Bioconductor version cannot be validated
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charlotte ▴ 10
@bbcc9ab6
Last seen 7 weeks ago
Hong Kong

Hi I have installed BiocManager,

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

but when I load this package,

library(BiocManager)

it occurs the following error:

Bioconductor version cannot be validated; no internet connection?
Warning message:
In file(con, "r") :
  unable to load shared object '/home/xyl/miniconda3/envs/Rbio/lib/R/modules//internet.so':
  /home/xyl/miniconda3/envs/Rbio/lib/R/modules//internet.so: undefined symbol: curl_multi_wait

How can I solve this problem? Thank you for your help!

BiocManager Bioconductor • 202 views
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Mike Smith ★ 5.1k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg / de.NBI

I think this is probably related to the conda issues discussed in Compilation fatal error: iostream.h: No such file or directory when installing Rhdf5lib package

Any time you see an error saying unable to load shared object ... undefined symbol is normally implies that whatever you're running is assuming you have some system library installed, but it's either missing or you have a different version from what it's expecting. Package managers like conda or apt-get should make sure that doesn't happen by installing everything you need, but it can get very messy if you mix two package managers and they start to conflict with each other.

If you're running R installed via conda, you probably don't want to install any R packages using install.packages() or BiocMananger::install(). Instead you should use the conda installation as you did for Rhdf5lib.

There's some additional details that might be helpful at https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/

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Entering edit mode

Thank you for your reply and help, Yes it is the problem that I missed some packages and I have solved it, thanks a lot!

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