Problems to install a package - Ubuntu
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@lelemraposo-7775
Last seen 6.4 years ago
Brazil

Hello everybody,

does anyone could help me with this problem?

I really need to install "VariantTools" in my machine but everytime appears this problem.

Thanks so much!

(...)

installing to /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/XML/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (XML)
ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/biomaRt’
ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/GenomicFeatures’
ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/BSgenome’
ERROR: dependencies ‘BSgenome’, ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/VariantAnnotation’
ERROR: dependencies ‘rtracklayer’, ‘GenomicFeatures’, ‘VariantAnnotation’, ‘BSgenome’ are not available for package ‘gmapR’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/gmapR’
ERROR: dependencies ‘VariantAnnotation’, ‘gmapR’, ‘GenomicFeatures’, ‘rtracklayer’, ‘BSgenome’ are not available for package ‘VariantTools’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/VariantTools’

The downloaded source packages are in
    ‘/tmp/RtmpD1G628/downloaded_packages’
Old packages: 'manipulate', 'MASS', 'spatial'
Update all/some/none? [a/s/n]:
n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘gmapR’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘VariantTools’ had non-zero exit status
> library("VariantTools")
Error in library("VariantTools") :
  there is no package called ‘VariantTools’
ubuntu package installation varianttools • 8.3k views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States

The error is slightly confusing, but I think it shouldn't be that difficult to interpret:

ERROR: dependency ‘RCurl’ is not available

Which means that you don't have RCurl installed. So your next step is

biocLite("RCurl")

and if that fails (which it may), then it will likely be due to missing headers for libcurl, in which case you will need to do something like

sudo apt-get install libcurl4-openssl-dev

at the terminal, or have your sysadmin do it for you.

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