R errors upon installation

[sandbardev]

Hello. I'm trying to install ballgown on Ubuntu 16.04 and I'm getting the following error messages:

SafetyError: The package for r-rcpp located at /home/mfl/miniconda3/pkgs/r-rcpp-0.12.17-r341h9d2a408_2
appears to be corrupted. The path 'lib/R/library/Rcpp/doc/Rcpp-introduction.pdf'
has a sha256 mismatch.
reported sha256: c8231d1db61b6cbd3128c50cb29020ed123cac64f359976d3c527e25e0706bfb
actual sha256: c272b3a49c68a3b93225ee20df2014d36c67772f160321512d17ecf6f647bb51

CondaVerificationError: The package for r-rcpp located at /home/mfl/miniconda3/pkgs/r-rcpp-0.12.17-r341h9d2a408_2
appears to be corrupted. The path 'lib/R/library/Rcpp/include/Rcpp/module/Module_generated_CppFunction.h'
specified in the package manifest cannot be found.

CondaVerificationError: The package for r-rcpp located at /home/mfl/miniconda3/pkgs/r-rcpp-0.12.17-r341h9d2a408_2
appears to be corrupted. The path 'lib/R/library/Rcpp/include/Rcpp/module/Module_generated_CppMethod.h'
specified in the package manifest cannot be found.

CondaVerificationError: The package for r-rcpp located at /home/mfl/miniconda3/pkgs/r-rcpp-0.12.17-r341h9d2a408_2
appears to be corrupted. The path 'lib/R/library/Rcpp/include/Rcpp/module/Module_generated_Pointer_CppMethod.h'
specified in the package manifest cannot be found.

CondaVerificationError: The package for r-rcpp located at /home/mfl/miniconda3/pkgs/r-rcpp-0.12.17-r341h9d2a408_2
appears to be corrupted. The path 'lib/R/library/Rcpp/libs/Rcpp.so'
specified in the package manifest cannot be found.

ClobberError: The package 'conda-forge::libgcc-7.2.0-h69d50b8_2' cannot be installed due to a
path collision for 'lib/libgfortran.so.3'.
This path already exists in the target prefix, and it won't be removed by
an uninstall action in this transaction. The path appears to be coming from
the package 'conda-forge::libgfortran-3.0.0-1', which is already installed in the prefix.

ClobberError: The package 'conda-forge::libgcc-7.2.0-h69d50b8_2' cannot be installed due to a
path collision for 'lib/libgfortran.so.3.0.0'.
This path already exists in the target prefix, and it won't be removed by
an uninstall action in this transaction. The path appears to be coming from
the package 'conda-forge::libgfortran-3.0.0-1', which is already installed in the prefix.

I have tried reinstalling R natively, in and out of the specific Conda env and nothing seemed to change de result. Installing ballgown through the github instructions also changed nothing, nor did installing r-rcpp directly through the conda repositories(ballgown asks the package to be downgraded).

[JMF47]

Hi Sanderson, just checking - what version of R is it being installed to?

[sandbardev]

During the conda installation:

The following packages will be DOWNGRADED:

r-base: 3.5.1-h4fe35fd_1 conda-forge --> 3.4.1-h4fe35fd_8 conda-forge
r-rcpp: 0.12.18-r351h29659fb_0 r --> 0.12.17-r341h9d2a408_2 conda-forge

Proceed ([y]/n)?

If I'm correct, it's asking to downgrade R from 3.5.1 to 3.4.1, and r-rcpp from 0.12.18 to 0.12.17.
On what I suppose to be the development version(this repository), after trying to install through R:

The downloaded source packages are in
‘/tmp/RtmpzB80cT/downloaded_packages’
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 ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘annotate’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘genefilter’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘sva’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘ballgown’ had non-zero exit status

I mentioned this second but I believe it to be it's own separate issue. If appropriate, I will submit another issue accordingly.