Rstudio on Galaxy.eu : installing new packages

usegalaxy.eu support
,
1

Hello,
I’m having trouble installing packages to RStudio on galaxy.eu.

I would like to install SNPRelate and its dependent package gdsfmt. I tried following the instructions in RStudio to use conda install : conda install -c bioconda bioconductor-gdsfmt but got the following error : Error: unexpected symbol in “conda install”
Not sure what I’m doing wrong here.

I also tried installing the package using biocManager: BiocManager::install("gdsfmt")
but that led to the following error:
/bin/sh: 1: x86_64-conda-linux-gnu-c++: not found
make: *** [/opt/miniconda/lib/R/etc/Makeconf:177: R_CoreArray.o] Error 127
ERROR: compilation failed for package ‘gdsfmt’

  • removing ‘/opt/miniconda/lib/R/library/gdsfmt’

I appreciate any advice on how to install these packages that I need for my analysis.
Thanks!

1 Like
2

May I know if you have solved this problem? I am encountering the same problem now. Thanks!

3

Same here. Would be nice to get an answer. I have that issue for several packages, such as zen4R.

4

I unfortunately never got an answer so decided to do this on my local version of RStudio.

5

Too bad. There is not much you can do with an RStudio instance if you cannot install packages…

my error msg:

Configuration failed to find the libv8 engine library. Try installing:
 * deb: libv8-dev or libnode-dev (Debian / Ubuntu)
 * rpm: v8-devel (Fedora, EPEL)
 * brew: v8 (OSX)
 * csw: libv8_dev (Solaris)
Alternatively, on Linux (x86_64) or MacOS you can set environment variable:
    DOWNLOAD_STATIC_LIBV8=1
to automatically download a static version of libv8.
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
---------------------------[ ERROR MESSAGE ]----------------------------
./configure: 97: x86_64-conda-linux-gnu-c++: not found
6

Yeah, those are the limits for now. We host at the public servers mostly for training purposes. Getting set up with a local Galaxy is one choice – can move data up to a public site when want to work with regular tools.

This may change but is how it works for now :slight_smile: