* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/annotate’ĮRROR: dependencies ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’ * removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/rhdf5’ĮRROR: dependency ‘XML’ is not available for package ‘annotate’ * removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/biomaRt’ĮRROR: dependency ‘Rhdf5lib’ is not available for package ‘rhdf5’ * removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/rtracklayer’ĮRROR: dependency ‘XML’ is not available for package ‘biomaRt’ * removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/XML’ĮRROR: dependency ‘XML’ is not available for package ‘rtracklayer’
noĮRROR: configuration failed for package ‘XML’ Here are a collection of them: cp: cannot stat 'hdf5/c++/src/.libs/libhdf5_cpp.a': No such file or directoryĮRROR: compilation failed for package ‘Rhdf5lib’Ĭhecking for xmlParseFile in -lxml2. All is going well until they try to install any of the R bioconductor packages. They then access R from the terminal and begin the process of installing Bioconductor’s biocmanager. Then user 2 set up a conda environment and install R-base and R-essentials. This machine has a fresh installation of Ubuntu, please don’t presume I have all the necessary dependencies.Īs sudo, user 1 (me) installed Anaconda, which then becomes executable by user 2. I have an Ubuntu machine with three accounts: root, user 1 with sudo privileges and part of group 1001, and user 2 also part of group 1001. I would appreciate some assistance resolving Bioconductor R package installation problems within a conda environment.
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