Question: Failed to install package(ASpli) in R
0
gravatar for qicaibiology
4 weeks ago by
qicaibiology40
qicaibiology40 wrote:

Hi all:

I am working through a terminal on the computation center in the University. Recently, I need to install a package in R to analyze my RNA-seq data.

I am under the anaconda2 environment. So I use conda install R to install R and call R by typing R. However, when I tried to install ASpli which is a package running in R(BiocManager::install("ASpli")), I get the following error(part of the error):

Error: package or namespace load failed for 'survival' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/caiqi/anaconda2/lib/R/library/Matrix/libs/Matrix.so':
libopenblas.so.0: cannot open shared object file: No such file or directory Error: package 'survival' could not be loaded Execution halted

Any advice on what should I do?

Thanks,

Cai

rna-seq R software error • 189 views
ADD COMMENTlink written 4 weeks ago by qicaibiology40

If you used conda to install R, why don't you use conda to install ASpli?

 conda install -c bioconda bioconductor-aspli
ADD REPLYlink written 4 weeks ago by h.mon28k

Thank your very much for your reply! I am trying your code to see what will happen. Can I ask another question because I don't understand very well about it: I saw I have anaconda2 folder and it contains lib which contains R : anaconda>lib>R, and I saw some packages in the R like edgeR and something like that. in my home folder I also see R>x86_64-pc-linux-gnu-library>3.5>edgeR/ASpli

I know previously I have been using R3.5 also under anaconda environment. Recently, the system got some mistake so I have to uninstall anaconda and reinstall anaconda and R. So this is how the question arise. My question is what is difference of R folder in my home and the R in the anaconda? How can use the R folder in my home folder? Appreciate a lot for your teaching.

ADD REPLYlink written 4 weeks ago by qicaibiology40

I tried your method, and I went into R and get the following:

> library(ASpli)
Loading required package: parallel
Loading required package: edgeR
Loading required package: limma
Error: package or namespace load failed for 'edgeR' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/caiqi/anaconda2/lib/R/library/edgeR/libs/edgeR.so':
  libopenblas.so.0: cannot open shared object file: No such file or directory
Error: package 'edgeR' could not be loaded
ADD REPLYlink written 4 weeks ago by qicaibiology40

First of all, I would suggest you create a conda environment for the R installation (note you may need to tweak version number):

conda create -n R-3.6-env R=3.6.1

To use this R, you must activate the environment:

 conda activate R-3.6-env

You can then install more packages

 conda install -c bioconda bioconductor-aspli

Install any other packages you need for this R environment. In case loading packages in this R environment still fails with "libopenblas.so.0: cannot open shared object file: No such file or directory", do:

conda install openblas

You can try the above command before creating a new environment, but this is a sign your conda install is somewhat broken. You may need to start from scratch again.

ADD REPLYlink written 4 weeks ago by h.mon28k

this is what I got :

(base) [caiqi@midway2-login2 ~]$ conda activate R-3.6-env
Could not find conda environment: R-3.6-env
You can list all discoverable environments with `conda info --envs`.

(base) [caiqi@midway2-login2 ~]$ conda info --envs
# conda environments:
#
base                  *  /home/caiqi/anaconda2
                         /home/caiqi/miniconda2
ADD REPLYlink written 4 weeks ago by qicaibiology40

it does not work out in the end. I can not even library(ASpli) in the end. Looks that it still has the same problem.

"> library(ASpli)

Loading required package: parallel Loading required package: edgeR Loading required package: limma Error: package or namespace load failed for 'ASpli' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/caiqi/anaconda2/lib/R/library/stringi/libs/stringi.so':
libicui18n.so.64: cannot open shared object file: No such file or directory"

Thanks a lot for your time,

Cai

ADD REPLYlink written 4 weeks ago by qicaibiology40
1
gravatar for qicaibiology
4 weeks ago by
qicaibiology40
qicaibiology40 wrote:

My friend and I checked the errors. What we did is : install.packages('Matrix')

Then we install ASpli again, and it does not show error. Going to give it a run to see what is going on.

Thanks for your help

ADD COMMENTlink written 4 weeks ago by qicaibiology40
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