How to install Bioconductor tximport R package in customized code env

Options
Go14
Go14 Registered Posts: 5 ✭✭✭

Hi

I want to install Bioconductor tximport R package in customized code env. But I am getting the below error.

Error: at least one package failed to install required versionIn addition: Warning message:package ‘tximport’ is not available (for R version 3.6.0) Execution halted

it seems the Bioconductor packages can be installed through Biocmanager and it is different from CRAN mirror.

When i try to install this package through notebook with the below commands,

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

BiocManager::install("tximport")

I am getting the below error

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.0 (2019-04-26)

Installing package(s) 'BiocVersion', 'tximport'

Warning message in install.packages(...):
“'lib = "/opt/dataiku/design-node/code-envs/R/test-R-env/R.lib"' is not writable”

Can you help me to fix this issue either in notebook or in code env ?

Answers

  • tgb417
    tgb417 Dataiku DSS Core Designer, Dataiku DSS & SQL, Dataiku DSS ML Practitioner, Dataiku DSS Core Concepts, Neuron 2020, Neuron, Registered, Dataiku Frontrunner Awards 2021 Finalist, Neuron 2021, Neuron 2022, Frontrunner 2022 Finalist, Frontrunner 2022 Winner, Dataiku Frontrunner Awards 2021 Participant, Frontrunner 2022 Participant, Neuron 2023 Posts: 1,595 Neuron
    Options

    @Go14

    First, I've never installed Bioconductor tximport in R.

    However, I do have a question/idea. Are you working on a local copy of Dataiku say installed on a Macintosh computer rather than say a production Linux Server? If so, are you able to install Bioconductor tximport on your computer outside of Dataiku DSS in an R environment directly or through say RStudio?

    In the past when working out an R or even Python library install problem with a Dataiku DSS code environment I would often find the answer when trying to install outside of a DSS Code environment.

    This is not guaranteed to help. However, it may offer a way forward for your current situration.

Setup Info
    Tags
      Help me…