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RGLab / FAUST

Full annotation using shape-constrained trees
GNU General Public License v3.0
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Installation failure #13

Closed zonglunli7515 closed 4 years ago

zonglunli7515 commented 4 years ago

Hi,

I have seemingly managed to install scamp. However, after running the suggested lines

tryCatch(installed.packages()["knitr","Version"], error = function(e){ install.packages("knitr") }) tryCatch(installed.packages()["rmarkdown","Version"], error = function(e){ install.packages("rmarkdown") }) tryCatch(installed.packages()["ggdendro","Version"], error = function(e){ install.packages("ggdendro") }) tryCatch(installed.packages()["remotes","Version"], error = function(e){ install.packages("remotes") }) remotes::install_github("RGLab/FAUST", force = TRUE, build_vignettes = TRUE)

I came across some suspicious/error messages

E creating vignettes (2m 22.4s) --- re-building ‘faustIntro.Rmd’ using rmarkdown Quitting from lines 70-83 (faustIntro.Rmd) Error: processing vignette 'faustIntro.Rmd' failed with diagnostics: there is no package called 'flowWorkspaceData' --- failed re-building ‘faustIntro.Rmd’

SUMMARY: processing the following file failed: ‘faustIntro.Rmd’

Error: Vignette re-building failed. Execution halted Error: Failed to install 'faust' from GitHub: System command 'R' failed, exit status: 1, stderr empty

Thanks in advance for your help.

Allen

gfinak commented 4 years ago 
Error: processing vignette 'faustIntro.Rmd' failed with diagnostics:
there is no package called 'flowWorkspaceData'

You need to install that package to build the vignettes.

zonglunli7515 commented 4 years ago 
Error: processing vignette 'faustIntro.Rmd' failed with diagnostics:
there is no package called 'flowWorkspaceData'

You need to install that package to build the vignettes.

Many thanks.

zonglunli7515 commented 4 years ago 
Error: processing vignette 'faustIntro.Rmd' failed with diagnostics:
there is no package called 'flowWorkspaceData'

You need to install that package to build the vignettes.

Hi,

Thanks again for your speedy help. I'm very new to R and mass cytometry data analysis. Btw, do you know how to import my own dataset(s) of fcs format? It seems to me that the example data are contained in package flowWorkspaceData:

gsPath <- system.file("extdata","gs_bcell_auto", package = "flowWorkspaceData") gs <- load_gs(gsPath)

Best,

Allen

gfinak commented 4 years ago

Sure. You need to leverage the cytoverse packages to create a GatingSet object containing your compensated, transformed and pre-gated data. If you try to do population discovery on raw data you'll get nonsense results.. garbage in garbage out still applies. https://cytoverse.org/ Has more details... see the various package Vignettes on Bioconductor to get started.

zonglunli7515 commented 4 years ago

Sure. You need to leverage the cytoverse packages to create a GatingSet object containing your compensated, transformed and pre-gated data. If you try to do population discovery on raw data you'll get nonsense results.. garbage in garbage out still applies. https://cytoverse.org/ Has more details... see the various package Vignettes on Bioconductor to get started.

Many thanks! It still sounds intricate but I will digest it!

Best,

Allen

evangreene commented 4 years ago

Closing this issue since it appears the installation difficulties have been resolved. Please open another issue if further installation difficulties are encountered.