search

gongx030 / DrImpute

Imputing dropout events in single-cell RNA-sequencing data
16 stars 4 forks source link

Cannot install DrImpute #1

Open galanisl opened 5 years ago

galanisl commented 5 years ago

Dear @gongx030 ,

I have been trying to install your imputation package in R without success. I get the following error:

libRblas.so: cannot open shared object file: No such file or directory

I've tried different 'solutions' posted online (e.g. https://groups.google.com/forum/#!msg/rapache/axLb5PsS9LY/7ZkP831LULkJ or http://promberger.info/linux/2009/03/20/r-lme4-matrix-not-finding-librlapackso/), but they haven't worked for me.

I am working under the following session:

R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS

Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_GB.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] devtools_1.13.5

loaded via a namespace (and not attached): [1] httr_1.3.1 compiler_3.4.4 R6_2.2.2 tools_3.4.4 withr_2.1.2 curl_3.2 yaml_2.1.18 memoise_1.1.0 git2r_0.21.0 digest_0.6.15

Thanks a lot in advance for your help!

galanisl commented 5 years ago

I managed to solve the problem:

In /usr/bin I created symbolic links to liblapack.so and libblas.so as follows:

sudo ln -s liblapack.so libRlapack.so
sudo ln -s libblas.so libRblas.so`

Then, I installed gfortran-7 like so:

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt update
sudo apt install gfortran-7

This solved all the error messages and allowed me to install the package.