Entering edit mode
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!
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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’