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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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Error: Invalid genome version given #44

Closed MoHallal closed 6 years ago

MoHallal commented 6 years ago

Hello, I am trying to run chimeraviz ( version 1.4.3) on some tsv files generated from defuse ( mouse RNA-seq data, mm10 genome version ) but I am getting an error : Invalid genome version. for some reason I am not able to update chimeraviz to the latest version and it seems the problem is related to not being able to update R( currently version 3.4.4) and Bioconductor on this version of Ubuntu any ideas on how to get around the above problems? Below are the requested information Thank you

  1. The output of sessionInfo().

    sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] chimeraviz_1.4.3 ensembldb_2.2.2 AnnotationFilter_1.2.0 GenomicFeatures_1.30.3 AnnotationDbi_1.40.0
[6] Biobase_2.38.0 Gviz_1.22.3 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 Biostrings_2.46.0
[11] XVector_0.18.0 IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0

loaded via a namespace (and not attached): [1] ProtGenerics_1.10.0 bitops_1.0-6 matrixStats_0.53.1 bit64_0.9-7
[5] RColorBrewer_1.1-2 progress_1.2.0 httr_1.3.1 rprojroot_1.3-2
[9] tools_3.4.4 backports_1.1.2 DT_0.4 R6_2.2.2
[13] rpart_4.1-13 Hmisc_4.1-1 DBI_1.0.0 lazyeval_0.2.1
[17] colorspace_1.3-2 nnet_7.3-12 gridExtra_2.3 prettyunits_1.0.2
[21] RMySQL_0.10.15 bit_1.1-14 curl_3.2 compiler_3.4.4
[25] htmlTable_1.12 DelayedArray_0.4.1 rtracklayer_1.38.3 scales_0.5.0
[29] checkmate_1.8.5 readr_1.1.1 RCircos_1.2.0 stringr_1.3.1
[33] digest_0.6.15 Rsamtools_1.30.0 foreign_0.8-70 rmarkdown_1.10
[37] base64enc_0.1-3 dichromat_2.0-0 pkgconfig_2.0.1 htmltools_0.3.6
[41] BSgenome_1.46.0 htmlwidgets_1.2 rlang_0.2.1 rstudioapi_0.7
[45] RSQLite_2.1.1 BiocInstaller_1.28.0 shiny_1.1.0 BiocParallel_1.12.0
[49] acepack_1.4.1 VariantAnnotation_1.24.5 RCurl_1.95-4.10 magrittr_1.5
[53] GenomeInfoDbData_1.0.0 Formula_1.2-3 Matrix_1.2-14 Rcpp_0.12.17
[57] munsell_0.5.0 stringi_1.2.3 yaml_2.1.19 SummarizedExperiment_1.8.1
[61] zlibbioc_1.24.0 org.Hs.eg.db_3.5.0 plyr_1.8.4 AnnotationHub_2.10.1
[65] blob_1.1.1 promises_1.0.1 crayon_1.3.4 lattice_0.20-35
[69] splines_3.4.4 hms_0.4.2 knitr_1.20 pillar_1.2.3
[73] biomaRt_2.34.2 XML_3.98-1.11 evaluate_0.10.1 biovizBase_1.26.0
[77] latticeExtra_0.6-28 data.table_1.11.4 httpuv_1.4.4.1 gtable_0.2.0
[81] assertthat_0.2.0 ggplot2_2.2.1 mime_0.5 xtable_1.8-2
[85] later_0.7.3 survival_2.42-3 tibble_1.4.2 GenomicAlignments_1.14.2
[89] memoise_1.1.0 cluster_2.0.7-1 interactiveDisplayBase_1.16.0 BiocStyle_2.6.1

  1. Which fusion-finder tool you are using, and its version. Defuse
  2. Which operating system you are using, and its version. Ubuntu 16.04 LTS
  3. Example code leading to the error (if you're experiencing an error). fusions <- importDefuse("results.filtered.tsv", "mm10", 100) Error in importDefuse("results.filtered.tsv", "mm10", 100) : Invalid genome version given
stianlagstad commented 6 years ago

Hi @Hallalster! Thank you for your interest in chimeraviz. Unfortunately mm10 was not supported before version 1.5.1 of chimeraviz.

I'm closing this issue, but maybe I can help you get to R version 3.5. Can you try following the instructions on this page: https://cran.r-project.org/bin/linux/ubuntu/ ? That is:

  1. Add deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ to the bottom of your /etc/apt/sources.list file.
  2. Execute sudo apt-get update && sudo apt-get install r-base

If that works out then you can install Bioconductor 3.7. Open R and execute:

  1. source("https://bioconductor.org/biocLite.R")
  2. biocLite()
  3. biocLite("chimeraviz")

If that works out as well you should be good to go :)

stianlagstad commented 6 years ago

Another option is using Docker. http://stianlagstad.no/developing-a-bioconductor-package-with-rstudio-and-docker/ might help you.