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7.9 years ago
viswanathrana29
▴
20
Hi all I heave insatlled then i install Bioconductor Packages through this command ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite() in R it show the following error Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) : unsupported URL scheme
biocLite() Error: could not find function "biocLite" How to solve this thank you
Thanx mbk0asis...now i am using this code source("http://bioconductor.org/biocLite.R") biocLite(c("GenomicFeatures", "AnnotationDbi")) then we get
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’ * removing ‘/home/vn/R/x86_64-pc-linux-gnu-library/3.0/rtracklayer’ ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’ * removing ‘/home/vn/R/x86_64-pc-linux-gnu-library/3.0/biomaRt’ ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’ * removing ‘/home/vn/R/x86_64-pc-linux-gnu-library/3.0/GenomicFeatures’
The downloaded source packages are in ‘/tmp/RtmpalrXpU/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘RCurl’ had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘rtracklayer’ had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘biomaRt’ had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘GenomicFeatures’ had non-zero exit status how to solve this error please help me.
I see that you are using Linux... you need to install XML and RCurl first, try this tutorial:
http://stackoverflow.com/questions/20671814/non-zero-exit-status-r-3-0-1-xml-and-rcurl
Note: the dependencies you need have to be installed as linux packages, not through R.