Installation issues
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ahwanpandey commented
Hello,
Thanks for getting this package together. I have been trying to install the miniconda version as well as each of the R libraries by itself but I am having no luck with either.
You are already aware of the SignIT issue here:
eyzhao/SignIT#3
I am anticipating that installing all the required R libraries will be enough to run the necessary scripts for HRDetect, but I can't get SignIT to install.
library(tidyverse)
library(devtools)
library(rstan)
library(signit) ***
library(argparse)
library(BSgenome)
library(BSgenome.Hsapiens.NCBI.GRCh38)
library(copynumber)
library(dbscan)
library(docopt)
library(doParallel)
library(futile.logger)
library(GenomicRanges)
library(nnls)
library(optparse)
library(plyr)
library(readr)
library(rjags)
library(RSvgDevice)
library(Rtsne)
library(snow)
library(stringr)
library(VariantAnnotation)
library(hrdtools)
So I tried with the miniconda pipeline, and had no luck there either.
- Firstly, when installing the miniconda version by running
make dependencies, the installation will not progress even after 24hrs unless I change the order of thedependencies/environment.yamlfile to be in the following order:
- r
- conda-forge
- bioconda
- main
- Then
dependencies/Makefilehas a svn checkout section that doesn't work:
packages/hrdtools/DESCRIPTION:
mkdir -p packages/hrdtools && \
svn checkout https://svn01.bcgsc.ca/svn/personal/ezhao/projects/signatures/trunk/hrdtools/ packages/hrdtools
instead, I replaced this with the following to make it work:
packages/hrdtools/DESCRIPTION:
mkdir -p packages/hrdtools && \
git clone https://github.com/eyzhao/hrdtools.git packages/hrdtools
Now even after this, I get a final error during the pipeline installation:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > conda activate dependencies
#
# To deactivate an active environment, use:
# > conda deactivate
#
echo "export R_LIBS=/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/library && export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:/gsc/software/linux-x86_64-centos6/JAGS-4.3.0/lib" > miniconda3/envs/dependencies/etc/conda/activate.d/env_vars.sh
mkdir -p packages/hrdtools && \
git clone https://github.com/eyzhao/hrdtools.git packages/hrdtools
Cloning into 'packages/hrdtools'...
remote: Enumerating objects: 97, done.
remote: Total 97 (delta 0), reused 0 (delta 0), pack-reused 97
Unpacking objects: 100% (97/97), done.
source /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/bin/activate dependencies && \
echo 'Installing R packages into this R install:' `which R` && \
export R_LIBS=/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/library && \
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/gsc/software/linux-x86_64-centos6/JAGS-4.3.0/lib
Installing R packages into this R install: /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/bin/R
/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/bin/Rscript r_dependencies.R && \
source /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/bin/deactivate && \
echo 'installed packages' > r_packages
/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/R: /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../../libgomp.so.1: version `GOMP_4.0' not found (required by /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/libR.so)
/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/R: /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../../libgomp.so.1: version `GOMP_4.0' not found (required by /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/./libRblas.so)
/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/R: /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../../libicuuc.so.58)
/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/R: /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../../libicuuc.so.58)
/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/R: /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../../libicui18n.so.58)
/home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/R: /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/apandey/Downloads/hrdetect-pipeline/dependencies/miniconda3/envs/dependencies/lib/R/bin/exec/../../lib/../../libicui18n.so.58)
make: *** [r_packages] Error 1
Another thing I noticed is that dependencies/Makefile has a hardcoded path to JAGS
$ head dependencies/Makefile
jags_lib := /gsc/software/linux-x86_64-centos6/JAGS-4.3.0/lib
makefile_path := $(abspath $(lastword $(MAKEFILE_LIST)))
makefile_dir := $(patsubst %/,%, $(dir $(makefile_path)))
Thanks in advance for your insights.