Xtfrm error with Maaslin2 default example in R

Downstream analysis and statistics MaAsLin
1

Maaslin2 1.13.0

I was running the ready-made example in the function Maaslin2 help page:

input_data <- system.file(
             'extdata','HMP2_taxonomy.tsv', package="Maaslin2")

input_metadata <-system.file(
             'extdata','HMP2_metadata.tsv', package="Maaslin2")

fit_data <- Maaslin2(
             input_data, input_metadata,'demo_output', transform = "AST",
             fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
             random_effects = c('site', 'subject'),
             normalization = 'NONE',
             reference = 'diagnosis,nonIBD',
             standardize = FALSE)

This leads to the following error:

....
2023-04-28 10:41:54.896843 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
In addition: Warning messages:
1: Model failed to converge with 1 negative eigenvalue: -5.6e+00 
2: Model failed to converge with 1 negative eigenvalue: -1.1e+01 
3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00291214 (tol = 0.002, component 1)
4: Model failed to converge with 1 negative eigenvalue: -2.1e+02 
5: Model failed to converge with 1 negative eigenvalue: -2.2e+02

Information my R session:

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /home/xxx/bin/R-4.3.0/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Mariehamn
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] doRNG_1.8.6                     rngtools_1.5.2                 
 [3] foreach_1.5.2                   ANCOMBC_2.2.0                  
 [5] lubridate_1.9.2                 forcats_1.0.0                  
 [7] stringr_1.5.0                   dplyr_1.1.2                    
 [9] purrr_1.0.1                     readr_2.1.4                    
[11] tidyr_1.3.0                     tibble_3.2.1                   
[13] ggplot2_3.4.2                   tidyverse_2.0.0                
[15] knitr_1.42                      MicrobiomeStat_1.1             
[17] Maaslin2_1.13.0                 ALDEx2_1.32.0                  
[19] zCompositions_1.4.0-1           truncnorm_1.0-9                
[21] NADA_1.6-1.1                    survival_3.5-5                 
[23] MASS_7.3-59                     tidySummarizedExperiment_1.10.0
[25] patchwork_1.1.2.9000            mia_1.8.0                      
[27] MultiAssayExperiment_1.26.0     TreeSummarizedExperiment_2.8.0 
[29] Biostrings_2.68.0               XVector_0.40.0                 
[31] SingleCellExperiment_1.22.0     SummarizedExperiment_1.30.0    
[33] Biobase_2.60.0                  GenomicRanges_1.52.0           
[35] GenomeInfoDb_1.36.0             IRanges_2.34.0                 
[37] S4Vectors_0.38.0                BiocGenerics_0.46.0            
[39] MatrixGenerics_1.12.0           matrixStats_0.63.0             
[41] BiocStyle_2.28.0                rebook_1.9.0                   

loaded via a namespace (and not attached):
  [1] bitops_1.0-7                DirichletMultinomial_1.42.0
  [3] doParallel_1.0.17           httr_1.4.5                 
  [5] numDeriv_2016.8-1.1         backports_1.4.1            
  [7] tools_4.3.0                 utf8_1.2.3                 
  [9] R6_2.5.1                    vegan_2.6-4                
 [11] lazyeval_0.2.2              mgcv_1.8-42                
 [13] rhdf5filters_1.12.0         permute_0.9-7              
 [15] withr_2.5.0                 gridExtra_2.3              
 [17] cli_3.6.1.9000              logging_0.10-108           
 [19] biglm_0.9-2.1               sandwich_3.0-2             
 [21] mvtnorm_1.1-3               robustbase_0.95-1          
 [23] pbapply_1.7-0               proxy_0.4-27               
 [25] yulab.utils_0.0.6           foreign_0.8-84             
 [27] scater_1.28.0               decontam_1.20.0            
 [29] readxl_1.4.2                rstudioapi_0.14            
 [31] RSQLite_2.3.1               generics_0.1.3             
 [33] Matrix_1.5-4                biomformat_1.28.0          
 [35] ggbeeswarm_0.7.1            fansi_1.0.4                
 [37] DescTools_0.99.48           DECIPHER_2.28.0            
 [39] lifecycle_1.0.3             multcomp_1.4-23            
 [41] yaml_2.3.7                  rhdf5_2.44.0               
 [43] grid_4.3.0                  blob_1.2.4                 
 [45] crayon_1.5.2                dir.expiry_1.8.0           
 [47] lattice_0.21-8              beachmat_2.16.0            
 [49] CodeDepends_0.6.5           pillar_1.9.0               
 [51] optparse_1.7.3              statip_0.2.3               
 [53] boot_1.3-28.1               gld_2.6.6                  
 [55] estimability_1.4.1          codetools_0.2-19           
 [57] glue_1.6.2                  data.table_1.14.8          
 [59] Rdpack_2.4                  vctrs_0.6.2                
 [61] treeio_1.24.0               cellranger_1.1.0           
 [63] gtable_0.3.3                cachem_1.0.7               
 [65] xfun_0.39                   rbibutils_2.2.13           
 [67] Rfast_2.0.7                 coda_0.19-4                
 [69] pcaPP_2.0-3                 modeest_2.4.0              
 [71] timeDate_4022.108           iterators_1.0.14           
 [73] statmod_1.5.0               gmp_0.7-1                  
 [75] TH.data_1.1-2               ellipsis_0.3.2             
 [77] nlme_3.1-162                phyloseq_1.44.0            
 [79] bit64_4.0.5                 filelock_1.0.2             
 [81] fBasics_4022.94             irlba_2.3.5.1              
 [83] vipor_0.4.5                 rpart_4.1.19               
 [85] colorspace_2.1-0            DBI_1.1.3                  
 [87] Hmisc_5.0-1                 nnet_7.3-18                
 [89] ade4_1.7-22                 Exact_3.2                  
 [91] tidyselect_1.2.0            emmeans_1.8.5              
 [93] timeSeries_4021.105         bit_4.0.5                  
 [95] compiler_4.3.0              graph_1.78.0               
 [97] htmlTable_2.4.1             BiocNeighbors_1.18.0       
 [99] expm_0.999-7                DelayedArray_0.25.0        
[101] plotly_4.10.1               checkmate_2.2.0            
[103] scales_1.2.1                DEoptimR_1.0-12            
[105] spatial_7.3-16              digest_0.6.31              
[107] minqa_1.2.5                 rmarkdown_2.21.3           
[109] base64enc_0.1-3             htmltools_0.5.5            
[111] pkgconfig_2.0.3             lme4_1.1-33                
[113] sparseMatrixStats_1.12.0    lpsymphony_1.28.0          
[115] stabledist_0.7-1            fastmap_1.1.1              
[117] rlang_1.1.0                 htmlwidgets_1.6.2          
[119] DelayedMatrixStats_1.22.0   energy_1.7-11              
[121] zoo_1.8-12                  jsonlite_1.8.4             
[123] BiocParallel_1.34.0         BiocSingular_1.16.0        
[125] RCurl_1.98-1.12             magrittr_2.0.3             
[127] Formula_1.2-5               scuttle_1.10.0             
[129] GenomeInfoDbData_1.2.10     Rhdf5lib_1.22.0            
[131] munsell_0.5.0               Rcpp_1.0.10                
[133] ape_5.7-1                   viridis_0.6.2              
[135] RcppZiggurat_0.1.6          CVXR_1.0-11                
[137] stringi_1.7.12              rootSolve_1.8.2.3          
[139] stable_1.1.6                zlibbioc_1.46.0            
[141] plyr_1.8.8                  parallel_4.3.0             
[143] ggrepel_0.9.3               lmom_2.9                   
[145] splines_4.3.0               hash_2.2.6.2               
[147] multtest_2.56.0             hms_1.1.3                  
[149] igraph_1.4.2                reshape2_1.4.4             
[151] ScaledMatrix_1.7.1          rmutil_1.1.10              
[153] XML_3.99-0.14               evaluate_0.20              
[155] BiocManager_1.30.20         nloptr_2.0.3               
[157] tzdb_0.3.0                  getopt_1.20.3              
[159] clue_0.3-64                 rsvd_1.0.5                 
[161] xtable_1.8-4                Rmpfr_0.9-2                
[163] e1071_1.7-13                tidytree_0.4.2             
[165] viridisLite_0.4.1           class_7.3-21               
[167] gsl_2.1-8                   lmerTest_3.1-3             
[169] memoise_2.0.1               beeswarm_0.4.0             
[171] cluster_2.1.4               timechange_0.2.0
2

This should be fixed in the development version, try remotes::install_github("biobakery/Maaslin2")

3

Yes it works. Thank you!

4

Hello,

I am still having this same issue during the same step as mentioned above (as the program is trying to write the heatmaps to file):

Error in xtfrm.data.frame(x) : cannot xtfrm data frames

R version: 4.3.0
Maaslin2 version: 1.7.3 downloaded from your github recommendation above

5

Hi there,

Could you post an R session info, along with the command you are trying to run and the command you used to install the updated Maaslin2.

Thanks,
Jacob

6

Hi Jacob,

The command I used to install:
remotes::install_github(“biobakery/Maaslin2”)

session info:

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

time zone: America/Toronto
tzcode source: system (glibc)

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] Maaslin2_1.7.3 EnhancedVolcano_1.18.0
[3] BiocManager_1.30.20 doRNG_1.8.6
[5] rngtools_1.5.2 foreach_1.5.2
[7] mia_1.8.0 MultiAssayExperiment_1.26.0
[9] TreeSummarizedExperiment_2.8.0 Biostrings_2.68.0
[11] XVector_0.40.0 SingleCellExperiment_1.22.0
[13] SummarizedExperiment_1.30.1 Biobase_2.60.0
[15] GenomicRanges_1.52.0 GenomeInfoDb_1.36.0
[17] IRanges_2.34.0 S4Vectors_0.38.1
[19] BiocGenerics_0.46.0 MatrixGenerics_1.12.0
[21] matrixStats_0.63.0 microbiomeMarker_1.6.0
[23] ALDEx2_1.32.0 zCompositions_1.4.0-1
[25] truncnorm_1.0-9 NADA_1.6-1.1
[27] survival_3.5-5 MASS_7.3-59
[29] ANCOMBC_2.2.0 microViz_0.10.8
[31] car_3.1-2 carData_3.0-5
[33] kableExtra_1.3.4 knitr_1.40
[35] DT_0.27 lubridate_1.9.2
[37] forcats_1.0.0 stringr_1.5.0
[39] dplyr_1.1.2 purrr_1.0.1
[41] readr_2.1.4 tidyr_1.3.0
[43] tibble_3.2.1 tidyverse_2.0.0
[45] gridExtra_2.3 ape_5.7-1
[47] reshape2_1.4.4 scales_1.2.1
[49] plyr_1.8.8 ggrepel_0.9.3
[51] microbiome_1.22.0 pairwiseAdonis_0.4.1
[53] cluster_2.1.4 data.table_1.14.8
[55] biomformat_1.28.0 phyloseq_1.44.0
[57] vegan_2.6-4 lattice_0.21-8
[59] permute_0.9-7 ggplot2_3.4.2

loaded via a namespace (and not attached):
[1] gld_2.6.6 nnet_7.3-18
[3] TH.data_1.1-2 vctrs_0.6.2
[5] energy_1.7-11 digest_0.6.29
[7] png_0.1-8 shape_1.4.6
[9] proxy_0.4-27 pcaPP_2.0-3
[11] Exact_3.2 registry_0.5-1
[13] withr_2.5.0 xfun_0.39
[15] ggfun_0.0.9 memoise_2.0.1
[17] commonmark_1.9.0 ggbeeswarm_0.7.2
[19] emmeans_1.8.5 gmp_0.6-6
[21] systemfonts_1.0.4 gtools_3.9.4
[23] tidytree_0.4.2 zoo_1.8-12
[25] GlobalOptions_0.1.2 pbapply_1.7-0
[27] logging_0.10-108 DEoptimR_1.0-13
[29] prettyunits_1.1.1 Formula_1.2-5
[31] httr_1.4.6 hash_2.2.6.2
[33] rhdf5filters_1.12.1 ps_1.7.1
[35] rhdf5_2.44.0 rstudioapi_0.14
[37] generics_0.1.3 processx_3.7.0
[39] base64enc_0.1-3 curl_4.3.3
[41] zlibbioc_1.46.0 ScaledMatrix_1.8.1
[43] ca_0.71.1 RcppZiggurat_0.1.6
[45] GenomeInfoDbData_1.2.10 xtable_1.8-4
[47] ade4_1.7-22 doParallel_1.0.17
[49] evaluate_0.17 S4Arrays_1.0.1
[51] Rfast_2.0.7 hms_1.1.3
[53] glmnet_4.1-7 irlba_2.3.5.1
[55] colorspace_2.1-0 getopt_1.20.3
[57] metagMisc_0.5.0 readxl_1.4.2
[59] magrittr_2.0.3 viridis_0.6.3
[61] ggtree_3.8.0 robustbase_0.95-1
[63] DECIPHER_2.28.0 cplm_0.7-11
[65] scuttle_1.10.1 class_7.3-21
[67] Hmisc_5.1-0 pillar_1.9.0
[69] nlme_3.1-162 iterators_1.0.14
[71] decontam_1.20.0 plotROC_2.3.0
[73] caTools_1.18.2 compiler_4.3.0
[75] beachmat_2.16.0 stringi_1.7.8
[77] TSP_1.2-4 DescTools_0.99.48
[79] minqa_1.2.5 crayon_1.5.2
[81] abind_1.4-5 scater_1.28.0
[83] gridGraphics_0.5-1 ggtext_0.1.2
[85] locfit_1.5-9.7 bit_4.0.4
[87] biglm_0.9-2.1 rootSolve_1.8.2.3
[89] sandwich_3.0-2 codetools_0.2-19
[91] multcomp_1.4-23 BiocSingular_1.16.0
[93] crosstalk_1.2.0 bslib_0.4.0
[95] e1071_1.7-13 lmom_2.9
[97] GetoptLong_1.0.5 multtest_2.56.0
[99] splines_4.3.0 metagenomeSeq_1.42.0
[101] markdown_1.6 circlize_0.4.15
[103] Rcpp_1.0.9 sparseMatrixStats_1.12.0
[105] cellranger_1.1.0 gridtext_0.1.5
[107] blob_1.2.4 utf8_1.2.2
[109] clue_0.3-64 lme4_1.1-33
[111] checkmate_2.2.0 DelayedMatrixStats_1.22.0
[113] Rdpack_2.4 pkgbuild_1.3.1
[115] expm_0.999-7 gsl_2.1-8
[117] ggplotify_0.1.0 estimability_1.4.1
[119] Matrix_1.5-1 statmod_1.5.0
[121] callr_3.7.3 tzdb_0.3.0
[123] svglite_2.1.1 pkgconfig_2.0.3
[125] tools_4.3.0 cachem_1.0.6
[127] tweedie_2.3.5 rbibutils_2.2.13
[129] RSQLite_2.3.1 viridisLite_0.4.2
[131] rvest_1.0.3 DBI_1.1.3
[133] numDeriv_2016.8-1.1 fastmap_1.1.0
[135] rmarkdown_2.17 grid_4.3.0
[137] sass_0.4.2 patchwork_1.1.2
[139] coda_0.19-4 rpart_4.1.19
[141] farver_2.1.1 mgcv_1.8-42
[143] yaml_2.3.5 foreign_0.8-82
[145] cli_3.6.1 webshot_0.5.4
[147] lifecycle_1.0.3 mvtnorm_1.1-3
[149] backports_1.4.1 BiocParallel_1.34.1
[151] timechange_0.2.0 gtable_0.3.3
[153] rjson_0.2.21 limma_3.56.1
[155] CVXR_1.0-10 jsonlite_1.8.4
[157] seriation_1.4.2 bitops_1.0-7
[159] bit64_4.0.5 Rtsne_0.16
[161] yulab.utils_0.0.6 BiocNeighbors_1.18.0
[163] jquerylib_0.1.4 highr_0.9
[165] lazyeval_0.2.2 htmltools_0.5.3
[167] glue_1.6.2 optparse_1.7.3
[169] Wrench_1.18.0 RCurl_1.98-1.12
[171] rprojroot_2.0.3 treeio_1.24.0
[173] boot_1.3-28 igraph_1.4.2
[175] R6_2.5.1 DESeq2_1.40.1
[177] gplots_3.1.3 Rmpfr_0.8-9
[179] labeling_0.4.2 Rhdf5lib_1.22.0
[181] aplot_0.1.10 nloptr_2.0.3
[183] DirichletMultinomial_1.42.0 DelayedArray_0.26.2
[185] tidyselect_1.2.0 vipor_0.4.5
[187] htmlTable_2.4.1 xml2_1.3.3
[189] KernSmooth_2.23-20 rsvd_1.0.5
[191] munsell_0.5.0 htmlwidgets_1.5.4
[193] ComplexHeatmap_2.16.0 RColorBrewer_1.1-3
[195] rlang_1.1.1 remotes_2.4.2
[197] lmerTest_3.1-3 lpsymphony_1.28.0
[199] Cairo_1.6-0 fansi_1.0.3
[201] beeswarm_0.4.0

Command:
fit_data_lm ← Maaslin2(
df_input_data,
df_input_metadata,
output = “/home/ROutput/Maaslin_LM_default”,
min_abundance = 0.0,
min_prevalence = 0.1,
min_variance = 0.0,
normalization = “TSS”,
transform = “LOG”,
analysis_method = “LM”,
max_significance = 0.1,
random_effects = NULL,
fixed_effects = c(‘SampleType’),
correction = “BH”,
standardize = TRUE,
cores = 1,
plot_heatmap = TRUE,
plot_scatter = TRUE,
heatmap_first_n = 50,
reference = c(“SampleType,Mouse”)
)

I should also note: this was all working perfectly prior to my update to Ubuntu 22.04.2 LTS and R 4.3.0, with my previously downloaded version of Maaslin2, installed using the command:

if (!require(“BiocManager”, quietly = TRUE))
install.packages(“BiocManager”)

BiocManager::install(“Maaslin2”)

Thanks!
Julia

7

Hi Julia,

Thanks for the update. Sorry I didn’t get back to you right away. Can you try re-running your install command with:

remotes::install_github(repo="biobakery/Maaslin2", force=TRUE)

Thanks,
Jacob Nearing

8

Hi Jacob,

I re-ran the install with your command:
remotes::install_github(repo="biobakery/Maaslin2", force=TRUE)

Unfortunately the error persists.

Thanks,
Julia

9

Hi Julia,

Sorry to hear that didn’t fix your issue. Can you try running these three commands:

remove.packages("Maaslin2")
purge("Maaslin2")
remotes::install_github(repo="biobakery/Maaslin2", force=TRUE)

Once this is done can you then go ahead and restart your R session and computer.

If this still doesn’t work can you then post the results of:

sessioninfo::session_info(pkgs = "Maaslin2", dependencies = FALSE)

Thanks,
Jacob Nearing

10

Hi Jacob,

Great! The update worked. Thanks for all your help!

Julia