I have some problems installing ggcyto from GitHub.

I have used openCyto previously, and I am hoping to be able to integrate this with ggplot, which is my preferred plotting system in R.

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Norwegian (Bokmål)_Norway.1252 
[2] LC_CTYPE=Norwegian (Bokmål)_Norway.1252   
[3] LC_MONETARY=Norwegian (Bokmål)_Norway.1252
[4] LC_NUMERIC=C                              
[5] LC_TIME=Norwegian (Bokmål)_Norway.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.1

loaded via a namespace (and not attached):
 [1] httr_1.0.0     R6_2.1.1       magrittr_1.5   tools_3.2.3    curl_0.9.4    
 [6] memoise_0.2.1  stringi_1.0-1  stringr_1.0.0  digest_0.6.8   devtools_1.9.1

> devtools::install_github('RGLab/ggcyto', ref="trunk")
Downloading GitHub repo RGLab/ggcyto@trunk
Installing ggcyto
Skipping 2 packages ahead of CRAN: ggplot2, ncdfFlow
"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save  \
  --no-restore CMD INSTALL  \
  "C:/Users/anderto/AppData/Local/Temp/RtmpCgJbpX/devtoolsc24670d6f5b/RGLab-ggcyto-9f63ca9"  \
  --library="C:/Program Files/R/R-3.2.3/library" --install-tests 

* installing *source* package 'ggcyto' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'jsonlite' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Warning: multiple methods tables found for 'lapply'
Warning: replacing previous import by 'grid::unit' when loading 'ggcyto'
Error in eval(expr, envir, enclos) : could not find function "eval"
Error : unable to load R code in package 'ggcyto'
ERROR: lazy loading failed for package 'ggcyto'
* removing 'C:/Program Files/R/R-3.2.3/library/ggcyto'
* restoring previous 'C:/Program Files/R/R-3.2.3/library/ggcyto'
Error: Command failed (1)

> traceback()
10: stop("Command failed (", status, ")", call. = FALSE)
9: system_check(r_path, options, c(r_profile(), r_env_vars(), env_vars), 
       ...)
8: force(code)
7: in_dir(path, system_check(r_path, options, c(r_profile(), r_env_vars(), 
       env_vars), ...))
6: R(paste("CMD INSTALL ", shQuote(built_path), " ", opts, sep = ""), 
       quiet = quiet)
5: install(source, ..., quiet = quiet)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = logical(1))
2: install_remotes(remotes, ...)
1: devtools::install_github("RGLab/ggcyto", ref = "trunk")
> 

By upgrading ncdfFlow to the GitHub version I am able to install ggcyto branch="fast" or "ggplot1.1", but not the "trunk" version. The ggcyto package seems to work then, but flowWorkspace command GetGatingset() returns error:

gs <- GatingSet(fs)
Error in as.list.default(X) : 
  no method for coercing this S4 class to a vector
> traceback()
10: as.list.default(X)
9: as.list(X)
8: lapply(x, function(gh) {
       sampleName <- sampleNames(gh)
       if (verbose) 
           message(paste("gating", sampleName, "..."))
       else message(".", appendLF = FALSE)
       if (alwaysLoadData) 
           isloadData <- TRUE
       else {
           isAllBoolGate <- all(sapply(y, .isBoolGate, x = gh))
           if (isAllBoolGate) {
               isloadData <- all(sapply(y, function(i) {
                   pid <- getParent(gh, i)
                   isParentGated <- isGated(gh, pid)
                   bf <- getGate(gh, i)
                   refNodes <- filterObject(bf)$refs
                   isRefGated <- all(sapply(refNodes, isGated, obj = gh))
                   !(isParentGated && isRefGated)
               }))
           }
           else isloadData <- TRUE
       }
       if (isloadData) {
           data <- getData(gh)
           mat <- exprs(data)
       }
       else {
           mat <- matrix(nrow = 0, ncol = 1, dimnames = list(NULL, 
               "dummy"))
       }
       lapply(y, function(i) {
           nodeID <- .getNodeInd(gh, i)
           nodeInd <- as.integer(nodeID) - 1
           recompute <- TRUE
           res <- try(.Call("R_gating", gh@pointer, mat, sampleName, 
               gains, nodeInd, recompute, extend_val, ignore_case, 
               leaf.bool), silent = TRUE)
           if (class(res) == "try-error") {
               if (!isloadData && grepl("not found in flowData", 
                   res)) 
                   stop("Found ungated upstream population. Set 'alwaysLoadData = TRUE' for 'recompute' method, and try again!")
               else stop(res)
           }
       })
   })
7: lapply(x, function(gh) {
       sampleName <- sampleNames(gh)
       if (verbose) 
           message(paste("gating", sampleName, "..."))
       else message(".", appendLF = FALSE)
       if (alwaysLoadData) 
           isloadData <- TRUE
       else {
           isAllBoolGate <- all(sapply(y, .isBoolGate, x = gh))
           if (isAllBoolGate) {
               isloadData <- all(sapply(y, function(i) {
                   pid <- getParent(gh, i)
                   isParentGated <- isGated(gh, pid)
                   bf <- getGate(gh, i)
                   refNodes <- filterObject(bf)$refs
                   isRefGated <- all(sapply(refNodes, isGated, obj = gh))
                   !(isParentGated && isRefGated)
               }))
           }
           else isloadData <- TRUE
       }
       if (isloadData) {
           data <- getData(gh)
           mat <- exprs(data)
       }
       else {
           mat <- matrix(nrow = 0, ncol = 1, dimnames = list(NULL, 
               "dummy"))
       }
       lapply(y, function(i) {
           nodeID <- .getNodeInd(gh, i)
           nodeInd <- as.integer(nodeID) - 1
           recompute <- TRUE
           res <- try(.Call("R_gating", gh@pointer, mat, sampleName, 
               gains, nodeInd, recompute, extend_val, ignore_case, 
               leaf.bool), silent = TRUE)
           if (class(res) == "try-error") {
               if (!isloadData && grepl("not found in flowData", 
                   res)) 
                   stop("Found ungated upstream population. Set 'alwaysLoadData = TRUE' for 'recompute' method, and try again!")
               else stop(res)
           }
       })
   })
6: .recompute(x, ...)
5: recompute(G)
4: recompute(G)
3: .local(x, ...)
2: GatingSet(fs)
1: GatingSet(fs)
> 

I am very thankfull for any help from this excellent community,

Anders Tøndell, PhD molecular medicine, NTNU, Norway

"" 

Given the the latest release of ggplot 2.0, I've merged 'ggplot1.1' branch to 'trunk', which is the version you should use. Don't use 'fast' branch since it is at the experimental stage.

Your 'GatingSet' error is a separate issue, without the context, I can't tell where went wrong. You want to check if 'fs' is a valid 'flowSet' or 'ncdfFlowSet' object.

Thank you for responding!

It now turns out that I was able to solve the issue. It seems that the binary version of flowCore was 'old', and I was unable to install the source version(1.36.5).

However, by upgrading flowCore to the RGLab-version: 'devtools::install_github('RGLab/flowCore', ref="trunk")'

and ncdfFlow:

'devtools::install_github('RGLab/ncdfFlow', ref="trunk")'

finally, 

'devtools::install_github('RGLab/ggcyto', ref="trunk")'

went through without errors!

The problem with 'GatingSet()' and several commands in flowWorkspace (Error in as.list.default(X) : 
  no method for coercing this S4 class to a vector) was also fixed, and everything is now working fine, apart from some warnings, (For example when installing ggcyto: Warning: multiple methods tables found for 'lapply').

I look forward to exploring openCyto and ggcyto further!

Anders Tøndell