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  • RnBeads (2.2.0) error when I run example 2

    I am going to run the example (2) on Linux server. After download completed, it showed me this error.

    > rnb.run.example(2)


    2019-08-12 09:10:14 1.6 STATUS STARTED Downloading and Unpacking Data Files
    2019-08-12 09:10:14 1.6 INFO Processing example 2
    trying URL 'http://rnbeads.mpi-inf.mpg.de/publication/data/example_2.tar.gz'
    Content type 'application/x-gzip' length 447342436 bytes (426.6 MB)
    ==================================================
    downloaded 426.6 MB

    2019-08-12 09:24:03 1.6 STATUS Downloaded http://rnbeads.mpi-inf.mpg.de/public...ample_2.tar.gz
    2019-08-12 09:25:09 1.7 STATUS Unpacked downloaded file
    2019-08-12 09:25:09 1.7 STATUS COMPLETED Downloading and Unpacking Data Files

    Error in (function (...) : invalid value for option assembly
    In addition: Warning messages:
    1: In structure(x$children, class = "XMLNodeList") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
    2: In structure(x$children, class = "XMLNodeList") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
    3: In structure(x$children, class = "XMLNodeList") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
    4: In structure(x$children, class = "XMLNodeList") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.

    My R session information is below

    > sessionInfo()


    R version 3.6.0 (2019-04-26)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Ubuntu 18.04.2 LTS

    Matrix products: default
    BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
    LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

    locale:
    [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

    other attached packages:
    [1] XML_3.98-1.20 RnBeads_2.2.0
    [3] plyr_1.8.4 methylumi_2.30.0
    [5] minfi_1.30.0 bumphunter_1.26.0
    [7] locfit_1.5-9.1 iterators_1.0.12
    [9] foreach_1.4.7 Biostrings_2.52.0
    [11] XVector_0.24.0 SummarizedExperiment_1.14.0
    [13] DelayedArray_0.10.0 BiocParallel_1.18.0
    [15] FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.8.2
    [17] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.36.4
    [19] AnnotationDbi_1.46.0 reshape2_1.4.3
    [21] scales_1.0.0 Biobase_2.44.0
    [23] illuminaio_0.26.0 matrixStats_0.54.0
    [25] limma_3.40.4 gridExtra_2.3
    [27] gplots_3.0.1.1 ggplot2_3.2.1
    [29] fields_9.8-3 maps_3.3.0
    [31] spam_2.2-2 dotCall64_1.0-0
    [33] ff_2.2-14 bit_1.1-14
    [35] cluster_2.0.8 MASS_7.3-51.1
    [37] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0
    [39] IRanges_2.18.1 S4Vectors_0.22.0
    [41] BiocGenerics_0.30.0

    loaded via a namespace (and not attached):
    [1] colorspace_1.4-1 siggenes_1.58.0 mclust_5.4.5
    [4] base64_2.0 rstudioapi_0.10 bit64_0.9-7
    [7] xml2_1.2.0 codetools_0.2-16 splines_3.6.0
    [10] scrime_1.3.5 zeallot_0.1.0 Rsamtools_2.0.0
    [13] annotate_1.62.0 HDF5Array_1.12.1 readr_1.3.1
    [16] compiler_3.6.0 httr_1.4.1 backports_1.1.4
    [19] assertthat_0.2.1 Matrix_1.2-17 lazyeval_0.2.2
    [22] prettyunits_1.0.2 tools_3.6.0 gtable_0.3.0
    [25] glue_1.3.1 GenomeInfoDbData_1.2.1 dplyr_0.8.3
    [28] doRNG_1.7.1 Rcpp_1.0.2 vctrs_0.2.0
    [31] multtest_2.40.0 nlme_3.1-141 preprocessCore_1.46.0
    [34] gdata_2.18.0 rtracklayer_1.44.2 DelayedMatrixStats_1.6.0
    [37] stringr_1.4.0 rngtools_1.4 gtools_3.8.1
    [40] beanplot_1.2 zlibbioc_1.30.0 hms_0.5.0
    [43] GEOquery_2.52.0 rhdf5_2.28.0 RColorBrewer_1.1-2
    [46] memoise_1.1.0 pkgmaker_0.27 biomaRt_2.40.3
    [49] reshape_0.8.8 stringi_1.4.3 RSQLite_2.1.2
    [52] genefilter_1.66.0 caTools_1.17.1.2 bibtex_0.4.2
    [55] rlang_0.4.0 pkgconfig_2.0.2 bitops_1.0-6
    [58] nor1mix_1.3-0 lattice_0.20-38 purrr_0.3.2
    [61] Rhdf5lib_1.6.0 GenomicAlignments_1.20.1 tidyselect_0.2.5
    [64] magrittr_1.5 R6_2.4.0 DBI_1.0.0
    [67] pillar_1.4.2 withr_2.1.2 survival_2.44-1.1
    [70] RCurl_1.95-4.12 tibble_2.1.3 crayon_1.3.4
    [73] KernSmooth_2.23-15 progress_1.2.2 data.table_1.12.2
    [76] blob_1.2.0 digest_0.6.20 xtable_1.8-4
    [79] tidyr_0.8.3 openssl_1.4.1 munsell_0.5.0
    [82] registry_0.5-1 quadprog_1.5-7 askpass_1.1

    Is anyone get idea about it?
    Thank you very much.

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