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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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Build Failing for Bioconductor #93

Closed gabrielodom closed 2 years ago

gabrielodom commented 3 years ago

Vignette 5 fails to build. https://master.bioconductor.org/checkResults/3.12/bioc-LATEST/pathwayPCA/malbec1-buildsrc.html

gabrielodom commented 3 years ago

Based on the line numbers, the error is something to do with the circlize:: function calls. However, I can't replicate the error on my Mac. The error is argument "y" is missing, with no default, which doesn't help me very much.

gabrielodom commented 3 years ago

I've made some minor changes, and I'm going to commit to see if Travis catches this same issue.

gabrielodom commented 3 years ago

So, good news: Travis will show the failing build for Ubuntu: https://travis-ci.org/github/gabrielodom/pathwayPCA/builds/746833254.

@jamesban2015, can you run Vignette 5 in Linux? Here is the message:

Quitting from lines 433-481 (Supplement5-Analyse_Results.Rmd) 
Error: processing vignette 'Supplement5-Analyse_Results.Rmd' failed with diagnostics:
argument "y" is missing, with no default
--- failed re-building ‘Supplement5-Analyse_Results.Rmd’

I can work on fixing the issue, but I need an idea of what's causing it. I haven't been able to replicate the issue on Mac.

jamesban2015 commented 3 years ago

@gabrielodom The file "circlePlotData.RDS" cannot be found. Where can I download it?

gabrielodom commented 3 years ago

In the vignettes folder: https://github.com/gabrielodom/pathwayPCA/tree/master/vignettes

gabrielodom commented 3 years ago

It should come with the package automatically if you clone the repo.

jamesban2015 commented 3 years ago

@gabrielodom I got the same error when running only the circos plot, and I think here you miss an argument,

circos.trackText function (sectors, x, y, labels, track.index = get.current.track.index(), direction = NULL, facing = c("inside", "outside", "reverse.clockwise", "clockwise", "downward", "bending", "bending.inside", "bending.outside"), niceFacing = FALSE, adj = par("adj"), cex = 1, col = par("col"), font = par("font"), factors = sectors) I am not sure if that this was changed due to the update of this package

gabrielodom commented 3 years ago

I'll try to track that down. Perhaps I don't have the updated version of the circlize:: package. Can you send me the version number for that package? I'm using 0.4.10. (Session.info() will show you.)

gabrielodom commented 3 years ago

I just checked Travis. It looks like circlize:: had an update recently to 0.4.11.

gabrielodom commented 3 years ago

I just built vignette 5 with no errors; then I restarted R, installed the newest version of circlize::, and built the same vignette. Here is the error:

Quitting from lines 433-481 (Supplement5-Analyse_Results.Rmd) 
Error in circos.trackText(rep(-3, nPathway), rep(-3.8, nPathway), labels = "PID_IL1",  : 
  argument "y" is missing, with no default
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> circos.trackText
gabrielodom commented 2 years ago

This should have been closed with commit bd6338f