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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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R version 4.0.2 and Bioconductor version 3.11 : dependencies 'europepmc' is not available. #629

Open nilanjana1996 opened 1 year ago

nilanjana1996 commented 1 year ago

BiocManager::install("clusterProfiler", INSTALL_opts = '--no-lock') The downloaded source packages are in 'C:\Users\nilanjan\AppData\Local\Temp\Rtmpq6tIDR\downloaded_packages' There were 50 or more warnings (use warnings() to see the first 50)

library(clusterProfiler) Error: package or namespace load failed for 'clusterProfiler' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'europepmc'

sessionInfo()

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=Finnish_Finland.1252 LC_CTYPE=Finnish_Finland.1252 [3] LC_MONETARY=Finnish_Finland.1252 LC_NUMERIC=C [5] LC_TIME=Finnish_Finland.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] readxl_1.3.1 biomaRt_2.44.4 loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.58.0 [3] bit64_4.0.5 RColorBrewer_1.1-2 [5] progress_1.2.2 httr_1.4.2 [7] GenomeInfoDb_1.24.2 tools_4.0.2 [9] utf8_1.1.4 R6_2.5.0 [11] DBI_1.1.1 BiocGenerics_0.34.0 [13] colorspace_2.0-0 withr_2.4.1 [15] tidyselect_1.1.0 gridExtra_2.3 [17] prettyunits_1.1.1 bit_4.0.4 [19] curl_4.3 compiler_4.0.2 [21] cli_2.3.1 Biobase_2.48.0 [23] xml2_1.3.2 DelayedArray_0.14.1 [25] rtracklayer_1.48.0 scales_1.1.1 [27] askpass_1.1 rappdirs_0.3.3 [29] stringr_1.4.0 digest_0.6.27 [31] Rsamtools_2.4.0 DOSE_3.14.0 [33] XVector_0.28.0 pkgconfig_2.0.3 [35] dbplyr_2.1.1 fastmap_1.1.0 [37] rlang_0.4.10 rstudioapi_0.13 [39] RSQLite_2.2.4 farver_2.1.0 [41] generics_0.1.0 BiocParallel_1.22.0 [43] GOSemSim_2.14.2 dplyr_1.0.5 [45] RCurl_1.98-1.2 magrittr_2.0.1 [47] GO.db_3.11.4 GenomeInfoDbData_1.2.3 [49] Matrix_1.4-1 Rcpp_1.0.6 [51] munsell_0.5.0 S4Vectors_0.26.1 [53] fansi_0.4.2 viridis_0.5.1 [55] lifecycle_1.0.0 stringi_1.5.3 [57] ggraph_2.0.5 MASS_7.3-51.6 [59] SummarizedExperiment_1.18.2 zlibbioc_1.34.0 [61] plyr_1.8.6 qvalue_2.20.0 [63] BiocFileCache_1.12.1 grid_4.0.2 [65] blob_1.2.1 ggrepel_0.9.1 [67] parallel_4.0.2 DO.db_2.9 [69] crayon_1.4.1 lattice_0.20-41 [71] cowplot_1.1.1 graphlayouts_0.8.0 [73] Biostrings_2.56.0 splines_4.0.2 [75] GenomicFeatures_1.40.1 hms_1.0.0 [77] pillar_1.5.1 igraph_1.3.0 [79] fgsea_1.14.0 GenomicRanges_1.40.0 [81] reshape2_1.4.4 stats4_4.0.2 [83] fastmatch_1.1-3 XML_3.99-0.5 [85] glue_1.4.2 downloader_0.4 [87] data.table_1.14.0 BiocManager_1.30.10 [89] tweenr_1.0.2 vctrs_0.3.6 [91] cellranger_1.1.0 polyclip_1.10-0 [93] tidyr_1.1.3 gtable_0.3.0 [95] openssl_1.4.3 purrr_0.3.4 [97] assertthat_0.2.1 cachem_1.0.4 [99] ggplot2_3.3.3 ggforce_0.3.3 [101] tidygraph_1.2.1 viridisLite_0.3.0 [103] tibble_3.1.0 GenomicAlignments_1.24.0 [105] AnnotationDbi_1.50.3 memoise_2.0.0 [107] IRanges_2.22.2 ellipsis_0.3.1 --   | >

guidohooiveld commented 11 months ago

Please use the latest version of R (=R-4.3.1) and Bioconductor (=3.17)! Development of packages goes on continuously, and you are using a very old version of R (and corresponding Bioconductor packages); these are more than 3 years old!

If you insist using this old version of R, you may want to install the package europepmc first (thus before installing clusterProfiler), but again, it is very much recommended to update! [For example, I know that the API of the KEGG website has changed several times after June 2020, so this will never work in R-4.0.2!]