Question

`ggbio` package can't be loaded

6

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Batool ▴ 370

@Batool-24467

Last seen 3.9 years ago

ggbio used to work perfectly fine for ages but recently I re-installed ggbio and I encounter this error:

Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

Which makes the console stuck forever in the RStudio. I tried the same thing on my sister's MacBook and had the same error.

I used the following to install the packages:

install.packages("ggplot2")
BiocManager::install("ggbio")
library(ggbio)

To resolve the problem, I re-installed both R, all RFrameworks, and RStudio at least 3 times but still, the same problem occurs after installing ggpolt2 after ggbio. Things go back to normal if I remove either ggplot2 or ggbio. I use R-4.0.3, RStudio v1.3.

I can't copy sessionInfo( ) because the console doesn't work anymore.

Is it possible that ggbio is pulling in an outdated version of GGally and overwriting the core functions of ggplot2 (such as +.gg)?

I'm stuck with this problem for 4 days and not sure how to resolve it.

Thanks, Batool

ggbio • 2.0k views

ADD COMMENT • link 3.9 years ago Batool ▴ 370

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Unfortunately, many problems in R package installation are MAC-specific (and I have never owned a MAC). R Studio adds another level of complexity on top of this, and I almost never use this, either. What were the error messages, do you know? - you have not shown them. If you do the usual thing and restart your computer to clear the cache and then install just ggbio via BiocManager::install("ggbio") and from within the standard R environment, what happens?

ADD REPLY • link 3.9 years ago Kevin Blighe ★ 4.0k

6

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Thank you Kevin Blighe for your reply. There wasn't any error message during the installation but after it's installed, it shows this message when it's loaded with library(ggbio):

Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

and then the console doesn't work anymore, stuck forever. Unfortunately, I only have a Mac machine. As I mentioned, I cleared all the cache, uninstalled R and R Studio at least 3-4 times but the same problem keeps going. This time, I didn't install RStudio on my machine but still got the same message.

ADD REPLY • link 3.9 years ago Batool ▴ 370

0

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How long have you waited for it to finish? I'm wondering whether it only _seems_ to be stuck forever.

ADD REPLY • link 3.9 years ago Michael Lawrence ★ 11k

6

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I tried two different machines (Mac), waited for 48 hours for the console to go back to normal, removed everything, and re-installed R and ggbio multiple times. I spent at least 3 days trying to figure out the problem before I posted the question.

This is sessionInfo():

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.0.3

and this for the second machine:

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3

Can I ask if you tried to re-install ggbio and loading it today library(ggbio)?

ADD REPLY • link 3.9 years ago Batool ▴ 370