summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
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@marpieraccioli-23381
Last seen 14 months ago
Italy

Hi,

this week I tried to run SAME exact code of R-Script tutorial which is provided as example data in the parathyroidSE data package, to perform counting reads with summerizeOverlaps to build an DEXSeqDataSet object. So running the code getting warnings when running summarizeOverlaps.

''' I copy code from terminal here

> library(GenomicRanges)
Carico il pacchetto richiesto: stats4
Carico il pacchetto richiesto: BiocGenerics
Carico il pacchetto richiesto: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter,
    Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit,
    which, which.max, which.min

Carico il pacchetto richiesto: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Carico il pacchetto richiesto: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Carico il pacchetto richiesto: GenomeInfoDb
> library(GenomicFeatures)
Carico il pacchetto richiesto: AnnotationDbi
Carico il pacchetto richiesto: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(GenomicAlignments)
Carico il pacchetto richiesto: SummarizedExperiment
Carico il pacchetto richiesto: DelayedArray
Carico il pacchetto richiesto: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Carico il pacchetto richiesto: Biostrings
Carico il pacchetto richiesto: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Carico il pacchetto richiesto: Rsamtools
> hse = makeTxDbFromBiomart( biomart="ensembl", dataset="hsapiens_gene_ensembl", host="grch37.ensembl.org" )
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> exonicParts = exonicParts( hse, linked.to.single.gene.only = TRUE )
> bamDir = system.file( "extdata", package="parathyroidSE", mustWork=TRUE )
> fls = list.files( bamDir, pattern="bam$", full=TRUE )
> bamlst = BamFileList( fls, index=character(), yieldSize=100000, obeyQname=TRUE )
**> SE = summarizeOverlaps( exonicParts, bamlst, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE )
Warning messages:
1: In serialize(data, node$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**

> sessionInfo()
R version 4.0.0 RC (2020-04-18 r78254)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252    LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C                  
[5] LC_TIME=Italian_Italy.1252    

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

other attached packages:
 [1] GenomicAlignments_1.23.2    Rsamtools_2.3.7             Biostrings_2.55.7           XVector_0.27.2             
 [5] SummarizedExperiment_1.17.5 DelayedArray_0.13.12        matrixStats_0.56.0          GenomicFeatures_1.39.7     
 [9] AnnotationDbi_1.49.1        Biobase_2.47.3              GenomicRanges_1.39.3        GenomeInfoDb_1.23.17       
[13] IRanges_2.21.8              S4Vectors_0.25.15           BiocGenerics_0.33.3        

loaded via a namespace (and not attached):
 [1] progress_1.2.2         tidyselect_1.0.0       purrr_0.3.4            lattice_0.20-41        vctrs_0.2.4           
 [6] snow_0.4-3             BiocFileCache_1.11.6   rtracklayer_1.47.0     blob_1.2.1             XML_3.99-0.3          
[11] rlang_0.4.5            pillar_1.4.3           glue_1.4.0             DBI_1.1.0              BiocParallel_1.21.2   
[16] rappdirs_0.3.1         bit64_0.9-7            dbplyr_1.4.3           GenomeInfoDbData_1.2.3 lifecycle_0.2.0       
[21] stringr_1.4.0          zlibbioc_1.33.1        memoise_1.1.0          biomaRt_2.43.5         curl_4.3              
[26] fansi_0.4.1            Rcpp_1.0.4.6           openssl_1.4.1          bit_1.1-15.2           hms_0.5.3             
[31] askpass_1.1            digest_0.6.25          stringi_1.4.6          dplyr_0.8.5            grid_4.0.0            
[36] cli_2.0.2              tools_4.0.0            bitops_1.0-6           magrittr_1.5           RCurl_1.98-1.1        
[41] RSQLite_2.2.0          tibble_3.0.0           crayon_1.3.4           pkgconfig_2.0.3        Matrix_1.2-18         
[46] ellipsis_0.3.0         prettyunits_1.1.1      assertthat_0.2.1       httr_1.4.1             R6_2.4.1              
[51] compiler_4.0.0

''' So to understand what is going on, downgraded back R version '3.6.0' and relative packages, but i had the same warning messages. I had the same problem also when i used pasilla package script tutorial. How to fix ?

Thanks, Marco

GenomicAlignments summerizeOverlaps-Method DEXSeq • 840 views
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