Closed MoHallal closed 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:
deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
to the bottom of your /etc/apt/sources.list
file.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:
source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite("chimeraviz")
If that works out as well you should be good to go :)
Another option is using Docker. http://stianlagstad.no/developing-a-bioconductor-package-with-rstudio-and-docker/ might help you.
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
sessionInfo()
.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