Hello,

I tried to re-run the same script on the same samples and I encountered this error. 

txi.rsem <- tximport(files, type = "rsem", reader = read_tsv)

Error in tximport(files, type = "rsem", reader = read_tsv) : 

  unused argument (reader = read_tsv)

The only thing that changed between the first time I ran it and this one is I downloaded the latest versions of R and RStudio. 

I tried importing with read.delim instead, but I got the same error.

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] DESeq2_1.16.1              SummarizedExperiment_1.6.4 DelayedArray_0.2.7       
[4] matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.5     
[7] GenomeInfoDb_1.12.2        IRanges_2.10.3             S4Vectors_0.14.4         
[10] BiocGenerics_0.22.0        readr_1.1.1                tximport_1.4.0           
[13] BiocInstaller_1.26.1       refGenome_1.7.3            RSQLite_2.0              
[16] doBy_4.5-15               

loaded via a namespace (and not attached):
[1] locfit_1.5-9.1          Rcpp_0.12.12            lattice_0.20-35       
[4] digest_0.6.12           R6_2.2.2                plyr_1.8.4            
[7] backports_1.1.0         acepack_1.4.1           ggplot2_2.2.1         
[10] zlibbioc_1.22.0         rlang_0.1.2             lazyeval_0.2.0        
[13] data.table_1.10.4       annotate_1.54.0         blob_1.1.0            
[16] rpart_4.1-11            Matrix_1.2-10           checkmate_1.8.3       
[19] splines_3.4.1           BiocParallel_1.10.1     geneplotter_1.54.0    
[22] stringr_1.2.0           foreign_0.8-69          htmlwidgets_0.9       
[25] RCurl_1.95-4.8          bit_1.1-12              munsell_0.4.3         
[28] compiler_3.4.1          base64enc_0.1-3         htmltools_0.3.6       
[31] nnet_7.3-12             tibble_1.3.4            gridExtra_2.3         
[34] htmlTable_1.9           GenomeInfoDbData_0.99.0 Hmisc_4.0-3           
[37] XML_3.98-1.9            MASS_7.3-47             bitops_1.0-6          
[40] grid_3.4.1              xtable_1.8-2            gtable_0.2.0          
[43] DBI_0.7                 magrittr_1.5            scales_0.5.0          
[46] stringi_1.1.5           XVector_0.16.0          genefilter_1.58.1     
[49] latticeExtra_0.6-28     Formula_1.2-2           RColorBrewer_1.1-2    
[52] tools_3.4.1             bit64_0.9-7             hms_0.3               
[55] survival_2.41-3         AnnotationDbi_1.38.2    colorspace_1.3-2      
[58] cluster_2.0.6           memoise_1.1.0           knitr_1.17 

You can just leave out the argument. This change is described in NEWS.