Entering edit mode
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