley_DECIPHER.Rmd

Closed this issue 6 years ago · 23 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.

Workshop is currently incomplete

Answer 1 · 2018-07-09T12:49:33.000Z

@npcooley this line won't work for others to build:

load("/Users/npc19/Desktop/WorkshopData.RData",
     verbose = TRUE)

Can you post your workshop data online somewhere to be accessed by download.file / BiocFileCache?

Answer 2 · 2018-07-14T21:52:15.000Z

Quitting from lines 80-86 (Cooley_DECIPHER.Rmd) 
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> load -> readChar
Execution halted

Answer 3 · 2018-07-19T15:52:41.000Z

processing file: Cooley_DECIPHER.Rmd
Quitting from lines 135-137 (Cooley_DECIPHER.Rmd) 
Error in GFFParser(GFFAddress = GeneCallAdds, Verbose = TRUE) : 
  could not find function "GFFParser"
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted

Answer 4 · 2018-07-19T16:19:32.000Z

Hi Levi, That function was added to the github package last night. If the github package is not update as of 14 hours ago, that function will not exist yet. Sorry for the hassle! Cheers, Nick

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On Thu, Jul 19, 2018 at 11:52 AM Levi Waldron ***@***.***> wrote: processing file: Cooley_DECIPHER.Rmd Quitting from lines 135-137 (Cooley_DECIPHER.Rmd) Error in GFFParser(GFFAddress = GeneCallAdds, Verbose = TRUE) : could not find function "GFFParser" Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval Execution halted — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlhJctS2Rn5b2r7hc7AapXJ_Ru2-7UuEks5uIKtKgaJpZM4VGf3p> .

Answer 5 · 2018-07-19T19:04:45.000Z

Could you specify what package? There is also clusterProfiler::GFFparser.

Answer 6 · 2018-07-19T19:09:55.000Z

Done, it now reads: FindHomology::GFFparser Cheers, Nick

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On Thu, Jul 19, 2018 at 3:04 PM, Marcel Ramos ***@***.***> wrote: Could you specify what package? There is also clusterProfiler::GFFparser. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlhJcuxlq6t6qqofmXtRB4i9OKzVfv5iks5uINhOgaJpZM4VGf3p> .

Answer 7 · 2018-07-19T19:20:14.000Z

My apologies, the "P" is capitalized... FindHomology::GFFParser

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On Thu, Jul 19, 2018 at 3:09 PM, Nicholas Cooley ***@***.***> wrote: Done, it now reads: FindHomology::GFFparser Cheers, Nick On Thu, Jul 19, 2018 at 3:04 PM, Marcel Ramos ***@***.***> wrote: > Could you specify what package? There is also clusterProfiler::GFFparser. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#26 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AlhJcuxlq6t6qqofmXtRB4i9OKzVfv5iks5uINhOgaJpZM4VGf3p> > . >

Answer 8 · 2018-07-19T20:03:52.000Z

Since not all versions of npcooley/FindHomology will work, please bump its version number (e.g. to 0.0.0.9001) and change the "Remotes:" in the DESCRIPTION here to:

  npcooley/FindHomology (>=0.0.0.9001),

Answer 9 · 2018-07-19T20:15:03.000Z

I've changed the version on both my package and in remotes. Is there more to do with that?

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On Thu, Jul 19, 2018 at 4:03 PM, Levi Waldron ***@***.***> wrote: Since not all versions of npcooley/FindHomology will work, please bump its version number (e.g. to 0.0.0.9001) and change the "Remotes:" in the DESCRIPTION here to: npcooley/FindHomology (>=0.0.0.9001), — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlhJcsYud8bhaVtUZW28a9wzrAA80bzmks5uIOYpgaJpZM4VGf3p> .

Answer 10 · 2018-07-19T20:20:43.000Z

I already updated the AMI (as of 2pm today), so the version from last night should be installed. Sean

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On Thu, Jul 19, 2018 at 4:15 PM npcooley ***@***.***> wrote: I've changed the version on both my package and in remotes. Is there more to do with that? On Thu, Jul 19, 2018 at 4:03 PM, Levi Waldron ***@***.***> wrote: > Since not all versions of npcooley/FindHomology will work, please bump its > version number (e.g. to 0.0.0.9001) and change the "Remotes:" in the > DESCRIPTION here to: > > npcooley/FindHomology (>=0.0.0.9001), > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < #26 (comment) >, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AlhJcsYud8bhaVtUZW28a9wzrAA80bzmks5uIOYpgaJpZM4VGf3p > > . > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFpE4eVKewnU_E6bD1oRImMtde46a6oks5uIOjHgaJpZM4VGf3p> .

-- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12

Answer 11 · 2018-07-19T21:27:25.000Z

Great! Can you let me know if I'm generating any other errors, or if the there are still problems with the that function/package? On Thu, Jul 19, 2018 at 4:20 PM, Sean Davis <notifications@github.com> wrote:

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I already updated the AMI (as of 2pm today), so the version from last night should be installed. Sean On Thu, Jul 19, 2018 at 4:15 PM npcooley ***@***.***> wrote: > I've changed the version on both my package and in remotes. Is there more > to do with that? > > On Thu, Jul 19, 2018 at 4:03 PM, Levi Waldron ***@***.***> > wrote: > > > Since not all versions of npcooley/FindHomology will work, please bump > its > > version number (e.g. to 0.0.0.9001) and change the "Remotes:" in the > > DESCRIPTION here to: > > > > npcooley/FindHomology (>=0.0.0.9001), > > > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub > > < > #26 (comment)- 406397308 > >, > > or mute the thread > > < > https://github.com/notifications/unsubscribe-auth/ AlhJcsYud8bhaVtUZW28a9wzrAA80bzmks5uIOYpgaJpZM4VGf3p > > > > . > > > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#26 (comment)- 406400314>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AAFpE4eVKewnU_ E6bD1oRImMtde46a6oks5uIOjHgaJpZM4VGf3p> > . > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlhJcnHLVSJ_dSxEHJsJoc3dJFcLmVdqks5uIOodgaJpZM4VGf3p> .

Answer 12 · 2018-07-19T21:33:45.000Z

Builds without errors now! There should be a version in the bookdown soon that you @npcooley can check to make sure everything looks OK.

Answer 13 · 2018-07-19T21:34:18.000Z

Great, thanks for your patience!

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On Thu, Jul 19, 2018 at 5:33 PM, Levi Waldron ***@***.***> wrote: Builds without errors now! There should be a version in the bookdown soon that you @npcooley <https://github.com/npcooley> can check to make sure everything looks OK. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlhJclYG6X093DjfzuydU1YpKXFHEawjks5uIPs5gaJpZM4VGf3p> .

Answer 14 · 2018-07-19T22:53:07.000Z

Note you only have two top-level sections in your chapter, "Overview" and "Workshop goals and objectives". See the TOC at https://bioconductor.github.io/BiocWorkshops/.

Answer 15 · 2018-07-20T02:18:45.000Z

That's ok, i don't think i want to make any more changes and mess anything up. Thanks for all your help!

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On Thu, Jul 19, 2018 at 6:53 PM, Levi Waldron ***@***.***> wrote: Note you only have two top-level sections in your chapter, "Overview" and "Workshop goals and objectives". See the TOC at https://bioconductor.github.io/BiocWorkshops/. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlhJcg9NtVm8Ry9viqKgPCJGiY8TXE_uks5uIQ3UgaJpZM4VGf3p> .

Answer 16 · 2018-07-20T21:19:05.000Z

In the book version of this workshop, any code chunks that uses plot(), pairs(), or hist() those plots aren't appearing. It looks like the objects those functions are being used with do exist, is there something i need to change to make them appear?

Additionally, when some data is being loaded from FindHomology, the function is returning a warning, despite the object data() is loading being used successfully in the next few chunks.

Answer 17 · 2018-07-21T17:40:32.000Z

R-generated images are missing, see https://bioconductor.github.io/BiocWorkshops/working-with-genomic-data-in-r-with-the-decipher-package.html

Answer 18 · 2018-07-21T17:57:39.000Z

I think this was caused by spaces in chunk names - we'll see with the next build.

Answer 19 · 2018-07-24T02:26:50.000Z

The images are still not showing and I'm not sure why, but I should be able to debug it before the workshop...

Answer 20 · 2018-07-25T13:52:42.000Z

@LiNk-NY could you help figure out why figures in this workshop are not rendering? E.g. see this pairs() command in the source file, and the corresponding broken image symbol in the book (see line pairs(SyntenyObject[2:3, 2:3], labels = GenomeIDs[2:3]))

Answer 21 · 2018-07-25T14:44:07.000Z

It was spaces in the chunk names, I think. I just checked in 6304f38 and things built successfully for me.

Answer 22 · 2018-07-25T15:10:02.000Z

Oh thanks Sean! I'd noticed the spaces problem and thought I'd fixed it, but I missed some others...

Answer 23 · 2018-07-25T17:24:00.000Z

Confirmed that the figures are all in place in the most recent gh-pages.