Regarding Maaslin2, an error occurred during the running process: Error in initializePtr() : The package 'cholmod_factor_ldetA' does not provide a function like 'Matrix'

Downstream analysis and statistics
1

Hello dear friends,
I’m a novice user of Maaslin2. I’m currently using Maaslin2 to analyze the abundance of gut microbiota in the MSM population. However, there’s an error that occurred during the model fitting process: Error in initializePtr() : The package ‘cholmod_factor_ldetA’ does not provide a function like ‘Matrix’. At first, I tried to install the ‘Matrix’ function, but it requires R >= 4.4, which is incompatible with the requirement of R <= 4.4 when I installed Maaslin2 before. Later, I suspected that there might be something wrong with the dataset I created. Here, I’m attaching my metadata and abundance data. I hope you guys can help me take a look! Thank you!

Xiao
cleaned_abundance_matrix.tsv (2.0 MB)
cleaned_metadata.tsv (12.7 KB)

2

Hi @Gal1nsoga

Could you let us know what the commands you used to run MaAsLin2 were?

Cheers,
Jacob

3

Thank you for your response!
Next, I’ll attach the code that I used to run MaAsLin2.
fit_data ← Maaslin2(
input_data = abundance,
input_metadata = metadata,
min_prevalence = 0,
output = output_dir,
fixed_effects = c(
“HIV_status”,
“sexual_behavior”,
“HIV_status:sexual_behavior”
),
random_effects = c(“age”, “BMI”),
normalization = “CLR”,
transform = “NONE”
)

4

ps. The output directory is already created:)

5

Hi @Gal1nsoga

It looks like the command is fine. What version of R are you using? I would suggest trying to install Maaslin2 from Github directly using devtools if you’re using 4.4 or above. If not you may need to install the Matrix package from source from the CRAN archive found here:

https://cran.r-project.org/src/contrib/Archive/Matrix/

Thanks,
Jacob