Hi,
I’m following the sPLS-DA vingette, when It comes to the part of prediction I get the following error with the predict function
predict ← mixOmics::predict
Error: ‘predict’ is not an exported object from ‘namespace:mixOmics’
sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] PCAtools_2.8.0 ggrepel_0.9.3 pheatmap_1.0.12
[4] edgeR_3.38.4 limma_3.52.4 mixOmics_6.23.4
[7] lattice_0.20-45 MASS_7.3-58 readr_2.1.3
[10] ggfortify_0.4.16 ggplot2_3.4.1 DESeq2_1.36.0
[13] SummarizedExperiment_1.26.1 MatrixGenerics_1.8.1 matrixStats_0.62.0
[16] tibble_3.1.8 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.20.2
[19] AnnotationFilter_1.20.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.15.0 GenomicFeatures_1.48.4
[22] AnnotationDbi_1.58.0 Biobase_2.56.0 GenomicRanges_1.48.0
[25] GenomeInfoDb_1.32.4 IRanges_2.30.1 S4Vectors_0.34.0
[28] BiocGenerics_0.42.0 tximport_1.24.0 stringr_1.5.0
[31] readxl_1.4.1 xlsx_0.6.5 plyr_1.8.7
[34] tidyr_1.3.0 dplyr_1.0.10
loaded via a namespace (and not attached):
[1] utf8_1.2.2 tidyselect_1.2.0 RSQLite_2.2.18 htmlwidgets_1.5.4
[5] grid_4.2.1 BiocParallel_1.30.4 devtools_2.4.5 munsell_0.5.0
[9] ScaledMatrix_1.4.1 codetools_0.2-18 miniUI_0.1.1.1 withr_2.5.0
[13] colorspace_2.0-3 filelock_1.0.2 knitr_1.40 rstudioapi_0.14
[17] rJava_1.0-6 labeling_0.4.2 GenomeInfoDbData_1.2.8 bit64_4.0.5
[21] farver_2.1.1 rprojroot_2.0.3 vctrs_0.5.2 generics_0.1.3
[25] xfun_0.34 BiocFileCache_2.4.0 R6_2.5.1 rsvd_1.0.5
[29] locfit_1.5-9.6 bitops_1.0-7 cachem_1.0.6 DelayedArray_0.22.0
[33] assertthat_0.2.1 promises_1.2.0.1 BiocIO_1.6.0 scales_1.2.1
[37] vroom_1.6.0 gtable_0.3.1 beachmat_2.12.0 processx_3.7.0
[41] rlang_1.0.6 genefilter_1.78.0 splines_4.2.1 rtracklayer_1.56.1
[45] GenVisR_1.28.0 lazyeval_0.2.2 yaml_2.3.6 reshape2_1.4.4
[49] httpuv_1.6.6 tools_4.2.1 usethis_2.1.6 ellipsis_0.3.2
[53] RColorBrewer_1.1-3 sessioninfo_1.2.2 Rcpp_1.0.9 sparseMatrixStats_1.8.0
[57] progress_1.2.2 zlibbioc_1.42.0 purrr_1.0.1 RCurl_1.98-1.9
[61] ps_1.7.1 prettyunits_1.1.1 viridis_0.6.2 cowplot_1.1.1
[65] urlchecker_1.0.1 fs_1.5.2 magrittr_2.0.3 data.table_1.14.4
[69] RSpectra_0.16-1 ProtGenerics_1.28.0 pkgload_1.3.0 hms_1.1.2
[73] xlsxjars_0.6.1 mime_0.12 evaluate_0.17 xtable_1.8-4
[77] XML_3.99-0.11 gridExtra_2.3 compiler_4.2.1 biomaRt_2.52.0
[81] ellipse_0.4.3 crayon_1.5.2 htmltools_0.5.4 corpcor_1.6.10
[85] later_1.3.0 tzdb_0.3.0 geneplotter_1.74.0 DBI_1.1.3
[89] dbplyr_2.2.1 rappdirs_0.3.3 Matrix_1.5-1 cli_3.4.1
[93] parallel_4.2.1 igraph_1.4.0 pkgconfig_2.0.3 GenomicAlignments_1.32.1
[97] xml2_1.3.3 rARPACK_0.11-0 annotate_1.74.0 dqrng_0.3.0
[101] XVector_0.36.0 VariantAnnotation_1.42.1 callr_3.7.2 digest_0.6.30
[105] Biostrings_2.64.1 rmarkdown_2.17 cellranger_1.1.0 DelayedMatrixStats_1.18.2
[109] restfulr_0.0.15 curl_4.3.3 shiny_1.7.2 Rsamtools_2.12.0
[113] gtools_3.9.3 rjson_0.2.21 FField_0.1.0 lifecycle_1.0.3
[117] jsonlite_1.8.3 viridisLite_0.4.1 BSgenome_1.64.0 fansi_1.0.3
[121] pillar_1.8.1 KEGGREST_1.36.3 fastmap_1.1.0 httr_1.4.4
[125] pkgbuild_1.3.1 survival_3.5-5 glue_1.6.2 remotes_2.4.2
[129] png_0.1-7 bit_4.0.4 stringi_1.7.8 profvis_0.3.7
[133] blob_1.2.3 BiocSingular_1.12.0 memoise_2.0.1 irlba_2.3.5.1