trackviewer gi2track not found
Entering edit mode
Last seen 8 weeks ago
United States

Hi Julie and Jianhong,

I just pulled trackviewer from BC today and noticed that gi2track is not available. Does this depend on R4.0?

Error in gi2track(gi) : could not find function "gi2track"
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] InteractionSet_1.14.0       SummarizedExperiment_1.16.1 DelayedArray_0.12.2        
 [4] BiocParallel_1.20.1         matrixStats_0.55.0          Biobase_2.46.0             
 [7] trackViewer_1.22.1          GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
[10] IRanges_2.20.2              S4Vectors_0.24.3            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.18.0      bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2      
 [5] progress_1.2.2           httr_1.4.1               Rgraphviz_2.30.0         backports_1.1.5         
 [9] tools_3.6.2              R6_2.4.1                 rpart_4.1-15             Hmisc_4.3-1             
[13] DBI_1.1.0                Gviz_1.30.3              lazyeval_0.2.2           colorspace_1.4-1        
[17] nnet_7.3-12              tidyselect_1.1.0         gridExtra_2.3            prettyunits_1.1.1       
[21] bit_1.1-15.2             curl_4.3                 compiler_3.6.2           graph_1.64.0            
[25] htmlTable_1.13.3         grImport_0.9-5           rtracklayer_1.46.0       checkmate_2.0.0         
[29] scales_1.1.0             askpass_1.1              rappdirs_0.3.1           stringr_1.4.0           
[33] digest_0.6.24            Rsamtools_2.2.2          foreign_0.8-72           XVector_0.26.0          
[37] dichromat_2.0-0          base64enc_0.1-3          jpeg_0.1-8.1             pkgconfig_2.0.3         
[41] htmltools_0.4.0          plotrix_3.8-2            ensembldb_2.10.2         BSgenome_1.54.0         
[45] dbplyr_1.4.4             htmlwidgets_1.5.1        rlang_0.4.8              rstudioapi_0.11         
[49] RSQLite_2.2.0            generics_0.0.2           acepack_1.4.1            dplyr_1.0.2             
[53] VariantAnnotation_1.32.0 RCurl_1.98-1.1           magrittr_1.5             GenomeInfoDbData_1.2.2  
[57] Formula_1.2-3            Matrix_1.2-18            Rcpp_1.0.3               munsell_0.5.0           
[61] lifecycle_0.2.0          stringi_1.4.6            zlibbioc_1.32.0          BiocFileCache_1.10.2    
[65] blob_1.2.1               crayon_1.3.4             lattice_0.20-38          Biostrings_2.54.0       
[69] splines_3.6.2            GenomicFeatures_1.38.2   hms_0.5.3                knitr_1.28              
[73] pillar_1.4.3             biomaRt_2.42.0           XML_3.99-0.3             glue_1.4.2              
[77] biovizBase_1.34.1        latticeExtra_0.6-29      data.table_1.12.8        BiocManager_1.30.10     
[81] png_0.1-7                vctrs_0.3.4              gtable_0.3.0             openssl_1.4.1           
[85] purrr_0.3.3              assertthat_0.2.1         ggplot2_3.2.1            xfun_0.21               
[89] AnnotationFilter_1.10.0  survival_3.1-8           tibble_3.0.4             GenomicAlignments_1.22.1
[93] AnnotationDbi_1.48.0     memoise_1.1.0            cluster_2.1.0            ellipsis_0.3.0
trackv trackViewer • 294 views
Entering edit mode

In all likelihood your package version is too old. Consider updating R and Bioconductor and install the recent package version.

Entering edit mode
Mike Smith ★ 5.6k
Last seen 4 hours ago
EMBL Heidelberg / de.NBI

Taking a look at the commit history for trackViewer ( we can see that gi2track was added in version 1.23.1.

It looks like you're getting trackViewer_1.22.1 and so the function isn't available. I'd echo doing as ATpoint suggests and consider using a newer version of R (and thus Bioconductor).

Entering edit mode

Thanks all for the comments. I was afraid that this would be the issue. So many of my currently installed BC packages fail install with newer R/BC versions, so not an option for me. People in a similar spot may want to try making a new docker image (the image associated with their manuscript has not been updated).


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