Spent a long time trying to install xps on Ubuntu 14.04. After successful installation of ROOT (root_v5.34.24.Linux-slc6_amd64-gcc4.8.tar.gz - specific to my system as gcc4.8 and 64bit). I got this error message from running either
R CMD INSTALL xps_1.30.0.tar.gz
or
source("http://bioconductor.org/biocLite.R") biocLite("xps", type="source")
I would get the following error:
** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/alex/R/library/xps/libs/xps.so': libcrypto.so.10: cannot open shared object file: No such file or directory Error: loading failed Execution halted ERROR: loading failed * removing ‘/home/alex/R/library/xps’
Attempted re-install R as I have had some permission issues installing certain packages (requiring sudo R). After setting up a personal package directory (/home/alex/R/library) I still got the issue above.
This askubuntu solved the issue for me. I've included the post below in case link is ever lost:
Lets make sure that you have your SSL installed and updated:
sudo apt-get update
sudo apt-get install libssl1.0.0 libssl-dev
Now lets fix the naming of the file by creating a link:
cd /lib/x86_64-linux-gnu
sudo ln -s libssl.so.1.0.0 libssl.so.10
sudo ln -s libcrypto.so.1.0.0 libcrypto.so.10
And finally, lets inform the developer about this flaw so he can fix it :)
Dear Christian,
I am new to XPS and following your paper on using XPS for my Gene St array (HuGene-2_0-st design). I need the degradation plot.
I used the listed code to create scheme object:
> scmdir <- "D:/GeneST_Analyse/CELFiles/schemes"
> libdir <- "D:/GeneST_Analyse/CELFiles/libraryfiles"
> anndir <- "D:/GeneST_Analyse/CELFiles/Annotation"
> scheme.hugene20stv1.na35 <- import.exon.scheme("Scheme_HuGene20stv1_na35",filedir=scmdir,layoutfile=paste(libdir,"HuGene-2_0-st.clf",sep="/"),schemefile=paste(libdir,"HuGene-2_0-st.pgf",sep="/"),probeset=paste(anndir,"HuGene-2_0-st-v1.na35.hg19.probeset.csv",sep="/"),transcript=paste(anndir,"HuGene-2_0-st-v1.na35.hg19.transcript.csv",sep="/"))
I got the following error. Could you please give me any suggestion?
Error Message:
Error in import.exon.scheme("Scheme_HuGene20stv1_na35", filedir = scmdir, :
error in function ‘ImportExonSchemes’
Thanks in Advance