installation problem

[mick42-star]

I use conda to install leafcutter and it seems installed successfully. I didn't see error message. but I cannot use the library.

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        mamba (1.4.2) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
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Looking for: ['r-leafcutter']

warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache
bioconda/osx-arm64                                          Using cache
bioconda/noarch                                             Using cache
r/osx-arm64                                                 Using cache
r/noarch                                                    Using cache
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not parse mod/etag header
warning  libmamba Could not parse mod/etag header
davidaknowles/osx-arm64                            134.0 B @ 755.0 B/s  0.2s
davidaknowles/noarch                               130.0 B @ 655.0 B/s  0.2s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk.. 113.0 B @ 108.0 B/s  0.8s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk.. 110.0 B @ 105.0 B/s  0.9s
pkgs/main/osx-arm64                                           No change
pkgs/r/noarch                                                 No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl.. 113.0 B @  93.0 B/s 404 failed  1.2s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..   5.1MB @   1.3MB/s  4.2s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk.. 113.0 B @  26.0 B/s 404 failed  0.3s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..   9.3MB @   2.0MB/s  4.8s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..   2.5MB @ 523.5kB/s  3.8s
pkgs/main/noarch                                              No change
pkgs/r/osx-arm64                                              No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..   2.4MB @ 450.5kB/s  4.2s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..   1.9kB @ 355.0 B/s  1.1s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk.. 113.0 B @  20.0 B/s 404 failed  0.3s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..  92.0 B @  15.0 B/s  0.3s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk.. 113.0 B @  19.0 B/s  0.9s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk.. 926.0kB @ 147.8kB/s  0.5s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..   9.3MB @   1.2MB/s  2.8s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..  15.6MB @   1.5MB/s  9.8s
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..  15.6MB @   1.4MB/s  6.6s

Pinned packages:
  - python 3.10.*

> library(leafcutter)
Error in library(leafcutter) : there is no package called ‘leafcutter’

[ryanyord]

I tried all the help on various github issues and reddit threads. Including the docker image from https://hub.docker.com/r/francois4/leafcutter/. This docker image would not load when using the argument library(leafcutter)

I found a solution using docker, starting from scratch in the terminal.

Pulling a clean environment from: https://hub.docker.com/r/mambaorg/micromamba , using the command
docker pull mambaorg/micromamba:1.5.5

then

docker run --rm -it mambaorg/micromamba:1.5.5

micromamba install -y -c conda-forge r-base=3.4.1
micromamba install -y -c conda-forge -c bioconda -c davidaknowles r-leafcutter

Now enter R
R
Now the library should load.
library(leafcutter)

As an additional note, you will likely want to mount your own directory when launching the docker container, here's an example with the -v flag:

docker run --rm -it -v /data/mybamfiles:/data/ mambaorg/micromamba:1.5.5

Additional note is that the --rm flag will completely wipe the image after shutting down. So you will likely need to store the image for the future.

[KuechlerO]

I tried all the help on various github issues and reddit threads. Including the docker image from https://hub.docker.com/r/francois4/leafcutter/. This docker image would not load when using the argument library(leafcutter)

I found a solution using docker, starting from scratch in the terminal.

Pulling a clean environment from: https://hub.docker.com/r/mambaorg/micromamba , using the command docker pull mambaorg/micromamba:1.5.5

then

docker run --rm -it mambaorg/micromamba:1.5.5

micromamba install -y -c conda-forge r-base=3.4.1 micromamba install -y -c conda-forge -c bioconda -c davidaknowles r-leafcutter

Now enter R R Now the library should load. library(leafcutter)

As an additional note, you will likely want to mount your own directory when launching the docker container, here's an example with the -v flag:

docker run --rm -it -v /data/mybamfiles:/data/ mambaorg/micromamba:1.5.5

Additional note is that the --rm flag will completely wipe the image after shutting down. So you will likely need to store the image for the future.

Amazing, big thanks!
On a side-note:
The preferred platform architecture of the pulled docker image is depending on your host OS.
Thus, to ensure the usage of the linux amd64 architecture use the following:

docker pull --platform linux/amd64 mambaorg/micromamba:1.5.5

[ryanyord]

I have now found a better method on R 4.2.1.

Using docker, starting from scratch in the terminal.

Pulling a clean environment from: https://hub.docker.com/r/mambaorg/micromamba , using the command
docker pull mambaorg/micromamba:1.5.5

then

docker run --rm -it mambaorg/micromamba:1.5.5

micromamba 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
micromamba install -c bioconda bioconductor-biobase bioconductor-dirichletmultinomial --freeze-installed

Now enter R
R
Enter:
devtools::install_github("davidaknowles/leafcutter/leafcutter")
When prompted type: 3 (3: None)
Now the library should load.
library(leafcutter)

As an additional note, you will likely want to mount your own directory when launching the docker container, here's an example with the -v flag:

docker run --rm -it -v /data/mybamfiles:/data/ mambaorg/micromamba:1.5.5

Additional note is that the --rm flag will completely wipe the image after shutting down. So you will likely need to store the image for the future.