komalsrathi
commented
3 years ago I updated to the latest R and updated all packages, as well as installed the dev version of signatureSearch (signatureSearch_1.7.3), and it seems to be working:
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6
Matrix products: default
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 methods base
other attached packages:
[1] signatureSearchData_1.6.0 signatureSearch_1.7.3 SummarizedExperiment_1.22.0 Biobase_2.52.0
[5] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 IRanges_2.26.0 S4Vectors_0.30.2
[9] MatrixGenerics_1.4.3 matrixStats_0.61.0 Rcpp_1.0.7 ExperimentHub_2.0.0
[13] AnnotationHub_3.0.2 BiocFileCache_2.0.0 dbplyr_2.1.1 BiocGenerics_0.38.0
loaded via a namespace (and not attached):
[1] shadowtext_0.0.9 fastmatch_1.1-3 plyr_1.8.6
[4] igraph_1.2.8 lazyeval_0.2.2 GSEABase_1.54.0
[7] splines_4.1.2 BiocParallel_1.26.2 usethis_2.1.3
[10] ggplot2_3.3.5 digest_0.6.28 yulab.utils_0.0.4
[13] htmltools_0.5.2 GOSemSim_2.18.1 viridis_0.6.2
[16] GO.db_3.13.0 fansi_0.5.0 magrittr_2.0.1
[19] memoise_2.0.0 limma_3.48.3 tzdb_0.2.0
[22] remotes_2.4.1 readr_2.1.0 Biostrings_2.60.2
[25] annotate_1.70.0 graphlayouts_0.7.1 R.utils_2.11.0
[28] enrichplot_1.12.3 prettyunits_1.1.1 colorspace_2.0-2
[31] blob_1.2.2 rappdirs_0.3.3 ggrepel_0.9.1
[34] dplyr_1.0.7 callr_3.7.0 crayon_1.4.2
[37] RCurl_1.98-1.5 jsonlite_1.7.2 scatterpie_0.1.7
[40] graph_1.70.0 ape_5.5 glue_1.5.0
[43] polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.38.0
[46] XVector_0.32.0 DelayedArray_0.18.0 pkgbuild_1.2.0
[49] Rhdf5lib_1.14.2 HDF5Array_1.20.0 scales_1.1.1
[52] DOSE_3.18.3 DBI_1.1.1 viridisLite_0.4.0
[55] xtable_1.8-4 tidytree_0.3.6 gridGraphics_0.5-1
[58] reactome.db_1.76.0 bit_4.0.4 preprocessCore_1.54.0
[61] htmlwidgets_1.5.4 httr_1.4.2 fgsea_1.18.0
[64] RColorBrewer_1.1-2 ellipsis_0.3.2 R.methodsS3_1.8.1
[67] pkgconfig_2.0.3 XML_3.99-0.8 farver_2.1.0
[70] utf8_1.2.2 ggplotify_0.1.0 tidyselect_1.1.1
[73] rlang_0.4.12 reshape2_1.4.4 later_1.3.0
[76] AnnotationDbi_1.54.1 munsell_0.5.0 BiocVersion_3.13.1
[79] tools_4.1.2 visNetwork_2.1.0 cachem_1.0.6
[82] downloader_0.4 cli_3.1.0 generics_0.1.1
[85] RSQLite_2.2.8 devtools_2.4.2 stringr_1.4.0
[88] fastmap_1.1.0 yaml_2.2.1 ggtree_3.0.4
[91] processx_3.5.2 bit64_4.0.5 fs_1.5.0
[94] tidygraph_1.2.0 purrr_0.3.4 KEGGREST_1.32.0
[97] ggraph_2.0.5 nlme_3.1-153 mime_0.12
[100] R.oo_1.24.0 aplot_0.1.1 DO.db_2.9
[103] compiler_4.1.2 rstudioapi_0.13 filelock_1.0.2
[106] curl_4.3.2 png_0.1-7 interactiveDisplayBase_1.30.0
[109] affyio_1.62.0 testthat_3.1.0 treeio_1.16.2
[112] tibble_3.1.6 tweenr_1.0.2 stringi_1.7.5
[115] ps_1.6.0 desc_1.4.0 lattice_0.20-45
[118] Matrix_1.3-4 vctrs_0.3.8 pillar_1.6.4
[121] lifecycle_1.0.1 rhdf5filters_1.4.0 BiocManager_1.30.16
[124] data.table_1.14.2 cowplot_1.1.1 bitops_1.0-7
[127] patchwork_1.1.1 httpuv_1.6.3 qvalue_2.24.0
[130] affy_1.70.0 R6_2.5.1 promises_1.2.0.1
[133] gridExtra_2.3 sessioninfo_1.2.1 MASS_7.3-54
[136] assertthat_0.2.1 pkgload_1.2.3 rhdf5_2.36.0
[139] rprojroot_2.0.2 withr_2.4.2 GenomeInfoDbData_1.2.6
[142] hms_1.1.1 clusterProfiler_4.0.5 ggfun_0.0.4
[145] grid_4.1.2 tidyr_1.1.4 ggforce_0.3.3
[148] shiny_1.7.1
Hi,
I have been using the package since quite some time but I just updated my OS to BigSur and looks like a bunch of things broke.
Here is my example code:
SessionInfo:
Please let me know how can I fix this error. I have tried to uninstall and reinstall both ExperimentHub and AnnotationHub several times now.