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r_session_info.txt
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# R Session info from
# R and all packages were freshly installed on a computer running macOS
# for these analyses in this manuscript
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] qgraph_1.6.9 ggfortify_0.4.12
[3] pbapply_1.4-3 gridExtra_2.3
[5] DESeq2_1.32.0 SummarizedExperiment_1.22.0
[7] Biobase_2.52.0 MatrixGenerics_1.4.2
[9] matrixStats_0.60.1 GenomicRanges_1.44.0
[11] GenomeInfoDb_1.28.1 IRanges_2.26.0
[13] S4Vectors_0.30.0 BiocGenerics_0.38.0
[15] ggrepel_0.9.1 Rphylopars_0.3.2
[17] forcats_0.5.1 stringr_1.4.0
[19] dplyr_1.0.7 purrr_0.3.4
[21] readr_2.0.1 tidyr_1.1.3
[23] tibble_3.1.4 ggplot2_3.3.5
[25] tidyverse_1.3.1 treeio_1.16.2
[27] jsonlite_1.7.2 ape_5.5
[29] agalmar_0.0.0.9000 digest_0.6.28
[31] hutan_0.5.1
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.1 Hmisc_4.5-0
[4] fastmatch_1.1-3 plyr_1.8.6 igraph_1.2.6
[7] lazyeval_0.2.2 splines_4.1.0 BiocParallel_1.26.2
[10] listenv_0.8.0 htmltools_0.5.2 fansi_0.5.0
[13] checkmate_2.0.0 magrittr_2.0.1 phytools_0.7-80
[16] memoise_2.0.0 cluster_2.1.2 tzdb_0.1.2
[19] globals_0.14.0 Biostrings_2.60.2 annotate_1.70.0
[22] modelr_0.1.8 jpeg_0.1-9 colorspace_2.0-2
[25] blob_1.2.2 rvest_1.0.1 xfun_0.25
[28] haven_2.4.3 crayon_1.4.1 RCurl_1.98-1.4
[31] microbenchmark_1.4-7 genefilter_1.74.0 survival_3.2-13
[34] phangorn_2.7.1 glue_1.4.2 gtable_0.3.0
[37] zlibbioc_1.38.0 geiger_2.0.7 XVector_0.32.0
[40] DelayedArray_0.18.0 future.apply_1.8.1 maps_3.3.0
[43] abind_1.4-5 scales_1.1.1 mvtnorm_1.1-2
[46] DBI_1.1.1 Rcpp_1.0.7 plotrix_3.8-1
[49] curry_0.1.1 htmlTable_2.2.1 xtable_1.8-4
[52] tmvnsim_1.0-2 tidytree_0.3.4 foreign_0.8-81
[55] bit_4.0.4 subplex_1.6 deSolve_1.28
[58] Formula_1.2-4 htmlwidgets_1.5.3 httr_1.4.2
[61] lavaan_0.6-9 RColorBrewer_1.1-2 ellipsis_0.3.2
[64] pkgconfig_2.0.3 XML_3.99-0.7 nnet_7.3-16
[67] dbplyr_2.1.1 locfit_1.5-9.4 utf8_1.2.2
[70] reshape2_1.4.4 tidyselect_1.1.1 rlang_0.4.11
[73] AnnotationDbi_1.54.1 munsell_0.5.0 cellranger_1.1.0
[76] tools_4.1.0 cachem_1.0.6 cli_3.0.1
[79] generics_0.1.0 RSQLite_2.2.8 broom_0.7.9
[82] fdrtool_1.2.16 fastmap_1.1.0 knitr_1.33
[85] bit64_4.0.5 fs_1.5.0 KEGGREST_1.32.0
[88] glasso_1.11 future_1.22.1 nlme_3.1-152
[91] xml2_1.3.2 doBy_4.6.11 compiler_4.1.0
[94] rstudioapi_0.13 png_0.1-7 reprex_2.0.1
[97] clusterGeneration_1.3.7 geneplotter_1.70.0 pbivnorm_0.6.0
[100] stringi_1.7.4 lattice_0.20-44 Matrix_1.3-4
[103] psych_2.1.6 vctrs_0.3.8 pillar_1.6.2
[106] lifecycle_1.0.1 combinat_0.0-8 data.table_1.14.0
[109] bitops_1.0-7 corpcor_1.6.9 latticeExtra_0.6-29
[112] R6_2.5.1 parallelly_1.27.0 codetools_0.2-18
[115] gtools_3.9.2 MASS_7.3-54 assertthat_0.2.1
[118] withr_2.4.2 phylolm_2.6.2 mnormt_2.0.2
[121] Deriv_4.1.3 GenomeInfoDbData_1.2.6 expm_0.999-6
[124] hms_1.1.0 rpart_4.1-15 quadprog_1.5-8
[127] grid_4.1.0 coda_0.19-4 base64enc_0.1-3
[130] numDeriv_2016.8-1.1 scatterplot3d_0.3-41 lubridate_1.7.10