Question: Error loading Gviz package object path is not exported by namespace:Rsamtools
0
gravatar for frequena.sanchez
5 months ago by
frequena.sanchez0 wrote:

Hello everyone,

I'm having a problem with the package Gviz. I can't load it and I get this error:

 library(Gviz)
 Error : package or namespace load failed for ‘Gviz’:
 object ‘path’ is not exported by 'namespace:Rsamtools'

Thank you in advance!!

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LCCOLLATE=SpanishSpain.1252 LCCTYPE=SpanishSpain.1252
[3] LCMONETARY=SpanishSpain.1252 LCNUMERIC=C
[5] LC
TIME=Spanish_Spain.1252

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

other attached packages: [1] stringr1.3.1 httr1.3.1
[3] biomaRt2.38.0 import1.1.0
[5] VariantAnnotation1.28.3 gridSVG1.6-0
[7] gridExtra2.3 gridBase0.4-7
[9] fpc2.1-11.1 RCurl1.95-4.11
[11] bitops1.0-6 PKI0.1-5.1
[13] base64enc0.1-3 rsconnect0.8.8
[15] cowplot0.9.3 prettydoc0.2.1
[17] reshape21.4.3 ggplot23.0.0
[19] seqinr3.4-5 rmarkdown1.10
[21] GenomicAlignments1.18.0 SummarizedExperiment1.12.0
[23] DelayedArray0.8.0 BiocParallel1.10.1
[25] matrixStats0.54.0 Biobase2.42.0
[27] shinydashboardPlus0.6.0.9000 dplyr0.7.8
[29] shinycssloaders0.2.0 shinydashboard0.7.0
[31] shiny1.1.0 Rsamtools1.34.0
[33] Biostrings2.50.1 XVector0.22.0
[35] GenomicRanges1.34.0 GenomeInfoDb1.18.1
[37] IRanges2.16.0 S4Vectors0.20.1
[39] BiocGenerics_0.28.0

loaded via a namespace (and not attached): [1] colorspace1.3-2 class7.3-14
[3] modeltools0.2-22 mclust5.4.2
[5] rprojroot1.3-2 htmlTable1.12
[7] dichromat2.0-0 rstudioapi0.7
[9] flexmix2.3-14 bit640.9-7
[11] mvtnorm1.0-8 interactiveDisplayBase1.14.0 [13] AnnotationDbi1.44.0 splines3.5.1
[15] robustbase0.93-3 knitr1.20
[17] ade41.7-13 Formula1.2-3
[19] jsonlite1.6 kernlab0.9-27
[21] cluster2.0.7-1 BiocManager1.30.4
[23] compiler3.5.1 backports1.1.2
[25] assertthat0.2.0 Matrix1.2-14
[27] lazyeval0.2.1 later0.7.5
[29] acepack1.4.1 htmltools0.3.6
[31] prettyunits1.0.2 tools3.5.1
[33] bindrcpp0.2.2 gtable0.2.0
[35] glue1.3.0 GenomeInfoDbData0.99.0
[37] Rcpp1.0.0 trimcluster0.1-2.1
[39] rtracklayer1.42.1 mime0.6
[41] XML3.98-1.16 DEoptimR1.0-8
[43] AnnotationHub2.14.1 zlibbioc1.28.0
[45] MASS7.3-51.1 scales1.0.0
[47] BSgenome1.50.0 hms0.4.2
[49] promises1.0.1 ProtGenerics1.8.0
[51] AnnotationFilter1.6.0 RColorBrewer1.1-2
[53] yaml2.2.0 curl3.2
[55] memoise1.1.0 rpart4.1-13
[57] latticeExtra0.6-28 stringi1.2.4
[59] RSQLite2.1.1 checkmate1.9.0
[61] GenomicFeatures1.34.1 prabclus2.2-6
[63] rlang0.3.0.1 pkgconfig2.0.2
[65] evaluate0.11 lattice0.20-35
[67] purrr0.2.5 bindr0.1.1
[69] htmlwidgets1.2 bit1.1-14
[71] tidyselect0.2.5 plyr1.8.4
[73] magrittr1.5 R62.2.2
[75] Hmisc4.1-1 DBI1.0.0
[77] pillar1.3.0 foreign0.8-70
[79] withr2.1.2 survival2.42-3
[81] nnet7.3-12 tibble1.4.2
[83] crayon1.3.4 progress1.2.0
[85] data.table1.11.8 blob1.1.1
[87] diptest0.75-7 digest0.6.18
[89] xtable1.8-2 httpuv1.4.5
[91] munsell_0.5.0

rsamtools gviz • 300 views
ADD COMMENTlink modified 5 months ago by solutionsweb7700 • written 5 months ago by frequena.sanchez0
1

Hi, what is the version of Gviz package you are using? Best Robert

ADD REPLYlink written 5 months ago by Robert Ivanek590

Hello Robert, thank you for your fast answer! This is the version of Gviz 1.26.4

ADD REPLYlink written 5 months ago by frequena.sanchez0
1

Make sure that your packages are from the correct version of Bioconductor. For your version of R / Bioconductor, use

BiocManager::valid()
ADD REPLYlink written 5 months ago by Martin Morgan ♦♦ 23k

Alright, it was solved. I just updated all the packages to the last version. Thank you!!

ADD REPLYlink written 5 months ago by frequena.sanchez0
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