Giter Club home page Giter Club logo

Comments (1)

bschilder avatar bschilder commented on June 2, 2024

Followup

Updating GenomicFeatures now causes an error when loading EnsDb.Hsapiens.v75 in get_transcripts() step.

Loading required package: ensembldb
Loading required package: GenomicFeatures
 Error in value[[3L]](cond) : 
  Package 'GenomicFeatures' version 1.42.1 cannot be unloaded:
 Error in unloadNamespace(package) : namespace 'GenomicFeatures' is imported by 'VariantAnnotation', 'Gviz', 'ensembldb', 'ggbio', 'biovizBase', 'OrganismDbi' so cannot be unloaded 
10.
stop(gettextf("Package %s version %s cannot be unloaded:\n %s", 
    sQuote(package), oldversion, paste0(P, conditionMessage(e), 
        "\n")), domain = NA) 
9.
value[[3L]](cond) 
8.
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 
7.
tryCatchList(expr, classes, parentenv, handlers) 
6.
tryCatch(unloadNamespace(package), error = function(e) {
    P <- if (!is.null(cc <- conditionCall(e))) 
        paste("Error in", deparse(cc)[1L], ": ")
    else "Error : " ... 
5.
library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
    quietly = quietly) 
4.
.getRequiredPackages2(pkgInfo, quietly = quietly) 
3.
library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
    quietly = quietly) 
2.
.getRequiredPackages2(pkgInfo, quietly = quietly) 
1.
library(EnsDb.Hsapiens.v75) 

Solution

After you upgrade GenomicFeatures, you must then also update EnsDb.Hsapiens.v75 (and, importantly, its dependencies). Then make sure to restart your R session to implement the changes.

from echolocator.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.