DiffBind installation error in R & Rstudio?

Question

[gskbioinfo143]

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

[steve]

we have been having issues installing many R packages under R version 3.3.0, with the culprit being an incompatible versions of zlib and the C++ compilers being used to compile the packages after download. Not sure if your system is using though so I cannot say what the exact fix for you would be, but I suspect this might be a good place to start looking.

Another potential issue is that you might not be running the latest version of R (3.3) and Bioconductor (3.3), so check on this. And make sure that you are using biocLite to install the Bioconductor packages, not R's install.packages (this is a common mistake). For reference:
http://bioconductor.org/packages/release/bioc/html/DiffBind.html
http://bioconductor.org/packages/release/bioc/html/ShortRead.html

[gskbioinfo143]

yes im using latest R & bioconductor. i followed the same procedure to install but still error comes

Answer 1

[Sinji]

You can use DiffReps as a stand alone command line program for ChIP-seq differential expression analysis.

It looks like you're missing some critical libraries so the packages will not download. The big ones I notice right away are the XML and RCurl libraries which can be solved by looking at this StackOverflow answer.