## Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
## 'DelayedArray::makeNindexFromArrayViewport' when loading 'SummarizedExperiment'
## R version 4.5.0 (2025-04-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 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/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] grid stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] deseq2pip_1.0.2 renv_1.1.4
## [3] enrichplot_1.28.2 ashr_2.2-63
## [5] sva_3.56.0 BiocParallel_1.42.0
## [7] genefilter_1.90.0 mgcv_1.9-1
## [9] nlme_3.1-168 labeling_0.4.3
## [11] limma_3.64.1 forcats_1.0.0
## [13] scales_1.4.0 ggpubr_0.6.0
## [15] fgsea_1.34.0 msigdbr_24.1.0
## [17] clusterProfiler_4.16.0 pheatmap_1.0.12
## [19] ggalt_0.4.0 DESeq2_1.48.1
## [21] SummarizedExperiment_1.38.1 Biobase_2.68.0
## [23] MatrixGenerics_1.20.0 matrixStats_1.5.0
## [25] GenomicRanges_1.60.0 GenomeInfoDb_1.44.0
## [27] IRanges_2.42.0 S4Vectors_0.46.0
## [29] BiocGenerics_0.54.0 generics_0.1.4
## [31] plotr_0.1.3 ggplotify_0.1.2
## [33] RColorBrewer_1.1-3 wesanderson_0.3.7
## [35] ggrepel_0.9.6 viridis_0.6.5
## [37] viridisLite_0.4.2 cowplot_1.1.3
## [39] patchwork_1.3.0 ggplot2_3.5.2
## [41] strpip_0.1.3 biomaRt_2.64.0
## [43] data.table_1.17.4 magrittr_2.0.3
## [45] rlang_1.1.6 stringr_1.5.1
## [47] tibble_3.2.1 tidyr_1.3.1
## [49] dplyr_1.1.4
##
## loaded via a namespace (and not attached):
## [1] splines_4.5.0 filelock_1.0.3 R.oo_1.27.1
## [4] XML_3.99-0.18 lifecycle_1.0.4 httr2_1.1.2
## [7] mixsqp_0.3-54 rstatix_0.7.2 edgeR_4.6.2
## [10] lattice_0.22-6 MASS_7.3-65 backports_1.5.0
## [13] sass_0.4.10 rmarkdown_2.29 jquerylib_0.1.4
## [16] yaml_2.3.10 ggtangle_0.0.6 DBI_1.2.3
## [19] maps_3.4.3 abind_1.4-8 purrr_1.0.4
## [22] R.utils_2.13.0 yulab.utils_0.2.0 rappdirs_0.3.3
## [25] GenomeInfoDbData_1.2.14 irlba_2.3.5.1 tidytree_0.4.6
## [28] annotate_1.86.0 pkgdown_2.1.3 codetools_0.2-20
## [31] DelayedArray_0.34.1 DOSE_4.2.0 xml2_1.3.8
## [34] tidyselect_1.2.1 aplot_0.2.5 UCSC.utils_1.4.0
## [37] farver_2.1.2 ash_1.0-15 BiocFileCache_2.16.0
## [40] jsonlite_2.0.0 Formula_1.2-5 survival_3.8-3
## [43] systemfonts_1.2.3 tools_4.5.0 progress_1.2.3
## [46] treeio_1.32.0 ragg_1.4.0 Rcpp_1.0.14
## [49] glue_1.8.0 gridExtra_2.3 Rttf2pt1_1.3.12
## [52] SparseArray_1.8.0 xfun_0.52 qvalue_2.40.0
## [55] withr_3.0.2 fastmap_1.2.0 truncnorm_1.0-9
## [58] digest_0.6.37 R6_2.6.1 gridGraphics_0.5-1
## [61] textshaping_1.0.1 GO.db_3.21.0 RSQLite_2.3.11
## [64] R.methodsS3_1.8.2 prettyunits_1.2.0 httr_1.4.7
## [67] htmlwidgets_1.6.4 S4Arrays_1.8.0 pkgconfig_2.0.3
## [70] gtable_0.3.6 blob_1.2.4 XVector_0.48.0
## [73] htmltools_0.5.8.1 carData_3.0-5 png_0.1-8
## [76] ggfun_0.1.8 knitr_1.50 reshape2_1.4.4
## [79] curl_6.2.3 cachem_1.1.0 KernSmooth_2.23-26
## [82] parallel_4.5.0 extrafont_0.19 AnnotationDbi_1.70.0
## [85] desc_1.4.3 pillar_1.10.2 vctrs_0.6.5
## [88] car_3.1-3 dbplyr_2.5.0 xtable_1.8-4
## [91] extrafontdb_1.0 evaluate_1.0.3 invgamma_1.1
## [94] cli_3.6.5 locfit_1.5-9.12 compiler_4.5.0
## [97] crayon_1.5.3 SQUAREM_2021.1 ggsignif_0.6.4
## [100] plyr_1.8.9 fs_1.6.6 stringi_1.8.7
## [103] assertthat_0.2.1 babelgene_22.9 Biostrings_2.76.0
## [106] lazyeval_0.2.2 proj4_1.0-15 GOSemSim_2.34.0
## [109] Matrix_1.7-3 hms_1.1.3 bit64_4.6.0-1
## [112] KEGGREST_1.48.0 statmod_1.5.0 igraph_2.1.4
## [115] broom_1.0.8 memoise_2.0.1 bslib_0.9.0
## [118] ggtree_3.16.0 fastmatch_1.1-6 bit_4.6.0
## [121] ape_5.8-1 gson_0.1.0