Is installation still possible?

[james-vincent]

This software seems like abandonware now. We have spent significant time trying to install in various ways with no success. It seems like there are many outdated parts and documentation.

Has anyone successfully built recently on a recent OS? Anyone willing to share a complete reproducible install script?

[qhauck16]

I was able to install it today - following the conda environment instructions in #239, only installing required packages and never updating packages when asked. I additionally had to install a few other R packages manually due to errors when attempting the devtools::install_github("davidaknowles/leafcutter/leafcutter") step: TailRank, DirichletMultinomial and BioBase. Here's the exact command I ran to setup the environment (taken from a comment in #239): mamba install -c conda-forge r-base=4.2.1 r-rcpp=1.0.10 r-rstan=2.21.7 r-stanheaders=2.21.0-7 r-devtools

[zhouyuan479]

I also installed this package today - follow #239 and qhauck16, but attempting the devtools::install_github("davidaknowles/leafcutter/leafcutter") step, I got the errors with installing the data.table due to version I guess. Here's the exact command I ran : mamba install -c conda-forge r-base=4.2.1 r-rcpp=1.0.10 r-rstan=2.21.7 r-stanheaders=2.21.0-7 r-devtools r-data.table=1.14.2, then install the TailRank, DirichletMultinomial and BioBase, the last, devtools::install_github("davidaknowles/leafcutter/leafcutter").

[jackhump]

Hi all, I had to re-install Leafcutter today due to my HPC updating R. I used the following recipe and it succeeded.

conda create -n leafcutter
conda activate leafcutter
mamba install -c conda-forge r-base=4.2.1 r-rcpp=1.0.10 r-rstan=2.21.7 r-stanheaders=2.21.0-7 r-devtools

>R
install.packages("BiocManager")

BiocManager::install("Biobase")

install.packages("TailRank")

BiocManager::install("DirichletMultinomial")

devtools::install_github("davidaknowles/leafcutter/leafcutter", ref = "psi_2019")

[LPChaumont]

I successfully installed LeafCutter today using the following Conda environment:

name: leafcutter
channels:
  - conda-forge
  - bioconda
  - nodefaults
dependencies:
  - samtools=1.10
  - regtools=1.0.0
  - python=2.7.15
  - r-base=3.6.3
  - r-rstan=2.19.2
  - r-devtools=2.4.1
  - r-hmisc=4.5_0
  - r-oompabase=3.2.9
  - r-oompadata=3.1.1
  - r-distributional=0.2.2
  - bioconductor-dirichletmultinomial=1.26.0
  - bioconductor-biobase=2.44.0

After setting up the environment, I installed LeafCutter in R with the following command:

devtools::install_github("davidaknowles/leafcutter/leafcutter", upgrade = "never")

[abhilashdasari]

@LPChaumont Your answer worked for me, thanks a lot.

Initially i got error related to R shiny, shinyjs, shinycssloaders and httpuv

Then i resolved using
remotes::install_version("shiny", version = "1.4.0", repos = "https://cran.r-project.org")
remotes::install_version("shinyjs", version = "1.1", repos = "https://cran.r-project.org")
remotes::install_version("shinycssloaders", version = "0.3", repos = "https://cran.r-project.org")
remotes::install_version("httpuv", version = "1.5.2", repos = "https://cran.r-project.org")

[josiegleeson]

I followed the steps @LPChaumont and @abhilashdasari suggested, then tried loading leafcutter and got an error about an rlang version. But I quit and re-started the rsession and then it worked!

[DylanMaxStermer]

I was also having issues and had to install some other packages not mentioned previously, but have it working – here is my workflow

Create and Configure Conda Environment

# Create environment with R and core dependencies
conda create -n leafcutter -c conda-forge \
  r-base=4.2.1 \
  r-rcpp=1.0.10 \
  r-rstan=2.21.7 \
  r-stanheaders=2.21.0-7 \
  r-devtools

# Activate environment
conda activate leafcutter

Install Required R Packages

R

# Install Bioconductor packages
install.packages("BiocManager")
BiocManager::install("Biobase")
BiocManager::install("DirichletMultinomial")

# Install specific versions of oompa/TailRank packages
install.packages("remotes")

remotes::install_version(
  "oompaBase",
  version = "3.2.9",
  repos = "https://cloud.r-project.org",
  type = "source"
)

remotes::install_version(
  "oompaData",
  version = "3.1.4",
  repos = "https://cloud.r-project.org",
  type = "source"
)

remotes::install_version(
  "TailRank",
  version = "3.2.2",
  repos = "https://cloud.r-project.org",
  type = "source"
)

# Install leafcutter from GitHub
devtools::install_github("davidaknowles/leafcutter/leafcutter", ref = "psi_2019")

[stonejr623]

@DylanMaxStermer Your solution worked best for me on my HPC. In order to make it load properly, I also needed to set r-rlang>=1.1.7 and r-data.table=1.14.2. Now it is working great!