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YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization
https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
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peakHeatmap returns ` Error: external pointer is not valid` in Rmarkdown #209

Closed h4rvey-g closed 1 year ago

h4rvey-g commented 1 year ago

The following code works fine in R but returns error in Rmarkdown code chunk.

for (i in seq(1, length(gr_list), by = 4)) {
    peakHeatmap(gr_list[i:(i + 3)], color = rainbow(n = 4), TxDb = txdb, upstream = 3000, downstream = 3000) +
        facet_grid(chr ~ .id)
}
Quitting from lines 54-58 (05_annotation.Rmd)                                                                                                  
Error: external pointer is not valid                                                                                                           
In addition: There were 50 or more warnings (use warnings() to see the first 50)
r$> traceback()                                                                                                                         
42: stop(structure(list(message = "external pointer is not valid",                                                                      
        call = NULL, cppstack = NULL), class = c("Rcpp::exception",                                                                     
    "C++Error", "error", "condition")))                                                                                                 
41: result_create(conn@ptr, statement)                                                                                                  
40: initialize(value, ...)                                                                                                              
39: initialize(value, ...)                                                                                                              
38: new("SQLiteResult", sql = statement, ptr = result_create(conn@ptr,                                                                  
        statement), conn = conn, bigint = conn@bigint)                                                                                  
37: .local(conn, statement, ...)                                                                                                        
36: dbSendQuery(conn, statement, ...)                                                                                                   
35: dbSendQuery(conn, statement, ...) 
34: .local(conn, statement, ...)                                                                                                        
33: dbGetQuery(conn, paste("SELECT", select.cols, "FROM", name),                                                                        
        row.names = row.names)                                                                                                          
32: dbGetQuery(conn, paste("SELECT", select.cols, "FROM", name),                                                                        
        row.names = row.names)                                                                                                          
31: .local(conn, name, ...)                                                                                                             
30: dbReadTable(dbconn(x), "metadata")                                                                                                  
29: dbReadTable(dbconn(x), "metadata") 
28: .local(x, ...)                                                                                                                      
27: metadata(TxDb)                                                                                                                      
26: metadata(TxDb)                                                                                                                      
25: unlist(metadata(TxDb))                                                                                                              
24: .ChIPseekerEnv(TxDb)                                                                                                                
23: getBioRegion(TxDb = TxDb, upstream = upstream, downstream = downstream,                                                             
        by = "gene", type = "start_site")                                                                                               
22: peakHeatmap(gr_list[i:(i + 3)], color = rainbow(n = 4), TxDb = txdb,
        upstream = 3000, downstream = 3000)                                                                                             
21: eval(expr, envir, enclos)                                                                                                           
20: eval(expr, envir, enclos)                                                                                                           
19: eval_with_user_handlers(expr, envir, enclos, user_handlers)                                                                         
18: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))                                                            
17: withCallingHandlers(withVisible(eval_with_user_handlers(expr,                                                                       
        envir, enclos, user_handlers)), warning = wHandler, error = eHandler,                                                           
        message = mHandler)
16: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,                                                          
        envir, enclos, user_handlers)), warning = wHandler, error = eHandler,                                                           
        message = mHandler))                                                                                                            
15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,                                                
        envir, enclos, user_handlers)), warning = wHandler, error = eHandler,                                                           
        message = mHandler)))                                                                                                           
14: 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)                                                               
13: evaluate::evaluate(...)                                                                                                             
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),                                           
        keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {                   
            if (options$error && options$include)                                                                                       
                0L                                                                                                                      
            else 2L
        }, output_handler = knit_handlers(options$render, options))                                                                     
11: in_dir(input_dir(), expr)                                                                                                           
10: in_input_dir(evaluate(code, envir = env, new_device = FALSE,                                                                        
        keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),                                             
        stop_on_error = if (is.numeric(options$error)) options$error else {                                                             
            if (options$error && options$include)                                                                                       
                0L                                                                                                                      
            else 2L       
 }, output_handler = knit_handlers(options$render, options)))                                                                    
9: eng_r(options)                                                                                                                       
8: block_exec(params)                                                                                                                   
7: call_block(x)                                                                                                                        
6: process_group.block(group)                                                                                                           
5: process_group(group)                                                                                                                 
4: 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$get("infile"),                                                                       
               ") ")                                                                                                                    
       })                                                                                                                               
3: process_file(text, output)                                                                                                           
2: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
1: rmarkdown::render("05_annotation.Rmd")
r$> sessionInfo()                                                                                                                              
R version 4.2.2 (2022-10-31)                                                                                                                   
Platform: x86_64-conda-linux-gnu (64-bit)                                                                                               
Running under: CentOS Linux 7 (Core)                                                                                                    

Matrix products: default                                                                                                                
BLAS/LAPACK: /xxx/.conda/envs/r/lib/libopenblasp-r0.3.21.so                                                                       

locale:                                                                                                                                 
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8                                   
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                                                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C                                      

attached base packages:            
other attached packages:           
 [1] doParallel_1.0.17                       iterators_1.0.14                        foreach_1.5.2                                             
 [4] TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0 GenomicFeatures_1.50.2                  AnnotationDbi_1.60.0                                      
 [7] Biobase_2.58.0                          optparse_1.7.3                          rtracklayer_1.58.0                                        
[10] GenomicRanges_1.50.0                    GenomeInfoDb_1.34.1                     IRanges_2.32.0                                            
[13] S4Vectors_0.36.0                        BiocGenerics_0.44.0                     ChIPseeker_1.34.0                                         
[16] forcats_0.5.2                           stringr_1.4.1                           dplyr_1.0.10                                              
[19] purrr_0.3.5                             readr_2.1.3                             tidyr_1.2.1                                               
[22] tibble_3.1.8                            ggplot2_3.4.0                           tidyverse_1.3.2                                           

loaded via a namespace (and not attached):                             
  [1] shadowtext_0.1.2                        readxl_1.4.1                            backports_1.4.1                                          
  [4] fastmatch_1.1-3                         BiocFileCache_2.6.0                     plyr_1.8.7                                               
  [7] igraph_1.3.5                            lazyeval_0.2.2                          splines_4.2.2                                            
 [10] BiocParallel_1.32.0                     digest_0.6.30                           yulab.utils_0.0.5                                        
 [13] htmltools_0.5.3                         GOSemSim_2.24.0                         viridis_0.6.2                                            
 [16] GO.db_3.16.0                            fansi_1.0.3                             magrittr_2.0.3                                           
 [19] memoise_2.0.1                           googlesheets4_1.0.1                     tzdb_0.3.0  
[22] Biostrings_2.66.0                       graphlayouts_0.8.3                      modelr_0.1.9                                             
 [25] matrixStats_0.62.0                      enrichplot_1.18.0                       prettyunits_1.1.1                                        
 [28] colorspace_2.0-3                        blob_1.2.3                              rvest_1.0.3                                              
 [31] rappdirs_0.3.3                          ggrepel_0.9.2                           haven_2.5.1                                              
 [34] xfun_0.34                               crayon_1.5.2                            RCurl_1.98-1.9                                           
 [37] jsonlite_1.8.3                          scatterpie_0.1.8                        TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2                  
 [40] ape_5.6-2                               glue_1.6.2                              polyclip_1.10-4                                          
 [43] gtable_0.3.1                            gargle_1.2.1                            zlibbioc_1.44.0                                          
 [46] XVector_0.38.0                          DelayedArray_0.24.0                     scales_1.2.1                                             
 [49] DOSE_3.24.0                             DBI_1.1.3                               Rcpp_1.0.9                                               
 [52] plotrix_3.8-2                           viridisLite_0.4.1                       progress_1.2.2                                           
 [55] tidytree_0.4.1                          gridGraphics_0.5-1                      bit_4.0.4                                                
 [58] getopt_1.20.3                           httr_1.4.4                              fgsea_1.24.0                                             
 [61] gplots_3.1.3                            RColorBrewer_1.1-3                      ellipsis_0.3.2                                           
 [64] pkgconfig_2.0.3                         XML_3.99-0.12                           farver_2.1.1                                             
 [67] sass_0.4.2                              dbplyr_2.2.1                            utf8_1.2.2                                               
 [70] labeling_0.4.2                          ggplotify_0.1.0                         tidyselect_1.2.0                                         
 [73] rlang_1.0.6                             reshape2_1.4.4                          munsell_0.5.0                                            
 [76] cellranger_1.1.0                        tools_4.2.2                             cachem_1.0.6                                             
 [79] cli_3.4.1                               generics_0.1.3                          RSQLite_2.2.18                                           
 [82] broom_1.0.1                             evaluate_0.18                           fastmap_1.1.0                                            
 [85] yaml_2.3.6                              ggtree_3.6.0                            knitr_1.40                                               
 [88] bit64_4.0.5                             fs_1.5.2                                tidygraph_1.2.2                                          
 [91] caTools_1.18.2                          KEGGREST_1.38.0                         ggraph_2.1.0                                             
 [94] nlme_3.1-160                            aplot_0.1.8                             xml2_1.3.3                                               
 [97] biomaRt_2.54.0                          compiler_4.2.2                          filelock_1.0.2                                           
[100] curl_4.3.3                              png_0.1-7                               treeio_1.22.0                                            
[103] reprex_2.0.2                            tweenr_2.0.2                            bslib_0.4.1                                              
[106] stringi_1.7.8                           highr_0.9                               lattice_0.20-45                                          
[109] Matrix_1.5-1                            vctrs_0.5.0                             pillar_1.8.1                                             
[112] lifecycle_1.0.3                         jquerylib_0.1.4                         data.table_1.14.4                                        
[115] cowplot_1.1.1                           bitops_1.0-7                            patchwork_1.1.2                                          
[118] qvalue_2.30.0                           R6_2.5.1                                BiocIO_1.8.0                                             
[121] KernSmooth_2.23-20                      gridExtra_2.3                           codetools_0.2-18                                         
[124] gtools_3.9.3                            boot_1.3-28                             MASS_7.3-58.1                                            
[127] assertthat_0.2.1                        SummarizedExperiment_1.28.0             rjson_0.2.21
[130] withr_2.5.0                             GenomicAlignments_1.34.0                Rsamtools_2.14.0                                         
[133] GenomeInfoDbData_1.2.9                  hms_1.1.2                               ggfun_0.0.8                                              
[136] grid_4.2.2                              HDO.db_0.99.1                           rmarkdown_2.18                                           
[139] MatrixGenerics_1.10.0                   googledrive_2.0.0                       ggforce_0.4.1                                            
[142] lubridate_1.8.0                         restfulr_0.0.15
h4rvey-g commented 1 year ago

Solved. The txdb object should be explicitly exported into foreach, using the argument .export=txdb. Or export the whole global environment with .export = ls(globalenv()).