gravatar for Assa Yeroslaviz

2 hours ago by


Im testing the Bisulphite-Seq workflow with RnBeads. When trying to save the rnbs object locally
I use the following commad

rnbs <- save.rnb.set(object = rnbs, path = rnbsSaveDir)

When doing so it deletes the object from memory, which is a very nice function.
While doing so it throws two warnings

Warning in doTryCatch(return(expr), name, parentenv, handler) :
  restarting interrupted promise evaluation
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  restarting interrupted promise evaluation

Would it be better to create an uncompressed output folder?

But for me to continue the analysis, it mean I need to reload the object from memory.

When I do this I get a lot more warnings:

> rnbs <- load.rnb.set(path = file.path(data.dir,""))
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In FUN(X[[i]], ...) : NOTE: did not overwrite file 'ff8fd9db6abc1.ff'
2: In FUN(X[[i]], ...) : NOTE: did not overwrite file 'ff8fd953c612ef.ff'
3: In FUN(X[[i]], ...) : NOTE: did not overwrite file 'ff8fd9710533e0.ff'
4: In FUN(X[[i]], ...) : NOTE: did not overwrite file 'ff8fd9c90f118.ff'
5: In FUN(X[[i]], ...) : NOTE: did not overwrite file 'ff8fd97fc46519.ff'
6: In FUN(X[[i]], ...) : NOTE: did not overwrite file 'ff8fd936c98dd7.ff'

I'm not sure what these warnings/messages suppose to tell me. Do I need to worry about something here, or are these just notifications of what is being uncompressed during the loading f the object?


R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (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/3.6/Resources/lib/libRlapack.dylib

[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] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RnBeads.hg38_1.18.0                     RnBeads_2.4.0                           plyr_1.8.6                             
 [4] methylumi_2.32.0                        minfi_1.32.0                            bumphunter_1.28.0                      
 [7] locfit_1.5-9.4                          iterators_1.0.12                        foreach_1.5.0                          
[10] Biostrings_2.54.0                       XVector_0.26.0                          SummarizedExperiment_1.16.1            
[13] DelayedArray_0.12.3                     BiocParallel_1.20.1                     FDb.InfiniumMethylation.hg19_2.2.0     
[16]                     TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.38.2                 
[19] AnnotationDbi_1.48.0                    reshape2_1.4.4                          scales_1.1.0                           
[22] Biobase_2.46.0                          illuminaio_0.28.0                       matrixStats_0.56.0                     
[25] limma_3.42.2                            gridExtra_2.3                           gplots_3.0.3                           
[28] ggplot2_3.3.0                           fields_10.3                             maps_3.3.0                             
[31] spam_2.5-1                              dotCall64_1.0-0                         ff_2.2-14.2                            
[34] bit_1.1-15.2                            cluster_2.1.0                           MASS_7.3-51.5                          
[37] GenomicRanges_1.38.0                    GenomeInfoDb_1.22.1                     IRanges_2.20.2                         
[40] S4Vectors_0.24.4                        BiocGenerics_0.32.0                    

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1         ellipsis_0.3.0           siggenes_1.60.0          mclust_5.4.6            
 [5] base64_2.0               rstudioapi_0.11          bit64_0.9-7              xml2_1.3.1              
 [9] codetools_0.2-16         splines_3.6.3            scrime_1.3.5             knitr_1.28              
[13] Rsamtools_2.2.3          annotate_1.64.0          dbplyr_1.4.3             HDF5Array_1.14.4        
[17] readr_1.3.1              compiler_3.6.3           httr_1.4.1               assertthat_0.2.1        
[21] Matrix_1.2-18            prettyunits_1.1.1        tools_3.6.3              gtable_0.3.0            
[25] glue_1.4.0               GenomeInfoDbData_1.2.2   dplyr_0.8.5              rappdirs_0.3.1          
[29] doRNG_1.8.2              Rcpp_1.0.4.6             vctrs_0.2.4              multtest_2.42.0         
[33] nlme_3.1-147             preprocessCore_1.48.0    gdata_2.18.0             rtracklayer_1.46.0      
[37] DelayedMatrixStats_1.8.0 xfun_0.13                stringr_1.4.0            lifecycle_0.2.0         
[41] rngtools_1.5             gtools_3.8.2             XML_3.99-0.3             beanplot_1.2            
[45] zlibbioc_1.32.0          hms_0.5.3                GEOquery_2.54.1          rhdf5_2.30.1            
[49] RColorBrewer_1.1-2       curl_4.3                 memoise_1.1.0            biomaRt_2.42.1          
[53] reshape_0.8.8            stringi_1.4.6            RSQLite_2.2.0            genefilter_1.68.0       
[57] caTools_1.18.0           rlang_0.4.5              pkgconfig_2.0.3          bitops_1.0-6            
[61] nor1mix_1.3-0            lattice_0.20-41          purrr_0.3.4              Rhdf5lib_1.8.0          
[65] GenomicAlignments_1.22.1 tidyselect_1.0.0         magrittr_1.5             R6_2.4.1                
[69] DBI_1.1.0                pillar_1.4.3             withr_2.2.0              survival_3.1-12         
[73] RCurl_1.98-1.2           tibble_3.0.1             crayon_1.3.4             KernSmooth_2.23-16      
[77] BiocFileCache_1.10.2     progress_1.2.2           data.table_1.12.8        blob_1.2.1              
[81] digest_0.6.25            xtable_1.8-4             tidyr_1.0.2              openssl_1.4.1           
[85] munsell_0.5.0            quadprog_1.5-8           askpass_1.1

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