Dear Users,

When I tried to install package SeqGSEA to R version 3.3.1, it has the error message as below.

shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/macosx/mavericks/contrib/3.3/DESeq_1.24.0.tgz'
Content type 'application/x-gzip' length 2172753 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/macosx/mavericks/contrib/3.3/SeqGSEA_1.12.0.tgz'
Content type 'application/x-gzip' length 1721423 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
Error in setwd(cDir) : character argument expected
Error in setwd(cDir) : character argument expected

It works find when I installed it to R version 3.2.3, but I would like to use new R version. Is it possible to install it?

Thanks in advance for any advise.

EL

> SessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.3 GenomicRanges_1.24.2 GenomeInfoDb_1.8.3   IRanges_2.6.1        S4Vectors_0.10.2    
[6] BiocGenerics_0.18.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.18.0 XVector_0.12.1  tools_3.3.1    

Thanks for your post. It is possible to install SeqGSEA in R version 3.3.1. See the SessionInfo() below. To resolve your issue, can you please test if you can install other R packages? If not, can you simply try to restart your computer, re-install R? Good luck!

> SessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)
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 stats graphics grDevices utils datasets methods base

other attached packages: 
[1] SeqGSEA_1.12.0 DESeq_1.24.0 lattice_0.20-33 locfit_1.5-9.1 doParallel_1.0.10 iterators_1.0.8 foreach_1.4.3 Biobase_2.32.0 
[9] BiocGenerics_0.18.0

loaded via a namespace (and not attached): 
[1] AnnotationDbi_1.34.4 splines_3.3.1 IRanges_2.6.1 xtable_1.8-2 tools_3.3.1 grid_3.3.1 DBI_0.4-1 genefilter_1.54.2 
[9] survival_2.39-5 Matrix_1.2-6 geneplotter_1.50.0 RColorBrewer_1.1-2 bitops_1.0-6 S4Vectors_0.10.2 codetools_0.2-14 RCurl_1.95-4.8 
[17] biomaRt_2.28.0 RSQLite_1.0.0 stats4_3.3.1 XML_3.98-1.4 annotate_1.50.0