Bioconductor version cannot be validated
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charlotte ▴ 10
@bbcc9ab6
Last seen 2.6 years 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 • 8.1k views
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Mike Smith ★ 6.4k
@mike-smith
Last seen 7 hours ago
EMBL Heidelberg

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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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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I have this problem now. How can I solve that. please guide me, Thanks

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Hi Sevda, Can you provide more information? Include the code you ran and the sessionInfo()

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Hello, when I used install.packages().I did not get any errors. but BiocManager do not work.

sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

time zone: Asia/Tehran tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] BiocManager_1.30.21.1 compiler_4.3.1 tools_4.3.1
Warning message: R graphics engine version 16 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.

library(BiocManager)

Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette Warning messages: 1: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error' 2: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'

BiocManager::install("WGCNA")

Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette

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Hi Sveda, If you are still having this issue, there are a few scenarios where you might get this error. For example,

Network Connectivity Issues:

Firewall or Proxy: Your network or system firewall/proxy settings might be blocking access to external repositories. Check your firewall settings and ensure that R and R packages are allowed to connect to the internet. Proxy Configuration: If you are behind a corporate network, you may need to configure proxy settings within R to allow access to external resources.

SSL/TLS Configuration:

The "SSL connect error" suggests there might be an issue with the SSL/TLS configuration. Ensure that your R installation has the necessary SSL libraries and certificates.

Best regards, Marcel

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Hello, I can install packages using install.packages(), which requires an internet connection. However, even with BiocManager, this issue still occurs. thank you for your guide.

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Hi Sevda,

The issue is most likely due to your internet configuration. Please make sure that your ISP or work internet is not blocking access to bioconductor.org. See this issue posted at BiocManager #183 for more information.

Best,

Marcel

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