Hi everyone,

im trying to install Diffbind to identify unique enriched peaks from treatment and control data.

i cant able to install diffbind in R it shows error(below)  i tried installing twice.

is there any tool to install to identify unique enriched peaks from chipseq data.

Need help

Thanks

ERROR: dependencies ‘GenomicRanges’, ‘Biobase’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’Alignments’, ‘Biobase’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘XVector’ are not available for package ‘ShortRead’

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IRanges’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XVector’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationForge’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Biostrings’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
11: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
12: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
13: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GSEABase’ had non-zero exit status
14: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
15: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
16: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
17: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Rsamtools’ had non-zero exit status
18: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Category’ had non-zero exit status
19: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
20: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status
21: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
22: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ShortRead’ had non-zero exit status
23: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GOstats’ had non-zero exit status
24: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome’ had non-zero exit status
25: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
26: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
27: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘systemPipeR’ had non-zero exit status
28: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DiffBind’ had non-zero exit status

What version of R are you using? Are you using the recommended method for installing Bioconductor packages?

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

Can you post a whole session, with R starting up (with the version), and biocLite loading?

-Rory