| title | date | output | ||||
|---|---|---|---|---|---|---|
envInfo.Rmd |
6/14/2021 |
|
# Gathering and loading all used packages
lf <- list.files(pattern="\\.Rmd$", recursive = TRUE, full.names = TRUE)
lf <- lf[!grepl("envInfo",lf)]
packages <- unique(unlist(lapply(lf, FUN=function(x){
trimws(grep("library",readLines(x),value=TRUE))
})))## Warning in readLines(x): incomplete final line found on './Figures/Supplement/
## Suppl_6/Suppl_6.Rmd'
packages <- gsub(")","",gsub("library(","",packages,fixed=TRUE),fixed=TRUE)
suppressPackageStartupMessages({
for(f in packages){
library(f, character.only=TRUE)
}
})## reset: creating "thermo" object
## OBIGT: loading default database with 1903 aqueous, 3443 total species
sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## 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
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] CHNOSZ_1.4.1
## [2] openxlsx_4.2.4
## [3] BSgenome.Hsapiens.UCSC.hg38_1.4.3
## [4] motifStack_1.34.0
## [5] ComplexHeatmap_2.6.2
## [6] TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6
## [7] org.Hs.eg.db_3.12.0
## [8] fst_0.9.4
## [9] readxl_1.3.1
## [10] AnnotationHub_2.22.0
## [11] BiocFileCache_1.14.0
## [12] dbplyr_2.1.0
## [13] scanMiRApp_0.99.22
## [14] gtable_0.3.0
## [15] gridExtra_2.3
## [16] ggpmisc_0.3.9
## [17] scales_1.1.1
## [18] data.table_1.14.0
## [19] ensembldb_2.14.0
## [20] AnnotationFilter_1.14.0
## [21] GenomicFeatures_1.42.2
## [22] AnnotationDbi_1.52.0
## [23] viridis_0.5.1
## [24] viridisLite_0.4.0
## [25] ggpointdensity_0.1.0
## [26] cowplot_1.1.1
## [27] ggrepel_0.9.1
## [28] Matrix_1.3-4
## [29] BSgenome.Mmusculus.UCSC.mm10_1.4.0
## [30] scanMiR_0.99.26
## [31] BiocParallel_1.24.1
## [32] BSgenome.Hsapiens.UCSC.hg19_1.4.3
## [33] BSgenome_1.58.0
## [34] Biostrings_2.58.0
## [35] XVector_0.30.0
## [36] rtracklayer_1.50.0
## [37] ggsci_2.9
## [38] scanMiRData_0.99.2
## [39] edgeR_3.32.1
## [40] limma_3.46.0
## [41] SummarizedExperiment_1.20.0
## [42] Biobase_2.50.0
## [43] GenomicRanges_1.42.0
## [44] GenomeInfoDb_1.26.7
## [45] IRanges_2.24.1
## [46] S4Vectors_0.28.1
## [47] BiocGenerics_0.36.1
## [48] MatrixGenerics_1.2.1
## [49] matrixStats_0.60.0
## [50] forcats_0.5.1
## [51] stringr_1.4.0
## [52] dplyr_1.0.5
## [53] purrr_0.3.4
## [54] readr_1.4.0
## [55] tidyr_1.1.3
## [56] tibble_3.1.0
## [57] ggplot2_3.3.4
## [58] tidyverse_1.3.0
##
## loaded via a namespace (and not attached):
## [1] circlize_0.4.13 backports_1.2.1
## [3] lazyeval_0.2.2 shinydashboard_0.7.1
## [5] digest_0.6.27 htmltools_0.5.1.1
## [7] fansi_0.5.0 magrittr_2.0.1
## [9] memoise_2.0.0 cluster_2.1.2
## [11] modelr_0.1.8 askpass_1.1
## [13] prettyunits_1.1.1 colorspace_2.0-2
## [15] blob_1.2.2 rvest_1.0.0
## [17] rappdirs_0.3.3 haven_2.3.1
## [19] xfun_0.24 crayon_1.4.1
## [21] RCurl_1.98-1.3 jsonlite_1.7.2
## [23] glue_1.4.2 zlibbioc_1.36.0
## [25] GetoptLong_1.0.5 DelayedArray_0.16.3
## [27] shape_1.4.6 DBI_1.1.1
## [29] Rcpp_1.0.7 xtable_1.8-4
## [31] progress_1.2.2 clue_0.3-59
## [33] bit_4.0.4 DT_0.18
## [35] htmlwidgets_1.5.3 httr_1.4.2
## [37] RColorBrewer_1.1-2 ellipsis_0.3.2
## [39] pkgconfig_2.0.3 XML_3.99-0.6
## [41] sass_0.4.0 ggseqlogo_0.1
## [43] locfit_1.5-9.4 utf8_1.2.2
## [45] tidyselect_1.1.0 rlang_0.4.11
## [47] later_1.2.0 munsell_0.5.0
## [49] BiocVersion_3.12.0 cellranger_1.1.0
## [51] tools_4.0.3 cachem_1.0.5
## [53] cli_3.0.1 generics_0.1.0
## [55] RSQLite_2.2.4 ade4_1.7-17
## [57] rintrojs_0.3.0 broom_0.7.5
## [59] evaluate_0.14 fastmap_1.1.0
## [61] yaml_2.2.1 knitr_1.31
## [63] bit64_4.0.5 fs_1.5.0
## [65] shinycssloaders_1.0.0 zip_2.2.0
## [67] mime_0.11 xml2_1.3.2
## [69] biomaRt_2.46.3 compiler_4.0.3
## [71] rstudioapi_0.13 png_0.1-7
## [73] plotly_4.9.3 interactiveDisplayBase_1.28.0
## [75] curl_4.3.2 waiter_0.2.3
## [77] reprex_1.0.0 bslib_0.2.5.1
## [79] stringi_1.7.3 lattice_0.20-44
## [81] ProtGenerics_1.22.0 vctrs_0.3.8
## [83] pillar_1.5.1 lifecycle_1.0.0
## [85] BiocManager_1.30.16 GlobalOptions_0.1.2
## [87] jquerylib_0.1.4 bitops_1.0-7
## [89] httpuv_1.5.5 R6_2.5.0
## [91] promises_1.2.0.1 MASS_7.3-54
## [93] assertthat_0.2.1 rjson_0.2.20
## [95] openssl_1.4.4 withr_2.4.2
## [97] GenomicAlignments_1.26.0 Rsamtools_2.6.0
## [99] GenomeInfoDbData_1.2.4 hms_1.1.0
## [101] rmarkdown_2.7 Cairo_1.5-12.2
## [103] shiny_1.6.0 lubridate_1.7.10