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USCbiostats / Methylation-variability

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Problems with running this #1

Closed pmarjora closed 3 years ago

pmarjora commented 3 years ago

Hi Emil, I am trying to run this but I am getting an error in target island150_gsea_upper_right copied below. Does this mean anything to you? Any ideas how to fix it? Thanks.

make(the_plan) ▶ target bulk_normal_genes Annotating... ▶ target bulk_tumor_genes Annotating... ▶ target tumor_list_b_metrics ▶ target normal_list_b_metrics ▶ target bulk_tumor_islands Annotating... ▶ target bulk_normal_promoters Annotating... ▶ target enhancers_annotations Building enhancers... ▶ target normal_list_a [dyeCorrection] Applying R/G ratio flip to fix dye bias ▶ target bulk_tumor_promoters Annotating... ▶ target bulk_normal_islands Annotating... ▶ target tumor_list_a [dyeCorrection] Applying R/G ratio flip to fix dye bias ▶ target tumor_roll_1000 'select()' returned 1:1 mapping between keys and columns Building cds... summarise() regrouping output by 'symbol' (override with .groups argument) Annotating... ▶ target bulk_normal_genes_metrics ▶ target bulk_tumor_genes_metrics ▶ target list_b ▶ target tumor_island150 New names:

  • seqnames -> seqnames...1
  • seqnames -> seqnames...48 ▶ target bulk_tumor_islands_metrics ▶ target bulk_normal_promoters_metrics ▶ target bulk_tumor_enhancers Annotating... ▶ target bulk_normal_enhancers Annotating... ▶ target normal_list_a_metrics ▶ target bulk_tumor_promoters_metrics ▶ target normal_island150 New names:
  • seqnames -> seqnames...1
  • seqnames -> seqnames...23 ▶ target bulk_normal_islands_metrics ▶ target tumor_list_a_metrics ▶ target bulk_genes ▶ target bulk_tumor_enhancers_metrics ▶ target bulk_normal_enhancers_metrics ▶ target bulk_promoters ▶ target combined_island150 Annotating... ▶ target bulk_islands ▶ target list_a ▶ target bulk_enhancers ▶ target island150_gsea_upper_right x fail island150_gsea_upper_right Error: target island150_gsea_upper_right failed. diagnose(island150_gsea_upper_right)$error$message: cannot add bindings to a locked environment. Please read the "Self-invalidation" section of the make() help file. diagnose(island150_gsea_upper_right)$error$calls: base::eval(quote(calc_island150_gsea(combined_island150, desc(tumor_variability normal_variability), island150_min_obs, island150_n_genes, genes_annotations, island_annotations)), new.env()) global::calc_island150_gsea(combined_island150, desc(tumor_variability normal_variability), island150_min_obs, island150_n_genes, genes_annotations, island_annotations) data %>% dplyr::filter(n_obs >= island150_min_obs) %>% arrange({ { order } }) %>% dplyr::slice(seq_len(island150_n_genes)) %>% annotate_nearest_gene_to_island(genes_annotations, island_annotations) %>% pull(gene_id) %>% enrichPathway() ReactomePA::enrichPathway(.) ReactomePA:::get_Reactome_DATA(organism) Reactome In addition: There were 50 or more warnings (use warnings() to see the first 50)
EmilHvitfeldt commented 3 years ago

Hmm, I'm not seeing this issue.

Can you paste what you get if you run:

sessionInfo()

Next, does the error persists if you run the drake plan with drake::r_make()?

pmarjora commented 3 years ago

Here's what I get when I enter sessionInfo():

R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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 datasets utils methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[2] GenomicFeatures_1.42.1
[3] org.Hs.eg.db_3.12.0
[4] AnnotationDbi_1.52.0
[5] ReactomePA_1.34.0
[6] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 [7] IlluminaHumanMethylationEPICmanifest_0.3.0
[8] minfi_1.36.0
[9] bumphunter_1.32.0
[10] locfit_1.5-9.4
[11] iterators_1.0.13
[12] foreach_1.5.1
[13] Biostrings_2.58.0
[14] XVector_0.30.0
[15] SummarizedExperiment_1.20.0
[16] Biobase_2.50.0
[17] MatrixGenerics_1.2.0
[18] matrixStats_0.57.0
[19] GenomicRanges_1.42.0
[20] GenomeInfoDb_1.26.2
[21] IRanges_2.24.1
[22] S4Vectors_0.28.1
[23] BiocGenerics_0.36.0
[24] annotatr_1.16.0
[25] bedslider_0.0.0.9000
[26] slider_0.1.5
[27] knitr_1.30
[28] recipes_0.1.15
[29] purrr_0.3.4
[30] tidyr_1.1.2
[31] stringr_1.4.0
[32] readr_1.4.0
[33] glue_1.4.2
[34] ggplot2_3.3.3
[35] tibble_3.0.4
[36] dplyr_1.0.2
[37] fs_1.5.0
[38] drake_7.13.0
[39] dotenv_1.0.2
[40] conflicted_1.0.4

loaded via a namespace (and not attached): [1] tidyselect_1.1.0 RSQLite_2.2.1 grid_4.0.3
[4] BiocParallel_1.24.1 scatterpie_0.1.5 munsell_0.5.0
[7] base64url_1.4 codetools_0.2-18 preprocessCore_1.52.0
[10] withr_2.3.0 colorspace_2.0-0 GOSemSim_2.16.1
[13] filelock_1.0.2 rstudioapi_0.13 DOSE_3.16.0
[16] GenomeInfoDbData_1.2.4 polyclip_1.10-0 farver_2.0.3
[19] bit64_4.0.5 rhdf5_2.34.0 txtq_0.2.3
[22] vctrs_0.3.6 generics_0.1.0 ipred_0.9-9
[25] xfun_0.19 BiocFileCache_1.14.0 regioneR_1.22.0
[28] R6_2.5.0 graphlayouts_0.7.1 illuminaio_0.32.0
[31] fgsea_1.16.0 bitops_1.0-6 rhdf5filters_1.2.0
[34] reshape_0.8.8 DelayedArray_0.16.0 assertthat_0.2.1
[37] promises_1.1.1 scales_1.1.1 ggraph_2.0.4
[40] enrichplot_1.10.1 nnet_7.3-14 gtable_0.3.0
[43] tidygraph_1.2.0 timeDate_3043.102 rlang_0.4.10
[46] genefilter_1.72.0 splines_4.0.3 rtracklayer_1.50.0
[49] GEOquery_2.58.0 checkmate_2.0.0 BiocManager_1.30.10
[52] yaml_2.2.1 reshape2_1.4.4 backports_1.2.1
[55] httpuv_1.5.4 qvalue_2.22.0 tools_4.0.3
[58] lava_1.6.8.1 nor1mix_1.3-0 ellipsis_0.3.1
[61] RColorBrewer_1.1-2 siggenes_1.64.0 Rcpp_1.0.5
[64] plyr_1.8.6 sparseMatrixStats_1.2.0 progress_1.2.2
[67] zlibbioc_1.36.0 RCurl_1.98-1.2 prettyunits_1.1.1
[70] rpart_4.1-15 openssl_1.4.3 viridis_0.5.1
[73] cowplot_1.1.1 ggrepel_0.9.0 magrittr_2.0.1
[76] data.table_1.13.6 DO.db_2.9 warp_0.2.0
[79] reactome.db_1.74.0 storr_1.2.5 hms_0.5.3
[82] mime_0.9 evaluate_0.14 xtable_1.8-4
[85] XML_3.99-0.5 mclust_5.4.7 gridExtra_2.3
[88] compiler_4.0.3 biomaRt_2.46.0 shadowtext_0.0.7
[91] crayon_1.3.4 htmltools_0.5.0 later_1.1.0.1
[94] lubridate_1.7.9.2 DBI_1.1.0 tweenr_1.0.1
[97] dbplyr_2.0.0 MASS_7.3-53 rappdirs_0.3.1
[100] Matrix_1.2-18 cli_2.2.0 quadprog_1.5-8
[103] gower_0.2.2 igraph_1.2.6 pkgconfig_2.0.3
[106] rvcheck_0.1.8 GenomicAlignments_1.26.0 xml2_1.3.2
[109] annotate_1.68.0 rngtools_1.5 multtest_2.46.0
[112] beanplot_1.2 prodlim_2019.11.13 doRNG_1.8.2
[115] scrime_1.3.5 digest_0.6.27 graph_1.68.0
[118] fastmatch_1.1-0 rmarkdown_2.6 base64_2.0
[121] DelayedMatrixStats_1.12.1 curl_4.3 graphite_1.36.0
[124] shiny_1.5.0 Rsamtools_2.6.0 lifecycle_0.2.0
[127] nlme_3.1-150 Rhdf5lib_1.12.0 viridisLite_0.3.0
[130] askpass_1.1 limma_3.46.0 BSgenome_1.58.0
[133] fansi_0.4.1 pillar_1.4.7 lattice_0.20-41
[136] fastmap_1.0.1 httr_1.4.2 survival_3.2-7
[139] GO.db_3.12.1 interactiveDisplayBase_1.28.0 BiocVersion_3.12.0
[142] bit_4.0.4 ggforce_0.3.2 class_7.3-17
[145] stringi_1.5.3 HDF5Array_1.18.0 blob_1.2.1
[148] AnnotationHub_2.22.0 memoise_1.1.0 renv_0.12.3

pmarjora commented 3 years ago

When I open the project in Rstudio I get the following messages. Is there an easy way to update all my packages?

Project '/Volumes/GoogleDrive/My Drive/2021/R21/Methylation-variability' loaded. [renv 0.12.3] Warning message: renv 0.12.3 was loaded from project library, but renv 0.11.0 is recorded in lockfile. Use renv::record("renv@0.12.3") to record this version in the lockfile. Use renv::restore(packages = "renv") to install renv 0.11.0 into the project library. The following folder(s) appear to be left-over temporary directories:

file5f816283c04e, file5f8171a6625c

Consider removing these folders from your library.

Consider removing these folders from your library.

The following package(s) are installed but not recorded in the lockfile: _ cowplot [1.1.1] shadowtext [0.0.7] enrichplot [1.10.1] viridis [0.5.1] RcppArmadillo [0.10.1.2.0] sparseMatrixStats [1.2.0] MatrixGenerics [1.2.0] RcppEigen [0.3.3.9.1] ggforce [0.3.2] checkmate [2.0.0] DOSE [3.16.0] tweenr [1.0.1] polyclip [1.10-0] graph [1.68.0] rhdf5filters [1.2.0] qvalue [2.22.0] reactome.db [1.74.0] graphite [1.36.0] scatterpie [0.1.5] GOSemSim [2.16.1] ggrepel [0.9.0] fastmatch [1.1-0] TxDb.Hsapiens.UCSC.hg19.knownGene [3.2.2] diffobj [0.3.2] gridExtra [2.3] ggraph [2.0.4] rvcheck [0.1.8] org.Hs.eg.db [3.12.0] brio [1.1.0] rematch2 [2.1.2] graphlayouts [0.7.1] tidygraph [1.2.0] cpp11 [0.2.4] fgsea [1.16.0] ReactomePA [1.34.0] waldo [0.2.3] GO.db [3.12.1] DO.db [2.9]

Use renv::snapshot() to add these packages to your lockfile.

The following package(s) are out of sync:

            Package   Lockfile Version   Library Version
      AnnotationDbi             1.50.1            1.52.0
      AnnotationHub             2.20.0            2.22.0
           BSgenome             1.56.0            1.58.0
            Biobase             2.48.0            2.50.0
      BiocFileCache             1.12.0            1.14.0
       BiocGenerics             0.34.0            0.36.0
       BiocParallel             1.22.0            1.24.1
        BiocVersion             3.11.1            3.12.0
         Biostrings             2.56.0            2.58.0
                 DT               0.14              0.16
       DelayedArray             0.14.0            0.16.0
 DelayedMatrixStats             1.10.1            1.12.1
           GEOquery             2.56.0            2.58.0
       GenomeInfoDb             1.24.2            1.26.2
   GenomeInfoDbData              1.2.3             1.2.4
  GenomicAlignments             1.24.0            1.26.0
    GenomicFeatures             1.40.1            1.42.1
      GenomicRanges             1.40.0            1.42.0
          HDF5Array             1.16.1            1.18.0
            IRanges             2.22.2            2.24.1
         KernSmooth            2.23-17           2.23-18
               MASS           7.3-51.6            7.3-53
                 R6              2.4.1             2.5.0
            RSQLite              2.2.0             2.2.1
           Rhdf5lib             1.10.0            1.12.0
            Rhtslib             1.20.0            1.22.0
          Rsamtools              2.4.0             2.6.0
          S4Vectors             0.26.1            0.28.1
            SQUAREM             2020.3            2020.5

SummarizedExperiment 1.18.1 1.20.0 XML 3.99-0.4 3.99-0.5 XVector 0.28.0 0.30.0 annotate 1.66.0 1.68.0 annotatr 1.14.0 1.16.0 backports 1.1.8 1.2.1 bedslider 0.0.0.9000 0.0.0.9000 biomaRt 2.44.1 2.46.0 bit 1.1-15.2 4.0.4 bit64 0.9-7 4.0.5 bumphunter 1.30.0 1.32.0 callr 3.4.3 3.5.1 cli 2.0.2 2.2.0 clipr 0.7.0 0.7.1 codetools 0.2-16 0.2-18 colorspace 1.4-1 2.0-0 data.table 1.12.8 1.13.6 dbplyr 1.4.4 2.0.0 digest 0.6.25 0.6.27 dplyr 1.0.0 1.0.2 drake 7.12.4 7.13.0 foreach 1.5.0 1.5.1 fs 1.4.2 1.5.0 genefilter 1.70.0 1.72.0 generics 0.0.2 0.1.0 ggplot2 3.3.2 3.3.3 glue 1.4.1 1.4.2 htmlwidgets 1.5.1 1.5.3 httr 1.4.1 1.4.2 igraph 1.2.5 1.2.6 illuminaio 0.30.0 0.32.0 interactiveDisplayBase 1.26.3 1.28.0 isoband 0.2.2 0.2.3 iterators 1.0.12 1.0.13 jsonlite 1.7.0 1.7.2 knitr 1.29 1.30 labeling 0.3 0.4.2 lava 1.6.7 1.6.8.1 lifecycle 0.2.0.9000 0.2.0 limma 3.44.3 3.46.0 lubridate 1.7.9 1.7.9.2 magrittr 1.5 2.0.1 matrixStats 0.56.0 0.57.0 mclust 5.4.6 5.4.7 mgcv 1.8-31 1.8-33 minfi 1.34.0 1.36.0 multtest 2.44.0 2.46.0 nlme 3.1-148 3.1-150 openssl 1.4.2 1.4.3 pillar 1.4.4 1.4.7 pkgbuild 1.0.8 1.2.0 preprocessCore 1.50.0 1.52.0 processx 3.4.3 3.4.5 ps 1.3.3 1.5.0 readr 1.3.1 1.4.0 recipes 0.1.13 0.1.15 regioneR 1.20.1 1.22.0 renv 0.11.0 0.12.3 rhdf5 2.32.2 2.34.0 rlang 0.4.6 0.4.10 rmarkdown 2.3 2.6 rprojroot 1.3-2 2.0.2 rstudioapi 0.11 0.13 rtracklayer 1.48.0 1.50.0 siggenes 1.62.0 1.64.0 slider 0.1.4 0.1.5 storr 1.2.1 1.2.5 stringi 1.4.6 1.5.3 survival 3.2-3 3.2-7 sys 3.3 3.4 testthat 2.3.2 3.0.1 tibble 3.0.2 3.0.4 tidyr 1.1.0 1.1.2 tinytex 0.24 0.28 vctrs 0.3.1 0.3.6 warp 0.1.0 0.2.0 withr 2.2.0 2.3.0 xfun 0.15 0.19 zlibbioc 1.34.0 1.36.0

Use renv::snapshot() to save the state of your library to the lockfile. Use renv::restore() to restore your library from the lockfile.

pmarjora commented 3 years ago

And here's what /I get when i use drake::r_make():

drake::r_make() Warning message: renv 0.12.3 was loaded from project library, but renv 0.11.0 is recorded in lockfile. Use renv::record("renv@0.12.3") to record this version in the lockfile. Use renv::restore(packages = "renv") to install renv 0.11.0 into the project library. [conflicted] Will prefer dplyr::select over any other package ▶ target normalized_genes ▶ target normalized_islands ▶ target island150_gsea_upper_right ▶ target island150_gsea_upper_left ▶ target island150_gsea_lower_right ▶ target island150_gsea_lower_left ▶ target normalized_list_b ▶ target normalized_enhancers ▶ target normalized_promoters ▶ target normalized_list_a ▶ target bulk_genes_variability ▶ target bulk_islands_variability ▶ target island150_gsea_report /

processing file: island150_gsea_analysis.Rmd |... | 4% inline R code fragments

|...... | 8% label: setup (with options) List of 1 logi FALSE

|........ | 12% ordinary text without R code

|........... | 16% label: unnamed-chunk-1 (with options) List of 1 logi FALSE

|.............. | 20% inline R code fragments

|................. | 24% label: unnamed-chunk-2 |.................... | 28% ordinary text without R code

|...................... | 32% label: unnamed-chunk-3 |......................... | 36% label: unnamed-chunk-4 Quitting from lines 34-35 (island150_gsea_analysis.Rmd) \ x fail island150_gsea_report Error : target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, envir = envir, run_pandoc = run_pandoc, quiet = quiet) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) knitr:::process_file(text, output) base::withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) knitr:::process_group(group) knitr:::process_group.block(group) knitr:::call_block(x) knitr:::block_exec(params) knitr:::in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))) knitr:::evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), tions$error && e = !isFALSE(options$message), stop_on_error = if (op options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) evaluate::evaluate(...) evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) evaluate:::timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) base:::handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) base::withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) base::withVisible(eval(expr, envir, enclos)) base::eval(expr, envir, enclos) base::eval(expr, envir, enclos) enrichplot::emapplot(island150_gsea_upper_right) enrichplot::emapplot(island150_gsea_upper_right) enrichplot:::emapplot.enrichResult(x, showCategory = showCategory, color = color, layout = layout, ...) enrichplot:::has_pairsim(x) base::stop(error_message) Error: callr subprocess failed: target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, [...] Type .Last.error.trace to see where the error occured

.Last.error.trace

Stack trace:

Process 55266:

  1. drake::r_make()
  2. drake:::r_drake(source, drake::make_impl, list(), r_fn, r_args)
  3. base:::do.call(r_fn, r_args)
  4. (function (func, args = list(), libpath = .libPaths(), repos = default_repos(), ...
  5. callr:::get_result(output = out, options)

  6. throw(newerr, parent = remerr[[2]])

    x callr subprocess failed: target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, envir = envir, run_pandoc = run_pandoc, quiet = quiet) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) knitr:::process_file(text, output) base::withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) knitr:::process_group(group) knitr:::process_group.block(group) knitr:::call_block(x) knitr:::block_exec(params) knitr:::in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))) knitr:::evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) evaluate::evaluate(...) evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) evaluate:::timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) base:::handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) base::withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) base::withVisible(eval(expr, envir, enclos)) base::eval(expr, envir, enclos) base::eval(expr, envir, enclos) enrichplot::emapplot(island150_gsea_upper_right) enrichplot::emapplot(island150_gsea_upper_right) enrichplot:::emapplot.enrichResult(x, showCategory = showCategory, color = color, layout = layout, ...) enrichplot:::has_pairsim(x) base::stop(error_message)

    Process 55370:

  7. (function (source, d_fn, d_args) ...
  8. BiocGenerics:::do.call(d_fn, d_args)
  9. base:::do.call(d_fn, d_args)
  10. (function (config) ...
  11. drake:::process_targets(config)
  12. drake:::run_backend(config)
  13. drake:::drake_backend(config)
  14. drake:::drake_backend_loop(config)
  15. drake:::loop_check(config)
  16. drake:::local_build(target = targets[1], config = config, downstream = targets[-1])
  17. drake:::conclude_build(build, config)
  18. drake:::conclude_build_impl(value, target, meta, config)
  19. drake:::conclude_build_impl.default(value, target, meta, config)
  20. drake:::handle_build_exceptions(target = target, meta = meta, ...
  21. drake:::handle_build_error(target, meta, config)
  22. drake:::log_failure(target, meta, config)
  23. drake:::stop0(msg)
  24. base:::stop(..., call. = FALSE)
  25. base:::.handleSimpleError(function (e) ...

  26. h(simpleError(msg, call))

    x target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, envir = envir, run_pandoc = run_pandoc, quiet = quiet) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) knitr:::process_file(text, output) base::withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) knitr:::process_group(group) knitr:::process_group.block(group) knitr:::call_block(x) knitr:::block_exec(params) knitr:::in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))) knitr:::evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) evaluate::evaluate(...) evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) evaluate:::timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) base:::handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) base::withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) base::withVisible(eval(expr, envir, enclos)) base::eval(expr, envir, enclos) base::eval(expr, envir, enclos) enrichplot::emapplot(island150_gsea_upper_right) enrichplot::emapplot(island150_gsea_upper_right) enrichplot:::emapplot.enrichResult(x, showCategory = showCategory, color = color, layout = layout, ...) enrichplot:::has_pairsim(x) base::stop(error_message)

pmarjora commented 3 years ago

I have now updated all my packages and retried. Here's what I get (I think it;'s just the same error as before I updated):

drake::r_make() Warning message: renv 0.12.5 was loaded from project library, but renv 0.11.0 is recorded in lockfile. Use renv::record("renv@0.12.5") to record this version in the lockfile. Use renv::restore(packages = "renv") to install renv 0.11.0 into the project library. [conflicted] Will prefer dplyr::select over any other package ▶ target bulk_promoters_variability ▶ target list_b_variability ▶ target island150_gsea_report \

processing file: island150_gsea_analysis.Rmd |... | 4% inline R code fragments

|...... | 8% label: setup (with options) List of 1 logi FALSE

|........ | 12% ordinary text without R code

|........... | 16% label: unnamed-chunk-1 (with options) List of 1 logi FALSE

|.............. | 20% inline R code fragments

|................. | 24% label: unnamed-chunk-2 |.................... | 28% ordinary text without R code

|...................... | 32% label: unnamed-chunk-3 |......................... | 36% label: unnamed-chunk-4 Quitting from lines 34-35 (island150_gsea_analysis.Rmd) \ x fail island150_gsea_report Error : target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, envir = envir, run_pandoc = run_pandoc, quiet = quiet) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) knitr:::process_file(text, output) base::withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) knitr:::process_group(group) knitr:::process_group.block(group) knitr:::call_block(x) knitr:::block_exec(params) knitr:::in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))) knitr:::evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), tions$error && e = !isFALSE(options$message), stop_on_error = if (op options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) evaluate::evaluate(...) evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) evaluate:::timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) base:::handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) base::withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) base::withVisible(eval(expr, envir, enclos)) base::eval(expr, envir, enclos) base::eval(expr, envir, enclos) enrichplot::emapplot(island150_gsea_upper_right) enrichplot::emapplot(island150_gsea_upper_right) enrichplot:::emapplot.enrichResult(x, showCategory = showCategory, color = color, layout = layout, ...) enrichplot:::has_pairsim(x) base::stop(error_message) Error: callr subprocess failed: target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, [...] Type .Last.error.trace to see where the error occured

.Last.error.trace

Stack trace:

Process 56492:

  1. drake::r_make()
  2. drake:::r_drake(source, drake::make_impl, list(), r_fn, r_args)
  3. base:::do.call(r_fn, r_args)
  4. (function (func, args = list(), libpath = .libPaths(), repos = default_repos(), ...
  5. callr:::get_result(output = out, options)

  6. throw(newerr, parent = remerr[[2]])

    x callr subprocess failed: target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, envir = envir, run_pandoc = run_pandoc, quiet = quiet) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) knitr:::process_file(text, output) base::withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) knitr:::process_group(group) knitr:::process_group.block(group) knitr:::call_block(x) knitr:::block_exec(params) knitr:::in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))) knitr:::evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) evaluate::evaluate(...) evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) evaluate:::timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) base:::handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) base::withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) base::withVisible(eval(expr, envir, enclos)) base::eval(expr, envir, enclos) base::eval(expr, envir, enclos) enrichplot::emapplot(island150_gsea_upper_right) enrichplot::emapplot(island150_gsea_upper_right) enrichplot:::emapplot.enrichResult(x, showCategory = showCategory, color = color, layout = layout, ...) enrichplot:::has_pairsim(x) base::stop(error_message)

    Process 56531:

  7. (function (source, d_fn, d_args) ...
  8. BiocGenerics:::do.call(d_fn, d_args)
  9. base:::do.call(d_fn, d_args)
  10. (function (config) ...
  11. drake:::process_targets(config)
  12. drake:::run_backend(config)
  13. drake:::drake_backend(config)
  14. drake:::drake_backend_loop(config)
  15. drake:::loop_check(config)
  16. drake:::local_build(target = targets[1], config = config, downstream = targets[-1])
  17. drake:::conclude_build(build, config)
  18. drake:::conclude_build_impl(value, target, meta, config)
  19. drake:::conclude_build_impl.default(value, target, meta, config)
  20. drake:::handle_build_exceptions(target = target, meta = meta, ...
  21. drake:::handle_build_error(target, meta, config)
  22. drake:::log_failure(target, meta, config)
  23. drake:::stop0(msg)
  24. base:::stop(..., call. = FALSE)
  25. base:::.handleSimpleError(function (e) ...

  26. h(simpleError(msg, call))

    x target island150_gsea_report failed. diagnose(island150_gsea_report)$error$message: Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis. diagnose(island150_gsea_report)$error$calls: base::eval(quote({ rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") file_out("doc/island150_gsea_analysis.html") file_out("doc/island150_gsea_analysis.pdf") }), new.env()) rmarkdown::render(knitr_in("doc/island150_gsea_analysis.Rmd"), output_format = "all") rmarkdown::render(input = input, output_format = output_format[i], output_file = output_file[i], output_dir = output_dir, output_options = output_options, intermediates_dir = intermediates_dir, knit_root_dir = knit_root_dir, runtime = runtime, clean = clean, params = params, knit_meta = knit_meta, envir = envir, run_pandoc = run_pandoc, quiet = quiet) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) knitr:::process_file(text, output) base::withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) knitr:::process_group(group) knitr:::process_group.block(group) knitr:::call_block(x) knitr:::block_exec(params) knitr:::in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))) knitr:::evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) evaluate::evaluate(...) evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) evaluate:::timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) base:::handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) base::withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) base::withVisible(eval(expr, envir, enclos)) base::eval(expr, envir, enclos) base::eval(expr, envir, enclos) enrichplot::emapplot(island150_gsea_upper_right) enrichplot::emapplot(island150_gsea_upper_right) enrichplot:::emapplot.enrichResult(x, showCategory = showCategory, color = color, layout = layout, ...) enrichplot:::has_pairsim(x) base::stop(error_message)

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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 datasets utils methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[2] GenomicFeatures_1.42.1
[3] org.Hs.eg.db_3.12.0
[4] AnnotationDbi_1.52.0
[5] ReactomePA_1.34.0
[6] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 [7] IlluminaHumanMethylationEPICmanifest_0.3.0
[8] minfi_1.36.0
[9] bumphunter_1.32.0
[10] locfit_1.5-9.4
[11] iterators_1.0.13
[12] foreach_1.5.1
[13] Biostrings_2.58.0
[14] XVector_0.30.0
[15] SummarizedExperiment_1.20.0
[16] Biobase_2.50.0
[17] MatrixGenerics_1.2.0
[18] matrixStats_0.57.0
[19] GenomicRanges_1.42.0
[20] GenomeInfoDb_1.26.2
[21] IRanges_2.24.1
[22] S4Vectors_0.28.1
[23] BiocGenerics_0.36.0
[24] annotatr_1.16.0
[25] bedslider_0.0.0.9000
[26] slider_0.1.5
[27] knitr_1.30
[28] recipes_0.1.15
[29] purrr_0.3.4
[30] tidyr_1.1.2
[31] stringr_1.4.0
[32] readr_1.4.0
[33] glue_1.4.2
[34] ggplot2_3.3.3
[35] tibble_3.0.4
[36] dplyr_1.0.2
[37] fs_1.5.0
[38] drake_7.13.0
[39] dotenv_1.0.2
[40] conflicted_1.0.4

loaded via a namespace (and not attached): [1] tidyselect_1.1.0 RSQLite_2.2.2 grid_4.0.3
[4] BiocParallel_1.24.1 scatterpie_0.1.5 munsell_0.5.0
[7] base64url_1.4 codetools_0.2-18 preprocessCore_1.52.0
[10] withr_2.3.0 colorspace_2.0-0 GOSemSim_2.16.1
[13] filelock_1.0.2 rstudioapi_0.13 DOSE_3.16.0
[16] GenomeInfoDbData_1.2.4 polyclip_1.10-0 farver_2.0.3
[19] bit64_4.0.5 rhdf5_2.34.0 txtq_0.2.3
[22] vctrs_0.3.6 generics_0.1.0 ipred_0.9-9
[25] xfun_0.20 BiocFileCache_1.14.0 regioneR_1.22.0
[28] R6_2.5.0 graphlayouts_0.7.1 illuminaio_0.32.0
[31] bitops_1.0-6 rhdf5filters_1.2.0 reshape_0.8.8
[34] fgsea_1.16.0 DelayedArray_0.16.0 assertthat_0.2.1
[37] promises_1.1.1 scales_1.1.1 ggraph_2.0.4
[40] enrichplot_1.10.1 nnet_7.3-14 gtable_0.3.0
[43] processx_3.4.5 tidygraph_1.2.0 timeDate_3043.102
[46] rlang_0.4.10 genefilter_1.72.0 splines_4.0.3
[49] rtracklayer_1.50.0 GEOquery_2.58.0 checkmate_2.0.0
[52] BiocManager_1.30.10 yaml_2.2.1 reshape2_1.4.4
[55] backports_1.2.1 httpuv_1.5.4 qvalue_2.22.0
[58] tools_4.0.3 lava_1.6.8.1 nor1mix_1.3-0
[61] ellipsis_0.3.1 RColorBrewer_1.1-2 siggenes_1.64.0
[64] Rcpp_1.0.5 plyr_1.8.6 sparseMatrixStats_1.2.0
[67] progress_1.2.2 zlibbioc_1.36.0 RCurl_1.98-1.2
[70] ps_1.5.0 prettyunits_1.1.1 rpart_4.1-15
[73] openssl_1.4.3 viridis_0.5.1 cowplot_1.1.1
[76] ggrepel_0.9.0 magrittr_2.0.1 data.table_1.13.6
[79] DO.db_2.9 warp_0.2.0 reactome.db_1.74.0
[82] storr_1.2.5 hms_0.5.3 mime_0.9
[85] xtable_1.8-4 XML_3.99-0.5 mclust_5.4.7
[88] gridExtra_2.3 compiler_4.0.3 biomaRt_2.46.0
[91] shadowtext_0.0.7 crayon_1.3.4 htmltools_0.5.0
[94] later_1.1.0.1 lubridate_1.7.9.2 DBI_1.1.0
[97] tweenr_1.0.1 dbplyr_2.0.0 MASS_7.3-53
[100] rappdirs_0.3.1 Matrix_1.3-2 cli_2.2.0
[103] quadprog_1.5-8 gower_0.2.2 igraph_1.2.6
[106] pkgconfig_2.0.3 rvcheck_0.1.8 GenomicAlignments_1.26.0
[109] xml2_1.3.2 annotate_1.68.0 rngtools_1.5
[112] multtest_2.46.0 beanplot_1.2 prodlim_2019.11.13
[115] doRNG_1.8.2 scrime_1.3.5 callr_3.5.1
[118] digest_0.6.27 graph_1.68.0 base64_2.0
[121] fastmatch_1.1-0 DelayedMatrixStats_1.12.1 curl_4.3
[124] graphite_1.36.0 shiny_1.5.0 Rsamtools_2.6.0
[127] lifecycle_0.2.0 nlme_3.1-151 Rhdf5lib_1.12.0
[130] viridisLite_0.3.0 askpass_1.1 limma_3.46.0
[133] BSgenome_1.58.0 fansi_0.4.1 pillar_1.4.7
[136] lattice_0.20-41 fastmap_1.0.1 httr_1.4.2
[139] survival_3.2-7 GO.db_3.12.1 interactiveDisplayBase_1.28.0 [142] BiocVersion_3.12.0 bit_4.0.4 ggforce_0.3.2
[145] class_7.3-17 stringi_1.5.3 HDF5Array_1.18.0
[148] blob_1.2.1 AnnotationHub_2.22.0 memoise_1.1.0
[151] renv_0.12.5

pmarjora commented 3 years ago

I've consolidated this and created a new issue.

pmarjora commented 3 years ago

Any news? I haven’t had any luck tracking down this error message online anywhere, so I’m kinda stuck.

On Jan 9, 2021, at 12:32 AM, Emil Hvitfeldt notifications@github.com wrote:

Hmm, I'm not seeing this issue.

Can you paste what you get if you run:

sessionInfo() Next, does the error persists if you run the drake plan with drake::r_make()?

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