Question mark after attaching packages in run_ichorCNA #12
Description
Hello,
I'm trying to run IchorCNA as a function for the first time (I used to run it as a command line).
I'm running with this sessionInfo():
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.66.1
[3] rtracklayer_1.58.0 Biostrings_2.66.0
[5] XVector_0.38.0 doMC_1.3.8
[7] iterators_1.0.14 foreach_1.5.2
[9] GenomicRanges_1.50.0 GenomeInfoDb_1.34.1
[11] IRanges_2.32.0 S4Vectors_0.36.0
[13] BiocGenerics_0.44.0 HMMcopy_1.40.0
[15] data.table_1.14.6 ichorCNA_0.5.0
loaded via a namespace (and not attached):
[1] compiler_4.2.2 restfulr_0.0.15
[3] MatrixGenerics_1.10.0 bitops_1.0-7
[5] tools_4.2.2 zlibbioc_1.44.0
[7] lattice_0.20-45 Matrix_1.5-3
[9] DelayedArray_0.24.0 yaml_2.3.6
[11] GenomeInfoDbData_1.2.9 grid_4.2.2
[13] Biobase_2.58.0 XML_3.99-0.13
[15] BiocParallel_1.32.5 Rsamtools_2.14.0
[17] codetools_0.2-18 matrixStats_0.63.0
[19] GenomicAlignments_1.34.0 SummarizedExperiment_1.28.0
[21] RCurl_1.98-1.9 crayon_1.5.2
[23] rjson_0.2.21 BiocIO_1.8.0
So in R, I run the commands:
> library(ichorCNA)
> run_ichorCNA("mix100.wig",gcWig = "gc_hg38_1000kb.wig",mapWig = "map_hg38_1000kb.wig")
And at some point, I got a question mark, and the run stoped, here is the output:
Loading required package: HMMcopy
Loading required package: data.table
data.table 1.14.6 using 1 threads (see ?getDTthreads). Latest news: r-datatable.com
Attaching package: ‘HMMcopy’
The following objects are masked from ‘package:ichorCNA’:
HMMsegment, plotParam
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object is masked from ‘package:ichorCNA’:
normalize
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, 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.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:data.table’:
first, second
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:data.table’:
shift
Loading required package: GenomeInfoDb
Loading required package: foreach
Loading required package: doMC
Loading required package: iterators
Loading required package: parallel
?
What is it? What can I do to solve it?