Question: Error loading Gviz package object path is not exported by namespace:Rsamtools
0
gravatar for frequena.sanchez
11 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 • 539 views
ADD COMMENTlink modified 11 months ago by solutionsweb7700 • written 11 months ago by frequena.sanchez0
1

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

ADD REPLYlink written 11 months ago by Robert Ivanek660

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

ADD REPLYlink written 11 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 11 months ago by Martin Morgan ♦♦ 24k

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

ADD REPLYlink written 11 months ago by frequena.sanchez0
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