Software Compatibility Issue Between phyloseq and lme4 Packages
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HULFRED • 0
@hul40-23955
Last seen 12 days ago
United States

Hi,

I've encountered a rather peculiar software issue involving the phyloseq package and the lme4 package when analyzing longitudinal microbiome data. Below, please find a reproducible example that triggers the error:

First, when I run the mixed effects model code provided by lme4, it works perfectly:

data("sleepstudy", package = "lme4")
m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
m

Linear mixed model fit by REML ['lmerModLmerTest']
Formula: Reaction ~ Days + (Days | Subject)
   Data: sleepstudy
REML criterion at convergence: 1743.628
Random effects:
 Groups   Name        Std.Dev. Corr
 Subject  (Intercept) 24.741       
          Days         5.922   0.07
 Residual             25.592       
Number of obs: 180, groups:  Subject, 18
Fixed Effects:
(Intercept)         Days  
     251.41        10.47

The above code runs without issues. However, when I load the phyloseq package and then attempt to run the same lme4 code, it results in errors:

library(phyloseq)
m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy)

Error in t(do.call(sparseMatrix, do.call(rbind, lapply(seq_along(blist),  : 
  invalid 'lazy' to R_sparse_transpose()

Even detaching the phyloseq package doesn't resolve the issue and leads to a different error message:

detach("package:phyloseq", unload = TRUE)
m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy)

Error in t.default(do.call(sparseMatrix, do.call(rbind, lapply(seq_along(blist),  : 
                                                                   argument is not a matrix

As of now, the only solution I've found is to restart the R session. Below is my sessionInfo():

 version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] gtable_0.3.4            ggplot2_3.4.3           rhdf5_2.44.0            Biobase_2.60.0          lattice_0.21-8         
 [6] rhdf5filters_1.12.1     vctrs_0.6.3             tools_4.3.1             bitops_1.0-7            generics_0.1.3         
[11] biomformat_1.28.0       stats4_4.3.1            parallel_4.3.1          tibble_3.2.1            fansi_1.0.4            
[16] cluster_2.1.4           pkgconfig_2.0.3         Matrix_1.6-1            data.table_1.14.8       S4Vectors_0.38.1       
[21] lifecycle_1.0.3         GenomeInfoDbData_1.2.10 compiler_4.3.1          stringr_1.5.0           Biostrings_2.68.1      
[26] munsell_0.5.0           codetools_0.2-19        permute_0.9-7           GenomeInfoDb_1.36.3     RCurl_1.98-1.12        
[31] pillar_1.9.0            nloptr_2.0.3            crayon_1.5.2            MASS_7.3-60             vegan_2.6-4            
[36] iterators_1.0.14        boot_1.3-28.1           foreach_1.5.2           nlme_3.1-163            tidyselect_1.2.0       
[41] digest_0.6.33           stringi_1.7.12          dplyr_1.1.3             reshape2_1.4.4          splines_4.3.1          
[46] ade4_1.7-22             grid_4.3.1              colorspace_2.1-0        cli_3.6.1               magrittr_2.0.3         
[51] survival_3.5-7          utf8_1.2.3              ape_5.7-1               scales_1.2.1            XVector_0.40.0         
[56] igraph_1.5.1            multtest_2.56.0         lme4_1.1-34             IRanges_2.34.1          mgcv_1.9-0             
[61] rlang_1.1.1             Rcpp_1.0.11             glue_1.6.2              BiocGenerics_0.46.0     rstudioapi_0.15.0      
[66] minqa_1.2.6             jsonlite_1.8.7          R6_2.5.1                Rhdf5lib_1.22.1         plyr_1.8.8             
[71] zlibbioc_1.46.0

Also, I using Bioconductor 3.17.

Any insights or advice on resolving this issue would be greatly appreciated.

Best regards,

Huang

phyloseq microbiome Software • 144 views
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Entering edit mode
ATpoint ★ 3.4k
@atpoint-13662
Last seen 1 day ago
Germany

Answered here https://github.com/lme4/lme4/issues/743

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