Comments (4)
Xinming9606
commented on September 27, 2024
2
Hi Stefanie,
I installed it successfully! Thanks for your reply!
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CarlaCristinaUranga
commented on September 27, 2024
1
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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Xinming9606
commented on September 27, 2024
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!
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stefpeschel
commented on September 27, 2024
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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Related Issues (20)
- How to look at sub-clusters? HOT 1
- output format for Gephi visualization HOT 2
- Colored by phylum HOT 2
- stability values using spieceasi HOT 1
- Problems while installing the NetCoMi HOT 1
- How to find a "good" algorithm and parameter set HOT 1
- RNA-seq data(Plant) HOT 1
- Error in length of dimnames after permutation testing HOT 1
- Labelling only certain taxa of interest HOT 1
- Will this package works for all lineage levels?
- Cross domain interactions HOT 3
- calculate the betweenness centrality as hubs HOT 2
- Looking for guidance on MANs Inference with samples from different metagenomics/metatranscriptomics studies HOT 4
- Error in NetConstruct for network comparison : "subscript out of bounds" HOT 4
- edges dont color correctly with negative correlations HOT 2
- Could I manually modify the color of each node? HOT 2
- Problem with the targets IDs in export to gephi HOT 4
- including correlations with environmental or experimental variables? HOT 3
- Understanding netConstruct() output HOT 1
- Issue with node size and netCompare HOT 5
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