*SOLVED*

restart of R after installing the package solved the error

*SOVED*

Hi,

I wanted to try using the GSVA package and when I used the example from the vignette I always get this error afer calling gsva:

library(GSEABase)
library(GSVAdata)
data(c2BroadSets)
c2BroadSets

library(Biobase)
library(genefilter)
library(limma)
library(RColorBrewer)
library(GSVA)

cacheDir <- system.file("extdata", package="GSVA")
cachePrefix <- "cache4vignette_"
file.remove(paste(cacheDir, list.files(cacheDir, pattern=cachePrefix), sep="/"))

data(leukemia)
leukemia_eset

filtered_eset <- nsFilter(leukemia_eset, require.entrez=TRUE, remove.dupEntrez=TRUE,
                           var.func=IQR, var.filter=TRUE, var.cutoff=0.5, filterByQuantile=TRUE,
                           feature.exclude="^AFFX")
filtered_eset
leukemia_filtered_eset <- filtered_eset$eset

cache(leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets,
 min.sz=10, max.sz=500, verbose=TRUE)$es.obs,
 dir=cacheDir, prefix=cachePrefix)

Mapping identifiers between gene sets and feature names
Estimating GSVA scores for 2023 gene sets.
Computing observed enrichment scores
Estimating ECDFs in microarray data with Gaussian kernels
Allocating cluster
Estimating enrichment scores in parallel
Taking diff of max KS.
Error in do.call(c, clusterApply(cl, x = splitList(X, length(cl)), fun = lapply,  : 
  second argument must be a list

My sessioninfo():

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GSVA_1.24.1          RColorBrewer_1.1-2   genefilter_1.58.1    GSVAdata_1.12.0      hgu95a.db_3.2.3     
 [6] org.Hs.eg.db_3.4.1   RTN_1.14.1           RedeR_1.24.1         biomaRt_2.32.1       limma_3.32.5        
[11] GSEABase_1.38.0      graph_1.54.0         annotate_1.54.0      XML_3.98-1.9         AnnotationDbi_1.38.2
[16] IRanges_2.10.2       S4Vectors_0.14.3     Biobase_2.36.2       BiocGenerics_0.22.0 

loaded via a namespace (and not attached):
 [1] splines_3.4.1      lattice_0.20-35    colorspace_1.3-2   snow_0.4-2         mgcv_1.8-18       
 [6] blob_1.1.0         survival_2.41-3    rlang_0.1.2        nloptr_1.0.4       DBI_0.7           
[11] bit64_0.9-7        plyr_1.8.4         MatrixModels_0.4-1 munsell_0.4.3      memoise_1.1.0     
[16] SparseM_1.77       quantreg_5.33      pbkrtest_0.4-7     Rcpp_0.12.12       xtable_1.8-2      
[21] scales_0.4.1       bit_1.1-12         lme4_1.1-13        digest_0.6.12      grid_3.4.1        
[26] tools_3.4.1        bitops_1.0-6       magrittr_1.5       RCurl_1.95-4.8     tibble_1.3.3      
[31] RSQLite_2.0        car_2.1-5          pkgconfig_2.0.1    MASS_7.3-47        Matrix_1.2-11     
[36] data.table_1.10.4  minet_3.34.0       minqa_1.2.4        nnet_7.3-12        igraph_1.1.2      
[41] nlme_3.1-131       compiler_3.4.1    

Thank yozu very much for your help!

Best

Felix