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jeroen / openssl

OpenSSL bindings for R
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Error with openssl when running a Rscript #25

Closed WPierrick closed 8 years ago

WPierrick commented 8 years ago

Hi,

I get this error when I want to run a Rscript on a cluster where R is installed (the script works, and every user on the cluster has personal R libraries) :

Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/myfilepath/R/x86_64-pc-linux-gnu-library/3.2/openssl/libs/openssl.so': /myfilepath/R/x86_64-pc-linux-gnu-library/3.2/openssl/libs/openssl.so: symbol EC_KEY_get0_group, version OPENSSL_1.0.1_EC not defined in file libcrypto.so.10 with link time reference Error: package or namespace load failed for 'missMethyl'

FYI, my version of openssl:

packageVersion("openssl") [1] ‘0.9.3’

Seems like it works when I manually load a package on R on a master head node of the cluster, but not when I run a job via bash on a cluster node.

Basically, R doesn't want to load any package because it seems there is a problem with incompatible openssl versions. Does that makes any sense? Any idea on how to solve this? The problem arise after I tried to install ShinyMethyl, a bioconductor package.

Cheers,

jeroen commented 8 years ago

Looks like a conflict on the server with multiple versions of libssl, where you compile against one version but then load another version. Can you show me the output of:

ldd /myfilepath/R/x86_64-pc-linux-gnu-library/3.2/openssl/libs/openssl.so

And of:

pkg-config --cflags openssl
pkg-config --libs openssl
WPierrick commented 8 years ago

Thank you for your reply!

There was indeed an incompatibility between openssl versions on my cluster's head node and other nodes following a security update. It's been fixed now. Thanks again.