Hi

I was doing a pathway analysis of RNA-Seq data using ToPASeq program. I ran the following commands :

> library("ToPASeq")
> library("gageData")
> DEXcounts = read.table("/home/febin/DEXcounts.txt", header = TRUE ,row.names = 1)
> DEXcounts = DEXcounts[,6:ncol(DEXcounts)]
> DEXcounts <- DEXcounts[rowSums(DEXcounts)>0,]
> grpTopDex = c(rep("cntrl",2),rep("dex2",2),rep("dex4",2))
> kegg<-pathways("hsapiens","kegg")
> spi<-SPIA(DEXcounts, grpTopDex, kegg,type="RNASeq")
    Error in .local(object, which, ...) :  unused argument (stringsAsFactors = FALSE)

Here is my  sessionInfo

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
[1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8      
[4] LC_COLLATE=en_IN.UTF-8     LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8  
[7] LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C             
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] gageData_2.16.0     ToPASeq_1.11.0      Rgraphviz_2.22.0    locfit_1.5-9.1      graph_1.56.0      
[6] BiocGenerics_0.24.0 gRbase_1.8-3        graphite_1.24.1     edgeR_3.20.9        limma_3.34.9       

loaded via a namespace (and not attached):
  [1] bitops_1.0-6               matrixStats_0.53.1         bit64_0.9-7              
  [4] progress_1.1.2             doParallel_1.0.11          RColorBrewer_1.1-2       
  [7] httr_1.3.1                 GenomeInfoDb_1.14.0        tools_3.4.3              
[10] backports_1.1.2            R6_2.2.2                   rpart_4.1-13             
[13] Hmisc_4.1-1                DBI_0.8                    lazyeval_0.2.1           
[16] colorspace_1.3-2           nnet_7.3-12                prettyunits_1.0.2        
[19] RMySQL_0.10.14             gridExtra_2.3              DESeq2_1.18.1            
[22] bit_1.1-12                 compiler_3.4.3             clipper_1.18.0           
[25] Biobase_2.38.0             htmlTable_1.11.2           DelayedArray_0.4.1       
[28] rtracklayer_1.38.3         KEGGgraph_1.38.0           scales_0.5.0             
[31] checkmate_1.8.5            mvtnorm_1.0-7              qpgraph_2.12.0           
[34] genefilter_1.60.0          RBGL_1.54.0                rappdirs_0.3.1           
[37] DESeq_1.30.0               Rsamtools_1.30.0           stringr_1.3.0            
[40] digest_0.6.15              foreign_0.8-69             R.utils_2.6.0            
[43] XVector_0.18.0             base64enc_0.1-3            pkgconfig_2.0.1          
[46] htmltools_0.3.6            maps_3.2.0                 htmlwidgets_1.0          
[49] rlang_0.2.0                rstudioapi_0.7             RSQLite_2.0              
[52] BiocParallel_1.12.0        acepack_1.4.1              R.oo_1.21.0              
[55] RCurl_1.95-4.10            magrittr_1.5               qtl_1.42-8               
[58] GenomeInfoDbData_1.0.0     Formula_1.2-2              dotCall64_0.9-5.2        
[61] Matrix_1.2-11              Rcpp_0.12.16               munsell_0.4.3            
[64] S4Vectors_0.16.0           R.methodsS3_1.7.1          stringi_1.1.7            
[67] yaml_2.1.18                SummarizedExperiment_1.8.1 zlibbioc_1.24.0          
[70] plyr_1.8.4                 blob_1.1.1                 lattice_0.20-35          
[73] Biostrings_2.46.0          splines_3.4.3              GenomicFeatures_1.30.3   
[76] annotate_1.56.2            knitr_1.20                 pillar_1.2.1             
[79] igraph_1.2.1               GenomicRanges_1.30.3       corpcor_1.6.9            
[82] biomaRt_2.34.2             codetools_0.2-15           geneplotter_1.56.0       
[85] stats4_3.4.3               XML_3.98-1.10              latticeExtra_0.6-28      
[88] data.table_1.10.4-3        spam_2.1-3                 foreach_1.4.4            
[91] gtable_0.2.0               assertthat_0.2.0           ggplot2_2.2.1            
[94] TeachingDemos_2.10         xtable_1.8-2               survival_2.41-3          
[97] tibble_1.4.2               iterators_1.0.9            GenomicAlignments_1.14.1 
[100] AnnotationDbi_1.40.0       memoise_1.1.0              IRanges_2.12.0           
[103] fields_9.6                 cluster_2.0.6      

How can I overcome this error? Thanks in advance.