trackviewer gi2track not found
1
0
Entering edit mode
@tomasrodriguez-21656
Last seen 27 days 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

locale:
[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 • 268 views
ADD COMMENT
2
Entering edit mode

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

ADD REPLY
2
Entering edit mode
Mike Smith ★ 5.6k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

Taking a look at the commit history for trackViewer (https://code.bioconductor.org/browse/trackViewer/commit/131ee5caa5f61dcad4c2572be3c9e61f958cbaa0#diff-1) 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).

ADD COMMENT
0
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).

ADD REPLY

Login before adding your answer.

Traffic: 149 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6