Question

error in package GenVisR while installing

0

Entering edit mode

abhisikta • 0

@600e8ea2

Last seen 2.4 years ago

India

I was trying to install GenVisR package for the R version 4.2.1. It showed the following error. When I tried to install "FField", it is showing again an error and library of GenVisR is not loaded. Please suggest what should I do? Thank You.

Code should be placed in three backticks as shown below

> ##installing the package called GenVisR (Genomic Visualisation in R)
> if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install("GenVisR")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.1/library
  packages:
    MASS, nlme
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'GenVisR' 
> ##loading the package in R
> library(GenVisR)
Error: package or namespace load failed for ‘GenVisR’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘FField’
> install.packages("FField")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/abhis/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘FField’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

GenVisR GenVis • 3.4k views

ADD COMMENT • link updated 12 months ago by zlskidmore ▴ 30 • written 2.4 years ago by abhisikta • 0

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Package ‘FField’ was removed from the CRAN repository.enter link description here I installed FField by using remotes::install_github("cran/FField"). Then I successfully installed by using BiocManager::install("GenVisR") .

ADD REPLY • link 2.3 years ago 堃 ▴ 10

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Have you tried to install Rtools as it was recommended ?

ADD REPLY • link 2.4 years ago Basti ▴ 780

score 2 · Answer 1 · 2022-09-04

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zlskidmore ▴ 30

@zlskidmore-9639

Last seen 12 months ago

United States

an update has been applied, removing the FField dependency, if you try the devel version there should not be an issue.

ADD COMMENT • link 2.2 years ago zlskidmore ▴ 30

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what does it mean the devel version ? I'm also gotting the same issue.

ADD REPLY • link 2.1 years ago kerkour • 0

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https://contributions.bioconductor.org/use-devel.html

ADD REPLY • link 2.1 years ago James W. MacDonald 67k

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And when will the dev. version be made available publicly? dev bioconductor requires updating R into the developmental, unreleased, version of R

ADD REPLY • link 12 months ago jon.klonowski ▴ 40

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You're commenting on an issue that is 12-month old. What was considered to be dev at the time has long been released. It will be more productive if you describe the problem you're having, show the error you get, and share your sessionInfo().

ADD REPLY • link 12 months ago Hervé Pagès 16k

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The same exact issue as OP, which is why I was following up.

My solution was to download the dev version through github:

# install and load devtools package
install.packages("devtools")
library(devtools)

# install GenVisR from github
install_github("griffithlab/GenVisR")

This solution bypasses the need to figure out which version of R is required to get the version of bioconductor that has the package version that does not have the same dependency with FField (or update to the most recent R).

ADD REPLY • link 12 months ago jon.klonowski ▴ 40

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Unfortunately, lolliplot() no longer functions and Lolliplot(), the replacement, is in development and non-functional.

I asked a question on their github: https://github.com/griffithlab/GenVisR/issues/394

ADD REPLY • link 12 months ago jon.klonowski ▴ 40

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Please try altering the host parameter within the Lolliplot() function. The function pulls from biomart and it looks like the default host has changed.

For example, try the us mirror using the provided example in the r documention:

object <- Lolliplot(dataset.mode1, transcript="ENST00000263967",
+                     species="hsapiens", txdb=txdb, BSgenome=BSgenome, host="https://useast.ensembl.org")

ADD REPLY • link 12 months ago zlskidmore ▴ 30