Error in if (outputType == "MAST" & !requireNamespace("MAST", quietly = TRUE)) stop("for outputType 'MAST', you must have package 'MAST' from Bioconductor installed.") : the condition has length > 1

[HenrikBengtsson]

I'm seeing the below error when running R CMD check --as-cran on clusterExperiment (1.3.2) with _R_CHECK_LENGTH_1_CONDITION_=true.

checking examples ... ERROR
Running examples in ‘clusterExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterContrasts,ClusterExperiment-method
> ### Title: Create contrasts for testing DE of a cluster
> ### Aliases: clusterContrasts,ClusterExperiment-method clusterContrasts
> ###   clusterContrasts,vector-method
> 
> ### ** Examples
> 
> data(simData)
> cl <- clusterMany(simData,nPCADims=c(5,10,50),  dimReduce="PCA",
+ clusterFunction="pam", ks=2:4, findBestK=c(FALSE), removeSil=TRUE,
+ subsample=FALSE)
> #Pairs:
> clusterContrasts(cl,contrastType="Pairs")
Error in if (outputType == "MAST" & !requireNamespace("MAST", quietly = TRUE)) stop("for outputType 'MAST', you must have package 'MAST' from Bioconductor installed.") : 
  the condition has length > 1
Calls: clusterContrasts ... .local -> clusterContrasts -> clusterContrasts -> .local
Execution halted

FYI, with _R_CHECK_LENGTH_1_CONDITION_=true we get:

> Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "true")
> if (1:2 == 1) TRUE
Error in if (1:2 == 1) TRUE : the condition has length > 1

whereas without we only get a warning:

> Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "false")

> if (1:2 == 1) TRUE
[1] TRUE
Warning message:
In if (1:2 == 1) TRUE :
  the condition has length > 1 and only the first element will be used

[epurdom]

Thanks. This was due to a missing match.arg in clusterContrasts when I added the argument of outputType to handle MAST format. I have committed a fix to this on both the master and develop branch (commit 125b7aa).