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stefpeschel / NetCoMi

Network construction, analysis, and comparison for microbial compositional data
https://netcomi.de
GNU General Public License v3.0
152 stars 27 forks source link

R version 4.1.1 NetCoMi not installing #27

Closed CarlaCristinaUranga closed 3 years ago

CarlaCristinaUranga commented 3 years ago

Hi, is anyone else having trouble downloading NetCoMi after updating to R 4.1.1?

Best, Carla

Xinming9606 commented 3 years ago

I have similar problem on installing, it say E> ERROR: dependencies 'SpiecEasi', 'SPRING' are not available for package 'NetCoMi' But pacakge SpiecEasi and SPRING were not installed, I'm not sure if it's the problem of updated R version. But please share if you solve the problem!

stefpeschel commented 3 years ago

Hi, I just updated my R version to 4.1.1 and installed NetCoMi into the empty library, which worked without any issues. Only devtools and BiocManager must have been previously installed. Here's the code:

install.packages("devtools") install.packages("BiocManager")

devtools::install_github("stefpeschel/NetCoMi", dependencies = TRUE, repos = c("https://cloud.r-project.org/", BiocManager::repositories()))

Dependencies that are only available on GitHub (such as SpiecEasi and SPRING) do sometimes cause problems so that they can't be installed automatically. If you encounter an error message regarding SpiecEasi or SPRING, I would recommend intalling them manually:

devtools::install_github("GraceYoon/SPRING") devtools::install_github("zdk123/SpiecEasi")

Please let me know if there are still problems with the installation process.

Best, Stefanie

Xinming9606 commented 3 years ago

Hi Stefanie,

I installed it successfully! Thanks for your reply!

CarlaCristinaUranga commented 3 years ago

I was also able to install it previously by installing each dependency individually. Thanks for an AWESOME package.

Best wishes,

Carla

On Thu, Oct 28, 2021, 12:15 AM Stefanie Peschel @.***> wrote:

Hi, I just updated my R version to 4.1.1 and installed NetCoMi into the empty library, which worked without any issues. Only devtools and BiocManager must have been previously installed. Here's the code:

install.packages("devtools") install.packages("BiocManager")

devtools::install_github("stefpeschel/NetCoMi", dependencies = TRUE, repos = c("https://cloud.r-project.org/", BiocManager::repositories()))

Dependencies that are only available on GitHub (such as SpiecEasi and SPRING) do sometimes cause problems so that they can't be installed automatically. If you encounter an error message regarding SpiecEasi or SPRING, I would recommend intalling them manually:

devtools::install_github("GraceYoon/SPRING") devtools::install_github("zdk123/SpiecEasi")

Please let me know if there are still problems with the installation process.

Best, Stefanie

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