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

**URL:** <https://forum.biobakery.org/t/regarding-maaslin2-an-error-occurred-during-the-running-process-error-in-initializeptr-the-package-cholmod-factor-ldeta-does-not-provide-a-function-like-matrix/7653>\
**Category:** Downstream analysis and statistics\
**Created:** [December 13, 2024, 5:31am UTC](https://forum.biobakery.org/t/regarding-maaslin2-an-error-occurred-during-the-running-process-error-in-initializeptr-the-package-cholmod-factor-ldeta-does-not-provide-a-function-like-matrix/7653 "2024-12-13T05:31:21Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Gal1nsoga](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/gal1nsoga/32/3104_2.png) [@Gal1nsoga](https://forum.biobakery.org/u/Gal1nsoga)\
**Post date:** [December 13, 2024, 5:31am UTC](https://forum.biobakery.org/t/regarding-maaslin2-an-error-occurred-during-the-running-process-error-in-initializeptr-the-package-cholmod-factor-ldeta-does-not-provide-a-function-like-matrix/7653/1 "2024-12-13T05:31:21Z")

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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](https://forum.biobakery.org/uploads/short-url/dyQjts4pDepR6TmohEKf5I8Oefr.tsv) (2.0 MB)  
[cleaned\_metadata.tsv](https://forum.biobakery.org/uploads/short-url/9nDCw9nPvq0p2GaZqbD0DIhFCss.tsv) (12.7 KB)

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**Author:** ![nearinj](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nearinj/32/2135_2.png) [@nearinj](https://forum.biobakery.org/u/nearinj)\
**Post date:** [December 16, 2024, 3:40pm UTC](https://forum.biobakery.org/t/regarding-maaslin2-an-error-occurred-during-the-running-process-error-in-initializeptr-the-package-cholmod-factor-ldeta-does-not-provide-a-function-like-matrix/7653/2 "2024-12-16T15:40:56Z")

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Hi @Gal1nsoga

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

Cheers,  
Jacob

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**Author:** ![Gal1nsoga](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/gal1nsoga/32/3104_2.png) [@Gal1nsoga](https://forum.biobakery.org/u/Gal1nsoga)\
**Post date:** [December 17, 2024, 12:09pm UTC](https://forum.biobakery.org/t/regarding-maaslin2-an-error-occurred-during-the-running-process-error-in-initializeptr-the-package-cholmod-factor-ldeta-does-not-provide-a-function-like-matrix/7653/3 "2024-12-17T12:09:02Z")

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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”  
)

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<div class="post-metadata">

**Author:** ![Gal1nsoga](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/gal1nsoga/32/3104_2.png) [@Gal1nsoga](https://forum.biobakery.org/u/Gal1nsoga)\
**Post date:** [December 17, 2024, 12:09pm UTC](https://forum.biobakery.org/t/regarding-maaslin2-an-error-occurred-during-the-running-process-error-in-initializeptr-the-package-cholmod-factor-ldeta-does-not-provide-a-function-like-matrix/7653/4 "2024-12-17T12:09:32Z")

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ps. The output directory is already created:)

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<div class="post-metadata">

**Author:** ![nearinj](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nearinj/32/2135_2.png) [@nearinj](https://forum.biobakery.org/u/nearinj)\
**Post date:** [December 20, 2024, 7:51pm UTC](https://forum.biobakery.org/t/regarding-maaslin2-an-error-occurred-during-the-running-process-error-in-initializeptr-the-package-cholmod-factor-ldeta-does-not-provide-a-function-like-matrix/7653/5 "2024-12-20T19:51:37Z")

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

Thanks,  
Jacob