summarizeOverlaps warnings

[sunta3iouxos]

It does not seem to be an isssue, since I am getting an ouptut but I am getting this:

>   se <- GenomicAlignments::summarizeOverlaps(features = tileTargetRegions, reads = bamfiles)
Warning messages:
1: In serialize(data, node$con) :
  'package:stats' may not be available when loading
2: In serialize(data, node$con) :
  'package:stats' may not be available when loading
3: In serialize(data, node$con) :
  'package:stats' may not be available when loading
4: In serialize(data, node$con) :
  'package:stats' may not be available when loading

Sesioninfo:

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ChIPpeakAnno_3.38.1  GenomicRanges_1.56.1 GenomeInfoDb_1.40.1  IRanges_2.38.1       S4Vectors_0.42.1    
[6] BiocGenerics_0.50.0 

loaded via a namespace (and not attached):
  [1] jsonlite_1.8.9                            magrittr_2.0.3                           
  [3] GenomicFeatures_1.56.0                    BiocIO_1.14.0                            
  [5] zlibbioc_1.50.0                           vctrs_0.6.5                              
  [7] multtest_2.60.0                           memoise_2.0.1                            
  [9] Rsamtools_2.20.0                          RCurl_1.98-1.16                          
 [11] polynom_1.4-1                             htmltools_0.5.8.1                        
 [13] S4Arrays_1.4.1                            progress_1.2.3                           
 [15] AnnotationHub_3.12.0                      lambda.r_1.2.4                           
 [17] curl_5.2.3                                CNEr_1.40.0                              
 [19] Rhdf5lib_1.26.0                           SparseArray_1.4.8                        
 [21] rhdf5_2.48.0                              pracma_2.4.4                             
 [23] KernSmooth_2.23-24                        htmlwidgets_1.6.4                        
 [25] plyr_1.8.9                                httr2_1.0.5                              
 [27] futile.options_1.0.1                      cachem_1.1.0                             
 [29] GenomicAlignments_1.40.0                  lifecycle_1.0.4                          
 [31] pkgconfig_2.0.3                           Matrix_1.7-0                             
 [33] R6_2.5.1                                  fastmap_1.2.0                            
 [35] GenomeInfoDbData_1.2.12                   MatrixGenerics_1.16.0                    
 [37] digest_0.6.37                             TFMPvalue_0.0.9                          
 [39] colorspace_2.1-1                          AnnotationDbi_1.66.0                     
 [41] ATACseqQC_1.28.0                          regioneR_1.36.0                          
 [43] RSQLite_2.3.7                             seqLogo_1.70.0                           
 [45] filelock_1.0.3                            randomForest_4.7-1.2                     
 [47] fansi_1.0.6                               httr_1.4.7                               
 [49] abind_1.4-8                               compiler_4.4.1                           
 [51] bit64_4.5.2                               BiocParallel_1.38.0                      
 [53] GenomicScores_2.16.0                      DBI_1.2.3                                
 [55] preseqR_4.0.0                             R.utils_2.12.3                           
 [57] HDF5Array_1.32.1                          biomaRt_2.60.1                           
 [59] MASS_7.3-60.2                             poweRlaw_0.80.0                          
 [61] rappdirs_0.3.3                            DelayedArray_0.30.1                      
 [63] rjson_0.2.23                              gtools_3.9.5                             
 [65] caTools_1.18.3                            tools_4.4.1                              
 [67] R.oo_1.26.0                               glue_1.8.0                               
 [69] VennDiagram_1.7.3                         restfulr_0.0.15                          
 [71] InteractionSet_1.32.0                     rhdf5filters_1.16.0                      
 [73] grid_4.4.1                                reshape2_1.4.4                           
 [75] ade4_1.7-22                               snow_0.4-4                               
 [77] TFBSTools_1.42.0                          generics_0.1.3                           
 [79] gtable_0.3.5                              BSgenome_1.72.0                          
 [81] tzdb_0.4.0                                R.methodsS3_1.8.2                        
 [83] tidyr_1.3.1                               ensembldb_2.28.1                         
 [85] data.table_1.16.0                         hms_1.1.3                                
 [87] xml2_1.3.6                                utf8_1.2.4                               
 [89] XVector_0.44.0                            BiocVersion_3.19.1                       
 [91] pillar_1.9.0                              stringr_1.5.1                            
 [93] limma_3.60.6                              splines_4.4.1                            
 [95] dplyr_1.1.4                               BiocFileCache_2.12.0                     
 [97] lattice_0.22-6                            survival_3.6-4                           
 [99] rtracklayer_1.64.0                        bit_4.5.0                                
[101] annotate_1.82.0                           DirichletMultinomial_1.46.0              
[103] universalmotif_1.22.3                     tidyselect_1.2.1                         
[105] RBGL_1.80.0                               GO.db_3.19.1                             
[107] locfit_1.5-9.10                           Biostrings_2.72.1                        
[109] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 ProtGenerics_1.36.0                      
[111] edgeR_4.2.1                               SummarizedExperiment_1.34.0              
[113] futile.logger_1.4.3                       Biobase_2.64.0                           
[115] statmod_1.5.0                             matrixStats_1.4.1                        
[117] stringi_1.8.4                             UCSC.utils_1.0.0                         
[119] lazyeval_0.2.2                            yaml_2.3.10                              
[121] codetools_0.2-20                          BSgenome.Mmusculus.UCSC.mm10_1.4.3       
[123] tibble_3.2.1                              BiocManager_1.30.25                      
[125] graph_1.82.0                              cli_3.6.3                                
[127] xtable_1.8-4                              munsell_0.5.1                            
[129] Rcpp_1.0.13                               dbplyr_2.5.0                             
[131] png_0.1-8                                 XML_3.99-0.17                            
[133] parallel_4.4.1                            readr_2.1.5                              
[135] ggplot2_3.5.1                             blob_1.2.4                               
[137] prettyunits_1.2.0                         AnnotationFilter_1.28.0                  
[139] bitops_1.0-9                              pwalign_1.0.0                            
[141] motifStack_1.48.0                         scales_1.3.0                             
[143] purrr_1.0.2                               crayon_1.5.3                             
[145] rlang_1.1.4                               KEGGREST_1.44.1                          
[147] formatR_1.14     

[hpages]

Can you provide a reproducible example? Thanks.

[sunta3iouxos]

Sorry for the delayed response.
What would you like to post? I could sent you the bed and bam file if possible.

[hpages]

Can't you reproduce with small publicly available bed and bam files? Sending things to me is not ideal. Showing a self-contained MRE (Minimal Reproducible Example) that uses data readily accessible by everybody is preferrable. This can be data from a Bioconductor data experiment package or data fetched from AnnotationHub and/or ExperimentHub. Thanks!