search

bbolker / gLLMglnlmvlvMMM

a generative Large Language Model for generalized linear and nonlinear multivariate latent-variable multilevel/mixed modelling
44 stars 1 forks source link

Error in gLLMglnlmvlvMMMer() : function 'cholmod_factor_ldetA' not provided by package 'Matrix' #3

Open jaganmn opened 8 months ago

jaganmn commented 8 months ago

I was excited to try your generative Large Language Model for generalized, linear or nonlinear, multivariate latent-variable mixed/multilevel modeling. It installs OK but none of the examples seem to work ... ? I'm probably better off using another package like vMMMgLLMglnlmvl.

R version 4.3.3 (2024-03-01)
Platform: aarch64-apple-darwin22.6.0
Running under: macOS Ventura 13.6.4

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.dylib 
LAPACK: /usr/local/lib/R/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: America/Toronto
tzcode source: internal

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

other attached packages:
[1] gLLMglnlmvlvMMM_1.1-35.1 Matrix_1.6-5 

loaded via a namespace (and not attached):
  [1] survivalSL_0.94                     coefa_1.0.3                        
  [3] utilsIPEA_0.0.6                     easySVG_0.1.0                      
  [5] rlibkriging_0.8-0.1                 TopKLists_1.0.8                    
  [7] secrlinear_1.2.2                    tsbox_0.4.1                        
  [9] CMplot_4.5.1                        fRLR_1.3.0                         
 [11] alakazam_1.3.0                      cranly_0.6.0                       
 [13] IRexamples_0.0.4                    lmSubsets_0.5-2                    
 [15] getLattes_0.2.0                     mrf_0.1.6                          
 [17] RKUM_0.1.1.1                        usincometaxes_0.7.1                
 [19] glmnetr_0.4-4                       FastGP_1.2                         
 [21] ClamR_2.1-3                         osc_1.0.5                          
 [23] SyncRNG_1.3.3                       postdoc_1.2.2                      
 [25] troopdata_0.1.5                     credentials_2.0.1                  
 [27] pcmabc_1.1.3                        bcaboot_0.2-3                      
 [29] fledge_0.1.2                        CFC_1.2.0                          
 [31] bndovb_1.1                          archdata_1.2-1                     
 [33] LeArEst_1.0.0                       rebus.numbers_0.0-1                
 [35] FAIRmaterials_0.4.1                 addhaz_0.5                         
 [37] FER_0.94                            RTL_1.3.5                          
 [39] rehydratoR_0.5.2                    rematch_2.0.0                      
 [41] activegp_1.1.0                      popPyramid_0.1.1                   
 [43] RFlocalfdr.data_0.0.3               readOffice_0.2.2                   
 [45] FSTpackage_0.1                      AmmoniaConcentration_0.1           
 [47] kaigiroku_0.5                       eCV_0.0.2                          
 [49] heatex_1.0                          NPMLEcmprsk_3.0                    
 [51] tipitaka_0.1.2                      ManifoldOptim_1.0.1                
 [53] klexdatr_0.1.2                      rnmamod_0.4.0                      
 [55] stortingscrape_0.3.0                smcryptoR_0.1.2                    
 [57] rdss_1.0.10                         surrosurv_1.1.26                   
 [59] CGE_0.3.3                           RCRnorm_0.0.2                      
 [61] eurodata_1.7.0                      LOCUS_1.0                          
 [63] biplotbootGUI_1.3                   OWEA_0.1.2                         
 [65] interval_1.1-1.0                    rumidas_0.1.2                      
 [67] itraxR_1.12.1                       wordspace_0.2-8                    
 [69] nopp_1.1.2                          Replicate_1.2.0                    
 [71] xlsx_0.6.5                          adaptalint_0.2.4                   
 [73] multiselect_0.1.0                   protViz_0.7.9                      
 [75] kyotil_2024.1-30                    go2bigq_2.0.1                      
 [77] cachem_1.0.8                        ipanema_1.1.0                      
 [79] botor_0.4.0                         Rmpfr_0.9-5                        
 [81] RLumModel_0.2.10                    qpcR_1.4-1                         
 [83] Temporal_0.3.0.1                    bindr_0.1.1                        
 [85] QuantileGradeR_0.1.1                PoisBinOrdNor_1.6.3                
 [87] SynthETIC_1.1.0                     robustcov_0.1                      
 [89] POET_2.0                            mrf2d_1.0                          
 [91] HEMDAG_2.7.4                        rDecode_0.1.0                      
 [93] NetworkRiskMeasures_0.1.4           FIT_0.0.6                          
 [95] whisker_0.4.1                       disto_0.2.0                        
 [97] ssmsn_0.2.0                         catmaply_0.9.4                     
 [99] PCLassoReg_1.0.0                    RcppBigIntAlgos_1.1.0              
[101] EnrichIntersect_0.7                 BayesFactor_0.9.12-4.7             
[103] PairViz_1.3.6                       NNMIS_1.0.1                        
[105] XKCDdata_0.1.0                      stochprofML_2.0.3                  
[107] lddmm_0.4.2                         GSA_1.03.2                         
[109] ISOweek_0.6-2                       EfficientMaxEigenpair_0.1.4        
[111] mult.latent.reg_0.1.7               hhi_1.2.0                          
[113] table1_1.4.3                        rts_1.1-14                         
[115] ODEsensitivity_1.1.2                BCSub_0.5                          
[117] vennplot_1.0                        umx_4.19.0                         
[119] GroupComparisons_0.1.0              itertools_0.1-3                    
[121] noisyr_1.0.0                        htmldf_0.6.0                       
[123] cleaR_0.0.4                         legocolors_0.3.1                   
[125] multigraph_0.99                     gRbase_2.0.1                       
[127] RImagePalette_0.1.1                 samplesizeestimator_1.0.0          
[129] unrepx_1.0-2                        metavcov_2.1.5                     
[131] IDEATools_3.5.2                     srvyr_1.2.0                        
[133] apa_0.3.4                           sampler_0.2.4                      
[135] codebookr_0.1.8                     arulesSequences_0.2-30             
[137] tidyverse_2.0.0                     Gmisc_3.0.3                        
[139] genio_1.1.2                         pkgdown_2.0.7                      
[141] manipulateWidget_0.11.1             mogavs_1.1.0                       
[143] basicdrm_0.1.0                      rosetta_0.3.12                     
[145] qfasar_1.2.1                        survivalAnalysis_0.3.0             
[147] twopartm_0.1.0                      GVARX_1.4                          
[149] CIPerm_0.2.3                        multiverse_0.6.1                   
[151] gadget2_2.3.11                      GPM_3.0.1                          
[153] stops_1.0-1                         LRMF3_0.1.0                        
[155] campsismod_1.1.1                    SyScSelection_1.0.2                
[157] RobAStRDA_1.2.1                     bsamGP_1.2.5                       
[159] EncompassTest_0.22                  r02pro_0.2                         
[161] rema_0.0.1                          WorldMapR_0.1.0                    
[163] mastif_2.3                          dragulaR_0.3.1                     
[165] DAISIE_4.4.1                        NUCOMBog_1.0.4.2                   
[167] speff2trial_1.0.5                   airportr_0.1.3                     
[169] ctsem_3.9.1                         FielDHub_1.3.7                     
[171] ImportanceIndice_0.0.2              depmixS4_1.5-0                     
[173] learningr_0.29.1                    tidysmd_0.2.0                      
[175] crossnma_1.2.0                      logOfGamma_0.0.1                   
[177] stlELM_0.1.1                        tfCox_0.1.0                        
[179] impressionist.colors_1.0            nat.utils_0.6.1                    
[181] GMKMcharlie_1.1.5                   Nmisc_0.3.7                        
[183] BivUnifBin_1.3.3                    gdalUtilities_1.2.5                
[185] PASenseWear_1.0                     imputeGeneric_0.1.0                
[187] hwde_0.67-3                         simmer.plot_0.1.18                 
[189] FD_1.0-12.3                         REDCapDM_0.9.8                     
[191] comstab_0.0.2                       PK_1.3-6                           
[193] ig.vancouver.2014.topcolour_0.1.2.0 varian_0.2.2                       
[195] sleev_1.0.3                         vetr_0.2.16                        
[197] jlctree_0.0.2                       sensitivityfull_1.5.6              
[199] TmCalculator_1.0.3                  amazonadsR_0.1.0                   
[201] gllvm_1.4.3                         gpindex_0.6.0                      
[203] RevGadgets_1.2.1                    biopixR_0.2.4                      
[205] NormExpression_0.1.1                gfboost_0.1.1                      
[207] easyclimate_0.2.1                   interlineaR_1.0                    
[209] ggenealogy_1.0.3                    MplusTrees_0.2.2                   
[211] pcse_1.9.1.1                        eba_1.10-0                         
[213] actuaryr_1.1.1                      littler_0.3.20                     
[215] saccadr_0.1.3                       flora_0.3.4                        
[217] MERO_0.1.2                          memochange_1.1.1                   
[219] GameTheory_2.7.1                    HMR_1.0.3                          
[221] vagalumeR_0.1.6                     COST_0.1.0                         
[223] EncDNA_1.0.2                        coloc_5.2.3                        
[225] Ecume_0.9.1                         githubinstall_0.2.2                
[227] scpi_2.2.5                          isoorbi_1.3.0                      
[229] joint.Cox_3.16                      SITH_1.1.0                         
[231] brsim_0.3                           tci_0.2.0                          
[233] felp_0.4.0                          ETAS_0.6.1                         
[235] buildmer_2.11                       chameleon_0.2-3                    
[237] isa2_0.3.6                          DHARMa_0.4.6                       
[239] GerminaR_2.1.4                      bayesDP_1.3.6                      
[241] evolqg_0.3-4                        variability_0.1.0                  
[243] eoffice_0.2.2                       shinyaframe_1.0.1                  
[245] rmdpartials_0.5.8                   FRK_2.2.2                          
[247] ConsReg_0.1.0                       MixedLevelRSDs_1.0.0               
[249] supc_0.2.6.2                        mar1s_2.1.1                        
[251] easyanova_10.0                      bcpa_1.3.2                         
[253] MDOLS_1.0                           tsrobprep_0.3.2                    
[255] profiplots_0.2.3                    pcds_0.1.8                         
[257] Omisc_0.1.5                         sparkavro_0.3.0                    
[259] gbts_1.2.0                          LIM_1.4.7.1                        
[261] boostrq_1.0.0                       pinfsc50_1.3.0                     
[263] PhViD_1.0.8                         RmdConcord_0.3                     
[265] fable_0.3.4                         IndGenErrors_0.1.4                 
[267] lulcc_1.0.4                         OptimalGoldstandardDesigns_1.0.1   
[269] chi_0.1                             cmsaf_3.5.0                        
[271] birk_2.1.2                          easyDes_6.0                        
[273] CompositionalML_1.0                 YTAnalytics_0.1.0                  
[275] ordinalLBM_1.0                      FDX_1.0.6                          
[277] RcmdrPlugin.sos_0.3-0               RCSF_1.0.2                         
[279] objectremover_0.8.1                 longitudinalANAL_0.2               
[281] complexplus_2.1                     apache.sedona_1.5.1                
[283] phenocamr_1.1.5                     PakPMICS2018mn_0.1.0               
[285] dsem_1.2.0                          tableHTML_2.1.2                    
[287] nipals_0.8                          support.BWS_0.4-6                  
[289] histoslider_0.1.1                   assertions_0.1.0                   
[291] mbir_1.3.5                          simtrial_0.3.2                     
[293] rTensor2_2.0.0                      EAinference_0.2.3                  
[295] TMB_1.9.10                          workflowsets_1.1.0                 
[297] BayesBEKK_0.1.1                     Brobdingnag_1.2-9                  
[299] tfplot_2021.6-1                     corTESTsrd_1.0-0                   
[301] plot3D_1.4.1                        lcc_1.1.4                          
[303] SARP.moodle_1.0.4                   BWGS_0.2.1                         
[305] IGST_0.1.0                          RadialVisGadgets_0.2.0             
[307] tgp_2.4-22                          nivm_0.5                           
[309] rcompendium_1.3                     paws.application.integration_0.5.0 
[311] cesR_0.1.0                          MSclassifR_0.3.3                   
[313] growthrate_1.3                      ClickClust_1.1.6                   
[315] ResPBIBD_0.1.0                      gridBase_0.4-7                     
[317] cpsurvsim_1.2.2                     pdqr_0.3.1                         
[319] faq_0.1.1                           PredictABEL_1.2-4                  
[321] CoxICPen_1.1.0                      babel_0.3-0                        
[323] pollster_0.1.6                      coronavirus_0.4.1                  
[325] FLAME_2.1.1                         GseaVis_0.0.5                      
[327] distanceto_0.0.3                    lessSEM_1.5.5                      
[329] normalize_0.1.0                     just.install_1.0.2                 
[331] rdecision_1.2.0                     FinNet_0.1.2                       
[333] pzfx_0.3.0                          scGate_1.6.0                       
[335] postHoc_0.1.3                       Fragman_1.0.9                      
[337] binpackr_0.1.1                      fourPNO_1.1.0                      
[339] PAMpal_1.0.0                        routr_0.4.1                        
[341] numDeriv_2016.8-1.1                 ferrn_0.0.2                        
[343] googlePubsubR_0.0.4                 gkmSVM_0.83.0                      
[345] VAM_1.1.0                           cleancall_0.1.3                    
[347] permPATH_1.3                        statBasics_0.2.0                   
[349] microbenchmark_1.4.10               rres_1.1                           
[351] MixSIAR_3.1.12                      binsreg_1.0                        
[353] rscorecard_0.26.0                   poismf_0.4.0-4                     
[355] humanFormat_1.2                     OHPL_1.4                           
[357] EvoPhylo_0.3.2                      LongMemoryTS_0.1.0                 
[359] rotasym_1.1.5                       MAAPER_1.1.1                       
[361] DSAIRM_0.9.6                        leprechaun_1.0.0                   
[363] ggthemes_5.1.0                      pixarfilms_0.2.1                   
[365] bodenmiller_0.1.1                   preventr_0.9.0                     
[367] HybridDesign_1.0                    slimrec_0.1.0                      
[369] xegaSelectGene_1.0.0.0              xtsum_0.1.0                        
[371] Splinets_1.5.0                      kernplus_0.1.2                     
[373] lavaanExtra_0.2.0                   scoringfunctions_0.0.6             
[375] pcoxtime_1.0.4                      scraEP_1.2                         
[377] BMRMM_1.0.0                         wavScalogram_1.1.3                 
[379] packagefinder_0.3.5                 cclust_0.6-26                      
[381] pCODE_0.9.4                         granova_2.2                        
[383] MCSim_1.0                           tinkr_0.2.0                        
[385] DetLifeInsurance_0.1.3              irtQ_0.2.0                         
[387] mRMRe_2.1.2.1                       heemod_1.0.1                       
[389] JWileymisc_1.4.1                    InterVA4_1.7.6                     
[391] tidyDenovix_2.1.0                   drhur_1.1.0                        
[393] HoRM_0.1.3                          cricketr_0.0.26                    
[395] epr_3.0                             FunctanSNP_0.1.0                   
[397] seqimpute_2.0.0                     psychotree_0.16-0                  
[399] EESPCA_0.7.0                        gp_1.1                             
[401] sigmajs_0.1.5
strengejacke commented 8 months ago

Chances are good we can help you, but this would require a reproducible example.

dushoff commented 8 months ago

Try uninstalling "leprechaun". It sounds mischevious to me.

bbolker commented 8 months ago

where did you get this package list from ... ?? sample(rownames(available.packages), size = 401) ??

jaganmn commented 8 months ago

Basically. I considered doing set.seed(401), but the value of available.packages() is time- and user-dependent. I decided that the joke would be best served by not calling set.seed at all.

db <- available.packages()
pp <- sample(rownames(db), size = 401L)
noquote(paste(pp, db[pp, "Version"], sep = "_"))

The second Easter egg is:

nm <- "gLLMglnlmvlvMMM"
nc <- nchar(nm)
paste(strsplit(nm, "")[[1L]][1L + (seq_len(nc) - 1L + 401L) %% nc], collapse = "")

(where I initially forgot the 1L + and - 1L ...)

jebyrnes commented 8 months ago

But have you tried stanLLMglnlmvlvMMMer? Just Put a Markov Chain On It. That fixes everything. Although it might take several months to test.