Tweet
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.
> 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.