problem installing biocLite, MotifDb.
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@mirzabiotech2000-10952
Last seen 5.3 years ago

Hello,

I am very new to linux. I am using Ubuntu 14.04, on 32 bit system.

I installed R-3.3.0 and when I am trying to installed biocLite and MotifDb using the following command lines given on your sites (https://www.bioconductor.org/help/workflows/generegulation/ and https://www.bioconductor.org/packages/3.3/bioc/html/MotifDb.html)

source("https://bioconductor.org/biocLite.R")
biocLite("MotifDb")
biocLite(c("MotifDb",  "GenomicFeatures", 
           "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene",
           "org.Sc.sgd.db", "BSgenome.Scerevisiae.UCSC.sacCer3",
           "motifStack", "seqLogo"))

Its is giving the following errors/ warnings:

There were 12 warnings (use warnings() to see them)

> warnings()

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 ‘rtracklayer’ had non-zero exit status

3: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘grImport’ had non-zero exit status

4: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘BSgenome’ had non-zero exit status

5: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘MotifDb’ had non-zero exit status

6: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘rGADEM’ 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 ‘BSgenome.Scerevisiae.UCSC.sacCer3’ had non-zero exit status

9: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘MotIV’ had non-zero exit status

10: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘GenomicFeatures’ had non-zero exit status

11: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘TxDb.Scerevisiae.UCSC.sacCer3.sgdGene’ had non-zero exit status

12: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘motifStack’ had non-zero exit status

Kindly help, its really imp and urgent.

Thank you,

 

motifdb bioclite • 794 views
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@herve-pages-1542
Last seen 3 days ago
Seattle, WA, United States

Hi,

It looks like the root of the problem is that the XML package could not be installed, probably because it could not be compiled. Compilation of XML needs to be able to link to a system library. Install this library (and its header files) with sudo apt-get install libxml2-dev on Ubuntu.

Cheers,

H.

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