problem in loading systemPipeR and RNASeqGene packages in R 3.4.1

Question

[nazaninhoseinkhan]

Dear all

I want to run RNASeq analysis in R.

Unfortunately when I try to load systemPipeR or RNASeqGene packages in R 3.4.1, I get the same error:

Error: package or namespace load failed for ‘GenomicRanges’:
 .onLoad failed in loadNamespace() for 'XVector', details:
  call: get(name, envir = asNamespace(pkg), inherits = FALSE)
  error: object 'setDefaultSlotValue' not found
Error: package ‘GenomicRanges’ could not be loaded

Can anybody help me to solve this problem?

Regards

Nazanin

[e.rempel]

What OS do you have?

[nazaninhoseinkhan]

I am trying to run RNASeq analysis on R 3.4.1 in windows 7

[h.mon]

What is the output of sessionInfo()?

[nazaninhoseinkhan]

I forgot to say that I get the error message when I want to install "airway" package which is a prerequisite of loading both sysytemPipeR and RNASeqGene packages.

The sessionInfo():

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
 [1] compiler_3.4.1  backports_1.1.0 magrittr_1.5    BiocStyle_2.4.1
 [5] rprojroot_1.2   htmltools_0.3.6 tools_3.4.1     yaml_2.1.14    
 [9] Rcpp_0.12.12    stringi_1.1.5   rmarkdown_1.6   knitr_1.17     
[13] stringr_1.2.0   digest_0.6.10   evaluate_0.10.1

[h.mon]

How are you trying to install airway?

source("https://bioconductor.org/biocLite.R")
biocLite("airway")

[nazaninhoseinkhan]

Using "source("https://bioconductor.org/biocLite.R") biocLite("airway")"

I get this message : Warning message: package ‘airway’ is not available (for R version 3.4.1)

And when I try to manually install it, I get the error that the package GenomicRanges can not be loaded.

[e.rempel]

Cannot tell for Windows, I was able to install airway package on OSX using R version 3.4.1

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   base     

other attached packages:
 [1] airway_0.110.0             SummarizedExperiment_1.6.3 DelayedArray_0.2.7        
 [4] matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.4      
 [7] GenomeInfoDb_1.12.2        IRanges_2.10.2             S4Vectors_0.14.3          
[10] BiocGenerics_0.22.0       

loaded via a namespace (and not attached):
 [1] lattice_0.20-35         bitops_1.0-6            grid_3.4.1              zlibbioc_1.22.0        
 [5] XVector_0.16.0          Matrix_1.2-11           tools_3.4.1             RCurl_1.95-4.8         
 [9] compiler_3.4.1          GenomeInfoDbData_0.99.0