Question mark after attaching packages in run_ichorCNA

[ekushele]

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?

[ekushele]

@gavinha Can you please help me with this?

[gavinha]

Hi @ekushele

I would recommend that you try the previous commit of ichorCNA and the snakemake workflow. GenomeInfoDb has been updated no longer works with our current implementation; however, if you are able to use the previous version of GenomeInfoDb_1.20.0 that should still work. Sorry for the inconvenience while we migrate to the Cromwell-WDL workflow.

Please see #13