cobra function missing - Githubissues

cobra() function is not included with NetZooR_1.6.0 package installed from Bioconductor in R 4.3.1 on WINDOWS:

<...>
batch <- metadata$tcga.cgc_case_batch_number
> length(unique(batch))
[1] 17
> number_of_samples <- dim(gene_expression)[2]
> X <- cbind(rep(1, number_of_samples), as.matrix(dummy_cols(batch)[, -c(1:2)]))
> dim(X)
[1] 572  17
> cobra_estimates <- cobra(X, gene_expression)
Error in cobra(X, gene_expression) : could not find function "cobra"
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] DESeq2_1.42.1               recount3_1.12.0             SummarizedExperiment_1.32.0 GenomicRanges_1.54.1        GenomeInfoDb_1.38.1         IRanges_2.36.0             
 [7] S4Vectors_0.40.2            MatrixGenerics_1.14.0       matrixStats_1.1.0           netZooR_1.6.0               matrixcalc_1.0-6            yarn_1.28.0                
[13] pandaR_1.34.0               Biobase_2.62.0              BiocGenerics_0.48.1         reticulate_1.31             igraph_2.0.2                fastDummies_1.7.4          

loaded via a namespace (and not attached):
  [1] STRINGdb_2.14.3           fs_1.6.3                  bitops_1.0-7              httr_1.4.6                RColorBrewer_1.1-3        doParallel_1.0.17        
  [7] Rgraphviz_2.46.0          repr_1.1.7                tools_4.3.1               doRNG_1.8.6               backports_1.4.1           utf8_1.2.3               
 [13] R6_2.5.1                  vegan_2.6-8               HDF5Array_1.30.1          mgcv_1.8-42               rhdf5filters_1.14.1       permute_0.9-7            
 [19] withr_2.5.0               prettyunits_1.1.1         base64_2.0.1              preprocessCore_1.64.0     cli_3.6.1                 penalized_0.9-52         
 [25] readr_2.1.5               genefilter_1.84.0         askpass_1.1               Rsamtools_2.18.0          pbdZMQ_0.3-12             siggenes_1.76.0          
 [31] illuminaio_0.44.0         R.utils_2.12.3            AnnotationForge_1.44.0    sessioninfo_1.2.2         scrime_1.3.5              plotrix_3.8-4            
 [37] limma_3.58.1              RSQLite_2.3.3             generics_0.1.3            GOstats_2.68.0            quantro_1.36.0            BiocIO_1.12.0            
 [43] gtools_3.9.5              dplyr_1.1.4               GO.db_3.18.0              Matrix_1.5-4.1            fansi_1.0.4               abind_1.4-5              
 [49] R.methodsS3_1.8.2         lifecycle_1.0.3           yaml_2.3.7                edgeR_4.0.16              gplots_3.1.3.1            rhdf5_2.46.1             
 [55] SparseArray_1.2.4         BiocFileCache_2.10.2      grid_4.3.1                blob_1.2.4                crayon_1.5.2              lattice_0.21-8           
 [61] GenomicFeatures_1.54.4    annotate_1.80.0           KEGGREST_1.42.0           pillar_1.9.0              beanplot_1.3.1            rjson_0.2.21             
 [67] codetools_0.2-19          glue_1.6.2                downloader_0.4            data.table_1.14.8         vctrs_0.6.5               png_0.1-8                
 [73] gtable_0.3.4              assertthat_0.2.1          gsubfn_0.7                cachem_1.0.8              S4Arrays_1.2.1            survival_3.5-5           
 [79] iterators_1.0.14          statmod_1.5.0             nlme_3.1-162              Category_2.68.0           bit64_4.0.5               progress_1.2.2           
 [85] filelock_1.0.3            nor1mix_1.3-3             KernSmooth_2.23-21        colorspace_2.1-0          DBI_1.1.3                 nnet_7.3-19              
 [91] tidyselect_1.2.1          bit_4.0.5                 compiler_4.3.1            curl_5.2.1                chron_2.3-61              graph_1.80.0             
 [97] xml2_1.3.5                ggdendro_0.2.0            DelayedArray_0.28.0       rtracklayer_1.62.0        scales_1.3.0              caTools_1.18.2           
[103] hexbin_1.28.4             quadprog_1.5-8            RBGL_1.78.0               rappdirs_0.3.3            stringr_1.5.1             digest_0.6.33            
[109] GEOquery_2.70.0           XVector_0.42.0            htmltools_0.5.5           pkgconfig_2.0.3           base64enc_0.1-3           sparseMatrixStats_1.14.0 
[115] dbplyr_2.5.0              fastmap_1.1.1             rlang_1.1.1               DelayedMatrixStats_1.24.0 jsonlite_1.8.7            BiocParallel_1.36.0      
[121] mclust_6.1.1              R.oo_1.25.0               RCurl_1.98-1.13           magrittr_2.0.3            GenomeInfoDbData_1.2.11   Rhdf5lib_1.24.2          
[127] IRkernel_1.3.2            munsell_0.5.0             Rcpp_1.0.11               proto_1.0.0               sqldf_0.4-11              stringi_1.7.12           
[133] RJSONIO_1.3-1.9           zlibbioc_1.48.0           MASS_7.3-60               plyr_1.8.9                bumphunter_1.44.0         org.Hs.eg.db_3.18.0      
[139] minfi_1.48.0              parallel_4.3.1            Biostrings_2.70.1         IRdisplay_1.1             splines_4.3.1             multtest_2.58.0          
[145] hash_2.2.6.3              hms_1.1.3                 locfit_1.5-9.10           uuid_1.2-1                RUnit_0.4.33              base64url_1.4            
[151] rngtools_1.5.2            reshape2_1.4.4            biomaRt_2.58.2            XML_3.99-0.17             evaluate_0.21             BiocManager_1.30.22      
[157] tzdb_0.4.0                foreach_1.5.2             tidyr_1.3.1               openssl_2.1.0             purrr_1.0.1               reshape_0.8.9            
[163] ggplot2_3.4.4             xtable_1.8-4              restfulr_0.0.15           viridisLite_0.4.2         RCy3_2.22.1               tibble_3.2.1             
[169] memoise_2.0.1             AnnotationDbi_1.64.1      GenomicAlignments_1.38.2  cluster_2.1.4             GSEABase_1.64.0
netZoo / netZooR

cobra function missing #328
