I am struggling installing R package DESeq. What I am doing is :

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2", dependencies = TRUE)

However, some dependencies are not available

ERROR: dependency ‘latticeExtra’ is not available for package ‘Hmisc’
* removing ‘/nfs/users/spoeta/R.packages/R.3.3.2/Hmisc’
* installing *source* package ‘airway’ ...
** data
** inst
** help
*** installing help indices
  converting help for package ‘airway’
    finding HTML links ... done
    airway                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (airway)
ERROR: dependency ‘Hmisc’ is not available for package ‘DESeq2’
* removing ‘/nfs/users/spoeta/R.packages/R.3.3.2/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmpOrNrqN/downloaded_packages’
installation path not writeable, unable to update packages: boot, class, cluster,
  codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, rpart
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IHW’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Hmisc’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

It seems that the problem is latticeExtra for Hmisc package, however cannot load it. I tried without success several things, one of them:

biocLite("latticeExtra")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘latticeExtra’
installation path not writeable, unable to update packages: boot, class, cluster,
  codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, rpart
Warning message:
package ‘latticeExtra’ is not available (for R version 3.3.2) 

However, I was using DESeq2 before, don't understand what is happening ...

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)

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

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

other attached packages:
 [1] BiocInstaller_1.24.0       EnhancedVolcano_1.1.3      ggrepel_0.8.1             
 [4] biomaRt_2.30.0             SummarizedExperiment_1.2.3 Biobase_2.32.0            
 [7] GenomicRanges_1.24.3       GenomeInfoDb_1.10.3        IRanges_2.6.1             
[10] S4Vectors_0.10.3           BiocGenerics_0.20.0        RColorBrewer_1.1-2        
[13] gplots_3.0.1.2             limma_3.28.21              dplyr_0.8.3               
[16] ggdendro_0.1-20            readr_1.3.1                plyr_1.8.5                
[19] reshape2_1.4.3             lattice_0.20-34            reshape_0.8.8             
[22] ggpubr_0.2.4               magrittr_1.5               ggplot2_3.2.1             

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3           gtools_3.8.1         assertthat_0.2.1    
 [4] zeallot_0.1.0        digest_0.6.12        R6_2.4.1            
 [7] backports_1.1.3      RSQLite_2.0          pillar_1.4.3        
[10] zlibbioc_1.20.0      rlang_0.4.2          lazyeval_0.2.2      
[13] rstudioapi_0.10      gdata_2.18.0         blob_1.1.0          
[16] stringr_1.4.0        RCurl_1.95-4.12      bit_1.1-12          
[19] munsell_0.5.0        pkgconfig_2.0.3      tidyselect_0.2.5    
[22] tibble_2.1.3         XML_3.98-1.9         crayon_1.3.4        
[25] withr_2.1.2          MASS_7.3-45          bitops_1.0-6        
[28] grid_3.3.2           gtable_0.3.0         lifecycle_0.1.0     
[31] DBI_0.7              scales_1.1.0         KernSmooth_2.23-15  
[34] stringi_1.2.3        XVector_0.12.1       ggsignif_0.6.0      
[37] vctrs_0.2.1          tools_3.3.2          bit64_0.9-7         
[40] glue_1.3.1           purrr_0.3.3          hms_0.5.3           
[43] AnnotationDbi_1.38.2 colorspace_1.4-0     BiocManager_1.30.10 
[46] caTools_1.17.1.2     memoise_1.1.0 

Your R version is almost 4 years old. Unfortunately your first step must be to install a modern version of R. It looks like you are working on an HPC cluster, so the cluster administrator should be able to help. (A typical DESeq2 analysis does not require an HPC, so you could also try to install R on your own computer, following instructions at https://cran.r-project.org/).