In RStudio Server I get an error when loading the bioconductor library GenomeInfoDb (actually as a dependency for DESeq2):
> library(GenomeInfoDb)
Error: package or namespace load failed for ‘GenomeInfoDb’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/balter/conda/envs/deseq/lib/R/library/RCurl/libs/RCurl.so':
/home/balter/conda/envs/deseq/lib/R/library/RCurl/libs/../../../.././libssl.so.1.0.0: undefined symbol: EVP_idea_cbc
There is a bit more to the story. I use conda and adjust my lib.Paths appropriately. I've never had problems with this.
After restarting my RStudio SErver session, I have:
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
current_conda_env:
current_conda_prefix:
[1] "no conda env"
> .libPaths()
[1] "/home/balter/conda/lib/R/library"
> "GenomeInfoDb" %in% installed.packages()
[1] FALSE
> startCondaEnv('deseq')
pointing to conda env: deseq and lib location /home/balter/R
[1] "/home/balter/conda/envs/deseq/lib/R/library" "/home/balter/R"
[3] "/home/balter/conda/lib/R/library"
> .libPaths()
[1] "/home/balter/conda/envs/deseq/lib/R/library" "/home/balter/R"
[3] "/home/balter/conda/lib/R/library"
> "GenomeInfoDb" %in% installed.packages()
[1] TRUE
> library(GenomeInfoDb)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames,
colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans,
rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit,
which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Error: package or namespace load failed for ‘GenomeInfoDb’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/balter/conda/envs/deseq/lib/R/library/RCurl/libs/RCurl.so':
/home/balter/conda/envs/deseq/lib/R/library/RCurl/libs/../../../.././libssl.so.1.0.0: undefined symbol: EVP_idea_cbc
However, at the command line I have:
Script started on 2019-01-07 14:20:14-08:00
(base) e[01;32mbalter@little-de[00m:e[01;34m~e[00m$ R
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
current_conda_env: base
current_conda_prefix: /home/balter/conda
pointing to conda env: base and lib location /home/balter/R35
[1] "/home/balter/conda/lib/R/library" "/home/balter/R35"
> .libPaths()
[1] "/home/balter/conda/lib/R/library" "/home/balter/R35"
> "Genomie[KeInfoDb" $e[K%in% installed.Pe[Kpackages()
[1] FALSE
> startCondaEnv('deseq')
pointing to conda env: deseq and lib location /home/balter/R
[1] "/home/balter/conda/envs/deseq/lib/R/library"
[2] "/home/balter/R"
[3] "/home/balter/conda/lib/R/library"
> .libPaths()
[1] "/home/balter/conda/envs/deseq/lib/R/library"
[2] "/home/balter/R"
[3] "/home/balter/conda/lib/R/library"
> .libPaths()
e[Ce[CstartCondaEnv('deseq')
e[Ce[C"GenomeInfoDb" %in% installed.packages()
[1] TRUE
> library(GenoameInfoDb)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
>
Save workspace image? [y/n/c]: n
(base) e[01;32mbalter@little-de[00m:e[01;34m~e[00m$ exit
exit
Script done on 2019-01-07 14:23:13-08:00