igvShiny/inst/demos/tiny.R fails on some stock genomes

[malcook]

In my hands, igvShiny/inst/demos/tiny. works in R 4.2.0 as provided (using genomeName="hg38" ).

I installed earlier today with remotes::install_github("paul-shannon/igvShiny")

From the documentation, I expect it should work with many other of the currently.supported.stock.genomes().

However, for me, changing to another stock genome with genomeName="danRer11" (or: sacCer3 hg19 dm3 dm6 chm13v2.0), fails with:

igvShiny.js:66 Uncaught TypeError: Cannot read properties of null (reading 'height')
    at Object.renderValue (igvShiny.js:66:77)
    at Object.renderValue (htmlwidgets.js:886:25)
    at shinyBinding.renderValue (htmlwidgets.js:541:20)
    at e.value (outputBinding.ts:48:12)
    at delegator.<computed> [as onValueChange] (htmlwidgets.js:112:23)
    at e.value (outputAdapter.ts:38:20)
    at e.value (shinyapp.ts:559:17)
    at e.<anonymous> (shinyapp.ts:736:20)
    at e.value (shinyapp.ts:717:29)
    at e.value (shinyapp.ts:700:12)
renderValue @ igvShiny.js:66
renderValue @ htmlwidgets.js:886
shinyBinding.renderValue @ htmlwidgets.js:541
value @ outputBinding.ts:48
delegator.<computed> @ htmlwidgets.js:112
value @ outputAdapter.ts:38
value @ shinyapp.ts:559
(anonymous) @ shinyapp.ts:736
value @ shinyapp.ts:717
value @ shinyapp.ts:700
i.onmessage @ shinyapp.ts:350

This is under Google Chrome (Version 105.0.5195.127 (Official Build) (64-bit)) .

Additionally there are warnings in the console of:

DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/igv-ui-1_3_0.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE
DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/circular-view.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE
DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/dom.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE

but these warnings are also present with "hg38".

The issue persists after updating all packages:

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /n/apps/CentOS7/install/r-4.2.0/lib64/R/lib/libRblas.so
LAPACK: /n/apps/CentOS7/install/r-4.2.0/lib64/R/lib/libRlapack.so

locale:
[1] C

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

other attached packages:
 [1] igvShiny_1.5.6         htmlwidgets_1.5.4      rtracklayer_1.56.1    
 [4] GenomeInfoDbData_1.2.8 GenomicRanges_1.48.0   GenomeInfoDb_1.32.3   
 [7] IRanges_2.30.1         S4Vectors_0.34.0       BiocGenerics_0.42.0   
[10] shiny_1.7.2           

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9                  lattice_0.20-45            
 [3] Rsamtools_2.12.0            Biostrings_2.64.1          
 [5] digest_0.6.29               V8_4.2.1                   
 [7] mime_0.12                   R6_2.5.1                   
 [9] httr_1.4.4                  zlibbioc_1.42.0            
[11] rlang_1.0.6                 curl_4.3.2                 
[13] jquerylib_0.1.4             Matrix_1.5-1               
[15] randomcoloR_1.1.0.1         BiocParallel_1.30.3        
[17] Rtsne_0.16                  stringr_1.4.1              
[19] RCurl_1.98-1.9              munsell_0.5.0              
[21] DelayedArray_0.22.0         compiler_4.2.0             
[23] httpuv_1.6.6                htmltools_0.5.3            
[25] SummarizedExperiment_1.26.1 codetools_0.2-18           
[27] matrixStats_0.62.0          XML_3.99-0.11              
[29] crayon_1.5.2                later_1.3.0                
[31] GenomicAlignments_1.32.1    bitops_1.0-7               
[33] grid_4.2.0                  jsonlite_1.8.2             
[35] xtable_1.8-4                lifecycle_1.0.2            
[37] magrittr_2.0.3              scales_1.2.1               
[39] cli_3.4.1                   stringi_1.7.8              
[41] cachem_1.0.6                XVector_0.36.0             
[43] promises_1.2.0.1            bslib_0.4.0                
[45] ellipsis_0.3.2              rjson_0.2.21               
[47] restfulr_0.0.15             tools_4.2.0                
[49] Biobase_2.56.0              MatrixGenerics_1.8.1       
[51] parallel_4.2.0              fastmap_1.1.0              
[53] yaml_2.3.5                  colorspace_2.0-3           
[55] cluster_2.1.4               memoise_2.0.1              
[57] sass_0.4.2                  BiocIO_1.6.0                

I tried it in R 4.1.2 and still get

Uncaught TypeError: Cannot read properties of null (reading 'height')
    at Object.renderValue (igvShiny.js:66:77)
    at Object.renderValue (htmlwidgets.js:886:25)
    at shinyBinding.renderValue (htmlwidgets.js:541:20)
    at e.value (outputBinding.ts:48:12)
    at delegator.<computed> [as onValueChange] (htmlwidgets.js:112:23)
    at e.value (outputAdapter.ts:38:20)
    at e.value (shinyapp.ts:559:17)
    at e.<anonymous> (shinyapp.ts:736:20)
    at e.value (shinyapp.ts:717:29)
    at e.value (shinyapp.ts:700:12)

again with updated packages:

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /n/apps/CentOS7/install/r-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /n/apps/CentOS7/install/r-4.1.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] igvShiny_1.5.6         htmlwidgets_1.5.4      rtracklayer_1.57.0    
 [4] GenomeInfoDbData_1.2.7 GenomicRanges_1.46.1   GenomeInfoDb_1.30.1   
 [7] IRanges_2.28.0         S4Vectors_0.30.2       BiocGenerics_0.40.0   
[10] shiny_1.7.2           

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.24.0 bslib_0.4.0                
 [3] lattice_0.20-45             V8_4.2.1                   
 [5] colorspace_2.0-3            htmltools_0.5.3            
 [7] yaml_2.3.5                  XML_3.99-0.9               
 [9] rlang_1.0.1                 jquerylib_0.1.4            
[11] later_1.3.0                 BiocParallel_1.28.3        
[13] randomcoloR_1.1.0.1         matrixStats_0.62.0         
[15] lifecycle_1.0.1             stringr_1.4.1              
[17] zlibbioc_1.40.0             MatrixGenerics_1.6.0       
[19] Biostrings_2.62.0           munsell_0.5.0              
[21] memoise_2.0.1               restfulr_0.0.13            
[23] Biobase_2.54.0              fastmap_1.1.0              
[25] httpuv_1.6.6                parallel_4.1.2             
[27] curl_4.3.2                  Rcpp_1.0.8                 
[29] xtable_1.8-4                promises_1.2.0.1           
[31] scales_1.2.1                cachem_1.0.6               
[33] DelayedArray_0.20.0         jsonlite_1.8.2             
[35] XVector_0.34.0              mime_0.12                  
[37] Rsamtools_2.10.0            rjson_0.2.21               
[39] digest_0.6.29               stringi_1.7.8              
[41] Rtsne_0.16                  BiocIO_1.4.0               
[43] grid_4.1.2                  cli_3.3.0                  
[45] tools_4.1.2                 bitops_1.0-7               
[47] sass_0.4.2                  magrittr_2.0.3             
[49] RCurl_1.98-1.6              cluster_2.1.2              
[51] crayon_1.5.2                ellipsis_0.3.2             
[53] Matrix_1.4-1                httr_1.4.4                 
[55] R6_2.5.1                    GenomicAlignments_1.30.0   
[57] compiler_4.1.2             

Similarly, igvShinyDemo.R fails when changing hg38 to e.g. danRer11.

What other diagnostics can I provide?

Or am I just using it incorrectly?

[paul-shannon]

Excellent bug report - thank you. Alas, I am traveling till 10/26 without a laptop, and so unable to track this down. I will explore and fix directly upon my return.

Sent from my iPhone

On Oct 5, 2022, at 5:58 AM, Malcolm Cook @.***> wrote:

 In my hands, igvShiny/inst/demos/tiny. works in R 4.2.0 as provided (using genomeName="hg38" ).

From the documentation, I expect it should work with many other of the currently.supported.stock.genomes().

However, for me, changing to another stock genome with genomeName="danRer11" (or: sacCer3 hg19 dm3 dm6 chm13v2.0), fails with:

Uncaught TypeError: Cannot read properties of null (reading 'height') at Object.renderValue (igvShiny.js:66:77) at Object.renderValue (htmlwidgets.js:886:25) at shinyBinding.renderValue (htmlwidgets.js:541:20) at e.value (outputBinding.ts:48:12) at delegator. [as onValueChange] (htmlwidgets.js:112:23) at e.value (outputAdapter.ts:38:20) at e.value (shinyapp.ts:559:17) at e. (shinyapp.ts:736:20) at e.value (shinyapp.ts:717:29) This is under Google Chrome (Version 105.0.5195.127 (Official Build) (64-bit)) .

Additionally there are warnings in the console of:

DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/igv-ui-1_3_0.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/circular-view.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/dom.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE but these warnings are also present with "hg38".

The issue persists after updating all packages:

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /n/apps/CentOS7/install/r-4.2.0/lib64/R/lib/libRblas.so LAPACK: /n/apps/CentOS7/install/r-4.2.0/lib64/R/lib/libRlapack.so

locale: [1] C

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

other attached packages: [1] igvShiny_1.5.6 htmlwidgets_1.5.4 rtracklayer_1.56.1
[4] GenomeInfoDbData_1.2.8 GenomicRanges_1.48.0 GenomeInfoDb_1.32.3
[7] IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.42.0
[10] shiny_1.7.2

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 lattice_0.20-45
[3] Rsamtools_2.12.0 Biostrings_2.64.1
[5] digest_0.6.29 V8_4.2.1
[7] mime_0.12 R6_2.5.1
[9] httr_1.4.4 zlibbioc_1.42.0
[11] rlang_1.0.6 curl_4.3.2
[13] jquerylib_0.1.4 Matrix_1.5-1
[15] randomcoloR_1.1.0.1 BiocParallel_1.30.3
[17] Rtsne_0.16 stringr_1.4.1
[19] RCurl_1.98-1.9 munsell_0.5.0
[21] DelayedArray_0.22.0 compiler_4.2.0
[23] httpuv_1.6.6 htmltools_0.5.3
[25] SummarizedExperiment_1.26.1 codetools_0.2-18
[27] matrixStats_0.62.0 XML_3.99-0.11
[29] crayon_1.5.2 later_1.3.0
[31] GenomicAlignments_1.32.1 bitops_1.0-7
[33] grid_4.2.0 jsonlite_1.8.2
[35] xtable_1.8-4 lifecycle_1.0.2
[37] magrittr_2.0.3 scales_1.2.1
[39] cli_3.4.1 stringi_1.7.8
[41] cachem_1.0.6 XVector_0.36.0
[43] promises_1.2.0.1 bslib_0.4.0
[45] ellipsis_0.3.2 rjson_0.2.21
[47] restfulr_0.0.15 tools_4.2.0
[49] Biobase_2.56.0 MatrixGenerics_1.8.1
[51] parallel_4.2.0 fastmap_1.1.0
[53] yaml_2.3.5 colorspace_2.0-3
[55] cluster_2.1.4 memoise_2.0.1
[57] sass_0.4.2 BiocIO_1.6.0
I tried it in R 4.1.2 and still get

Uncaught TypeError: Cannot read properties of null (reading 'height') at Object.renderValue (igvShiny.js:66:77) at Object.renderValue (htmlwidgets.js:886:25) at shinyBinding.renderValue (htmlwidgets.js:541:20) at e.value (outputBinding.ts:48:12) at delegator. [as onValueChange] (htmlwidgets.js:112:23) at e.value (outputAdapter.ts:38:20) at e.value (shinyapp.ts:559:17) at e. (shinyapp.ts:736:20) at e.value (shinyapp.ts:717:29) at e.value (shinyapp.ts:700:12) again with updated packages:

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /n/apps/CentOS7/install/r-4.1.2/lib64/R/lib/libRblas.so LAPACK: /n/apps/CentOS7/install/r-4.1.2/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

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

other attached packages: [1] igvShiny_1.5.6 htmlwidgets_1.5.4 rtracklayer_1.57.0
[4] GenomeInfoDbData_1.2.7 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[7] IRanges_2.28.0 S4Vectors_0.30.2 BiocGenerics_0.40.0
[10] shiny_1.7.2

loaded via a namespace (and not attached): [1] SummarizedExperiment_1.24.0 bslib_0.4.0
[3] lattice_0.20-45 V8_4.2.1
[5] colorspace_2.0-3 htmltools_0.5.3
[7] yaml_2.3.5 XML_3.99-0.9
[9] rlang_1.0.1 jquerylib_0.1.4
[11] later_1.3.0 BiocParallel_1.28.3
[13] randomcoloR_1.1.0.1 matrixStats_0.62.0
[15] lifecycle_1.0.1 stringr_1.4.1
[17] zlibbioc_1.40.0 MatrixGenerics_1.6.0
[19] Biostrings_2.62.0 munsell_0.5.0
[21] memoise_2.0.1 restfulr_0.0.13
[23] Biobase_2.54.0 fastmap_1.1.0
[25] httpuv_1.6.6 parallel_4.1.2
[27] curl_4.3.2 Rcpp_1.0.8
[29] xtable_1.8-4 promises_1.2.0.1
[31] scales_1.2.1 cachem_1.0.6
[33] DelayedArray_0.20.0 jsonlite_1.8.2
[35] XVector_0.34.0 mime_0.12
[37] Rsamtools_2.10.0 rjson_0.2.21
[39] digest_0.6.29 stringi_1.7.8
[41] Rtsne_0.16 BiocIO_1.4.0
[43] grid_4.1.2 cli_3.3.0
[45] tools_4.1.2 bitops_1.0-7
[47] sass_0.4.2 magrittr_2.0.3
[49] RCurl_1.98-1.6 cluster_2.1.2
[51] crayon_1.5.2 ellipsis_0.3.2
[53] Matrix_1.4-1 httr_1.4.4
[55] R6_2.5.1 GenomicAlignments_1.30.0
[57] compiler_4.1.2
What other diagnostics can I provide?

Or am I just using it incorrectly?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[paul-shannon]

Another thought. Genome name is no longer a direct argument in the igvShiny constrictor. Maybe you already know that…

Can you run inst/demos/igvShinyDemo.R?

Forgive me if you have already traveled this route

Sent from my iPhone

On Oct 5, 2022, at 6:55 AM, Paul Shannon @.***> wrote:

 Excellent bug report - thank you. Alas, I am traveling till 10/26 without a laptop, and so unable to track this down. I will explore and fix directly upon my return.

Sent from my iPhone

On Oct 5, 2022, at 5:58 AM, Malcolm Cook @.***> wrote:

 In my hands, igvShiny/inst/demos/tiny. works in R 4.2.0 as provided (using genomeName="hg38" ).

From the documentation, I expect it should work with many other of the currently.supported.stock.genomes().

However, for me, changing to another stock genome with genomeName="danRer11" (or: sacCer3 hg19 dm3 dm6 chm13v2.0), fails with:

Uncaught TypeError: Cannot read properties of null (reading 'height') at Object.renderValue (igvShiny.js:66:77) at Object.renderValue (htmlwidgets.js:886:25) at shinyBinding.renderValue (htmlwidgets.js:541:20) at e.value (outputBinding.ts:48:12) at delegator. [as onValueChange] (htmlwidgets.js:112:23) at e.value (outputAdapter.ts:38:20) at e.value (shinyapp.ts:559:17) at e. (shinyapp.ts:736:20) at e.value (shinyapp.ts:717:29) This is under Google Chrome (Version 105.0.5195.127 (Official Build) (64-bit)) .

Additionally there are warnings in the console of:

DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/igv-ui-1_3_0.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/circular-view.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE DevTools failed to load source map: Could not load content for http://hd1991356yb:9998/dom.css.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE but these warnings are also present with "hg38".

The issue persists after updating all packages:

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /n/apps/CentOS7/install/r-4.2.0/lib64/R/lib/libRblas.so LAPACK: /n/apps/CentOS7/install/r-4.2.0/lib64/R/lib/libRlapack.so

locale: [1] C

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] igvShiny_1.5.6 htmlwidgets_1.5.4 rtracklayer_1.56.1 [4] GenomeInfoDbData_1.2.8 GenomicRanges_1.48.0 GenomeInfoDb_1.32.3 [7] IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.42.0 [10] shiny_1.7.2

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 lattice_0.20-45 [3] Rsamtools_2.12.0 Biostrings_2.64.1 [5] digest_0.6.29 V8_4.2.1 [7] mime_0.12 R6_2.5.1 [9] httr_1.4.4 zlibbioc_1.42.0 [11] rlang_1.0.6 curl_4.3.2 [13] jquerylib_0.1.4 Matrix_1.5-1 [15] randomcoloR_1.1.0.1 BiocParallel_1.30.3 [17] Rtsne_0.16 stringr_1.4.1 [19] RCurl_1.98-1.9 munsell_0.5.0 [21] DelayedArray_0.22.0 compiler_4.2.0 [23] httpuv_1.6.6 htmltools_0.5.3 [25] SummarizedExperiment_1.26.1 codetools_0.2-18 [27] matrixStats_0.62.0 XML_3.99-0.11 [29] crayon_1.5.2 later_1.3.0 [31] GenomicAlignments_1.32.1 bitops_1.0-7 [33] grid_4.2.0 jsonlite_1.8.2 [35] xtable_1.8-4 lifecycle_1.0.2 [37] magrittr_2.0.3 scales_1.2.1 [39] cli_3.4.1 stringi_1.7.8 [41] cachem_1.0.6 XVector_0.36.0 [43] promises_1.2.0.1 bslib_0.4.0 [45] ellipsis_0.3.2 rjson_0.2.21 [47] restfulr_0.0.15 tools_4.2.0 [49] Biobase_2.56.0 MatrixGenerics_1.8.1 [51] parallel_4.2.0 fastmap_1.1.0 [53] yaml_2.3.5 colorspace_2.0-3 [55] cluster_2.1.4 memoise_2.0.1 [57] sass_0.4.2 BiocIO_1.6.0 I tried it in R 4.1.2 and still get

Uncaught TypeError: Cannot read properties of null (reading 'height') at Object.renderValue (igvShiny.js:66:77) at Object.renderValue (htmlwidgets.js:886:25) at shinyBinding.renderValue (htmlwidgets.js:541:20) at e.value (outputBinding.ts:48:12) at delegator. [as onValueChange] (htmlwidgets.js:112:23) at e.value (outputAdapter.ts:38:20) at e.value (shinyapp.ts:559:17) at e. (shinyapp.ts:736:20) at e.value (shinyapp.ts:717:29) at e.value (shinyapp.ts:700:12) again with updated packages:

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /n/apps/CentOS7/install/r-4.1.2/lib64/R/lib/libRblas.so LAPACK: /n/apps/CentOS7/install/r-4.1.2/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] igvShiny_1.5.6 htmlwidgets_1.5.4 rtracklayer_1.57.0 [4] GenomeInfoDbData_1.2.7 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 [7] IRanges_2.28.0 S4Vectors_0.30.2 BiocGenerics_0.40.0 [10] shiny_1.7.2

loaded via a namespace (and not attached): [1] SummarizedExperiment_1.24.0 bslib_0.4.0 [3] lattice_0.20-45 V8_4.2.1 [5] colorspace_2.0-3 htmltools_0.5.3 [7] yaml_2.3.5 XML_3.99-0.9 [9] rlang_1.0.1 jquerylib_0.1.4 [11] later_1.3.0 BiocParallel_1.28.3 [13] randomcoloR_1.1.0.1 matrixStats_0.62.0 [15] lifecycle_1.0.1 stringr_1.4.1 [17] zlibbioc_1.40.0 MatrixGenerics_1.6.0 [19] Biostrings_2.62.0 munsell_0.5.0 [21] memoise_2.0.1 restfulr_0.0.13 [23] Biobase_2.54.0 fastmap_1.1.0 [25] httpuv_1.6.6 parallel_4.1.2 [27] curl_4.3.2 Rcpp_1.0.8 [29] xtable_1.8-4 promises_1.2.0.1 [31] scales_1.2.1 cachem_1.0.6 [33] DelayedArray_0.20.0 jsonlite_1.8.2 [35] XVector_0.34.0 mime_0.12 [37] Rsamtools_2.10.0 rjson_0.2.21 [39] digest_0.6.29 stringi_1.7.8 [41] Rtsne_0.16 BiocIO_1.4.0 [43] grid_4.1.2 cli_3.3.0 [45] tools_4.1.2 bitops_1.0-7 [47] sass_0.4.2 magrittr_2.0.3 [49] RCurl_1.98-1.6 cluster_2.1.2 [51] crayon_1.5.2 ellipsis_0.3.2 [53] Matrix_1.4-1 httr_1.4.4 [55] R6_2.5.1 GenomicAlignments_1.30.0 [57] compiler_4.1.2 What other diagnostics can I provide?

Or am I just using it incorrectly?

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[malcook]

Yes, in my hands inst/demos/igvShinyDemo.R suffers similarly - hg38 works fine and the sidebar pane buttons show the various tracks, but upon changing to danRer11, the app loads and shows the side bar pane (with Search, Add As Bed, etc) but the genome pane is blank.

Of possible additional diagnostic value to you is that upon initial display I see in R console:

Listening on http://0.0.0.0:9997
--- starting renderIgvShiny
--- ending renderIgvShiny
[1] --- igvReady
[1] igv ready, igvShiny_0
[1] --- igvReady
[1] igv ready, igvShiny_0

whereas changing to danRer11 shows only

Listening on http://0.0.0.0:9997
--- starting renderIgvShiny
--- ending renderIgvShiny

(you will note I changed the port to 9997 and host to 0.0.0.0, but it happens with original values too)

[malcook]

while I have your attention, once this works, should I expect to be able to display bigbed tracks?

[paul-shannon]

Please run inst/unitTests/test_genomeSpec.R. That may locate the problem.

Any track type supported by igv.js can be - of already is - supported by igvShiny.

I am sorry I cannot be more directly helpful this month - away from home, no laptop.

• Paul

On Oct 5, 2022, at 3:56 PM, Malcolm Cook @.***> wrote:

 Yes, in my hands inst/demos/igvShinyDemo.R suffers similarly - hg38 works fine and the sidebar pane buttons show the various tracks, but upon changing to danRer11, the app loads and shows the side bar pane (with Search, Add As Bed, etc) but the genome pane is blank.

Of possible additional diagnostic value to you is that upon initial display I see in R console:

Listening on http://0.0.0.0:9997 --- starting renderIgvShiny --- ending renderIgvShiny [1] --- igvReady [1] igv ready, igvShiny_0 [1] --- igvReady [1] igv ready, igvShiny_0 whereas changing to danRer11 shows only

Listening on http://0.0.0.0:9997 --- starting renderIgvShiny --- ending renderIgvShiny (you will note I changed the port to 9997 and host to 0.0.0.0, but it happens with original values too)

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[malcook]

sleuthing a little in your codebase for refereneces to hg38, I find this which leads me to test the other genomes similarly hardcoded (mm10, tair10, rhos) and find that:

• hg19 and mm10 both work
• tair10 - works, except for CORS related error [1]
• rhos fails with

  Currently supported: chm13v2.0,chm13v1.1,hg38,hg38_1kg,hg19,hg18,mm39,mm10,mm9,rn7,rn6,gorGor6,gorGor4,panTro6,panTro5,panTro4,macFas5,panPan2,canFam3,canFam5,bosTau9,bosTau8,susScr11,galGal6,danRer11,danRer10,ce11,dm6,dm3,dmel_r5.9,sacCer3,ASM294v2,ASM985889v3,tair10,GCA_003086295.2

So it seems that as written there is some hardcoded rigging needed in igvGenomes.js

[malcook]

inst/unitTests/test_genomeSpec.R yields:

runTests()
--- test_url.exists
--- test_supportedGenomes
Error in currently.supported.genomes() (from test_genomeSpec.R!W7QDWR#30) : 
  could not find function "currently.supported.genomes"

Commenting out that test - all others succeed.

Changing it to call currently.supported.stock.genomes instead of currently.supported.genomes (referencing igvR manual) and it now succeeds along with all other tests. i'm pretty sure my observation above about hardcoded options in the javascript library is where the issue lies.

Also, it continues to pass after adding "danRer11" to the list of stock genomes it asserts must be included.

[paul-shannon]

@malcook - Malcolm,

I hacked together a usable macbook/RStudio setup, but lack a git client. So I offer the fixed stock Genome code - a modified igvShiny.js and stockGenomesDemo.R - as a clumsy zip file here.

I hope that this is easy for you to blend with your current local version of igvShiny. When I get back to Seattle at the end of the month I will push this code to the master branch, run the tests, make more changes, to include:

• doing a long overdue refactoring of igvShiny.js genomeSpecificOptions function
• creating a new class for BedGraph tracks, supporting both local files and urls.

patch.zip

[paul-shannon]

@malcook - any feedback on this patch? I am now back in Seattle, about to push the changes, and I'd be grateful to hear from you if you made any use of the patch.

[paul-shannon]

igvShiny 1.5.8 supports all igv.js-provided stock genomes, test/demo in inst/demos/stockGenomesDemo.R

[malcook]

Hi. I wound up not using the patch as I had a workaround of using a local genome and it was easier to wait for this release, which I can confirm now works as expected for danRer11.

[paul-shannon]

Glad to hear this, Malcolm. I welcome other requests and bug reports.