##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cytofast.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cytofast_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cytofast.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytofast/DESCRIPTION’ ... OK
* this is package ‘cytofast’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cytofast’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'cytofast' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.13-bioc/meat/cytofast.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cytofast-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cfList-class
> ### Title: Class cfList
> ### Aliases: cfList-class cfList samples samples,cfList-method expr
> ###   expr,cfList-method counts counts,cfList-method results
> ###   results,cfList-method show,cfList-method
> 
> ### ** Examples
> 
> ### manually create instance of cfList class
> library(FlowSOM)
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Thanks for using FlowSOM. From version 2.1.4 on, the scale 
parameter in the FlowSOM function defaults to FALSE
> 
> ## Cluster with FlowSOM
> dirFCS <- system.file("extdata", package="cytofast")
> fSOM <- FlowSOM(input = dirFCS, 
+                 transform = FALSE,
+                 scale = FALSE,
+                 colsToUse = c(9:11, 15:52),
+                 nClus = 10, # Note that this is an ambiguous choice
+                 seed = 123)
> 
> ## expr slot
> # retrieve clusters
> clusterID <- as.factor(fSOM$FlowSOM$map$mapping[,1])
> levels(clusterID) <- fSOM$metaclustering
> 
> # retrieve samples (As example, we assume each FCS file is its own sample)
> sampleID <- lapply(fSOM$FlowSOM$metaData, function(x){rep(x[1], each = length(x[1]:x[2]))})
> attr(sampleID, 'names') <- NULL
> sampleID <- as.factor(unlist(sampleID)) 
> levels(sampleID) <- paste("ID", 1:10, sep="_")
> 
> exprD <- data.frame(clusterID, 
+                     sampleID, 
+                     fSOM$FlowSOM$data[, c(9:11, 15:52)])
> 
> ## samples slot
> samplesD <- data.frame(sampleID = levels(sampleID), 
+                        group = rep(c("group1", "group1"), each=5)) 
> 
> ## create cfList
> cfList(samples = samplesD,
+        expr = exprD)
Error in validObject(.Object) : 
  invalid class “cfList” object: 1: expr slot is missing a "sampleID" column
invalid class “cfList” object: 2: expr slot is missing a "clusterID" column
Calls: cfList -> new -> initialize -> initialize -> validObject
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/cytofast.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cytofast
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘cytofast’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘expr’ in package ‘cytofast’
** help
Loading required namespace: cytofast
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'cytofast' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'cytofast' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package keeps a record of temporary installation path
* DONE (cytofast)