error, unsupported genome: 'hg19'
duleise opened this issue · 12 comments
duleise commented
My used-to-working-fine codes gave me this error. I hope it is temporary. Anyone else has the same?
> setGenome(igv, "hg19")
error, unsupported genome: 'hg19'
paul-shannon commented
Hi Otto,
Sorry for the trouble. Can you run
sessionInfo()
and provide the results? That will help me track down the problem.
- Paul
… On Oct 18, 2019, at 5:22 AM, Otto Bergman ***@***.***> wrote:
My used-to-working-fine codes gave me this error. I hope it is temporary. Anyone else has the same?
> setGenome(igv, "hg19")
error, unsupported genome: 'hg19'
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duleise commented
hi, Paul, thank you for such a prompt reply.
I restarted a clean session and had the same error. Here is my sessionInfo.
The only suspicious action I can think of is, I updated to macOS Catalina.
/Otto
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] igvR_1.5.34 BrowserViz_2.7.18 httpuv_1.5.2 jsonlite_1.6
[5] GenomicAlignments_1.21.7 Rsamtools_2.1.7 Biostrings_2.53.2 XVector_0.25.0
[9] SummarizedExperiment_1.15.9 DelayedArray_0.11.8 BiocParallel_1.19.4 matrixStats_0.55.0
[13] Biobase_2.45.1 GenomicRanges_1.37.17 GenomeInfoDb_1.21.2 IRanges_2.19.17
[17] S4Vectors_0.23.25 BiocGenerics_0.31.6
loaded via a namespace (and not attached):
[1] httr_1.4.1 bit64_0.9-7 assertthat_0.2.1 askpass_1.1 BiocFileCache_1.9.1
[6] blob_1.2.0 BSgenome_1.53.2 GenomeInfoDbData_1.2.1 progress_1.2.2 pillar_1.4.2
[11] RSQLite_2.1.2 backports_1.1.5 lattice_0.20-38 glue_1.3.1 digest_0.6.21
[16] promises_1.1.0 colorspace_1.4-1 Matrix_1.2-17 XML_3.98-1.20 pkgconfig_2.0.3
[21] biomaRt_2.41.9 zlibbioc_1.31.0 purrr_0.3.2 scales_1.0.0 later_1.0.0
[26] Rtsne_0.15 tibble_2.1.3 openssl_1.4.1 GenomicFeatures_1.37.4 randomcoloR_1.1.0
[31] splitstackshape_1.4.8 magrittr_1.5 crayon_1.3.4 memoise_1.1.0 tools_3.6.1
[36] data.table_1.12.2 prettyunits_1.0.2 hms_0.5.1 stringr_1.4.0 V8_2.3
[41] munsell_0.5.0 cluster_2.1.0 AnnotationDbi_1.47.1 compiler_3.6.1 rlang_0.4.0
[46] MotifDb_1.27.0 grid_3.6.1 RCurl_1.95-4.12 VariantAnnotation_1.31.6 rappdirs_0.3.1
[51] bitops_1.0-6 DBI_1.0.0 curl_4.2 R6_2.4.0 dplyr_0.8.3
[56] seqLogo_1.51.0 rtracklayer_1.45.6 bit_1.1-14 zeallot_0.1.0 stringi_1.4.3
[61] Rcpp_1.0.2 vctrs_0.2.0 dbplyr_1.4.2 tidyselect_0.2.5
paul-shannon commented
Thanks, Otto. I am puzzled. Your versions are quite (but not completely) up to date. And setGenome(igv, “hg19”) is the most basic test - which (for me) runs daily.
Can I trouble you to upgrade to yesterday’s version, 1.5.36? For that version I added more genomes.
intall_github(“paul-shannon/igvR”) ought to do it.
Then:
igv <- igvR()
getSupportedGenomes(igv)
"hg38" "hg19" "hg18" "mm10" "gorgor4" "pantro4”
"panpan2" "susscr11" "bostau8" "canfam3" "rn6" "danrer11”
"danrer10" "dm6" "ce11" "saccer3" "tair10" "pfal3d7”
setGenome(igv, "hg19”) # works
- Paul
… On Oct 18, 2019, at 6:10 AM, Otto Bergman ***@***.***> wrote:
hi, Paul, thank you for such a prompt reply.
I restarted a clean session and had the same error. Here is my sessionInfo.
The only suspicious action I can think of is, I updated to macOS Catalina.
/Otto
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] igvR_1.5.34 BrowserViz_2.7.18 httpuv_1.5.2 jsonlite_1.6
[5] GenomicAlignments_1.21.7 Rsamtools_2.1.7 Biostrings_2.53.2 XVector_0.25.0
[9] SummarizedExperiment_1.15.9 DelayedArray_0.11.8 BiocParallel_1.19.4 matrixStats_0.55.0
[13] Biobase_2.45.1 GenomicRanges_1.37.17 GenomeInfoDb_1.21.2 IRanges_2.19.17
[17] S4Vectors_0.23.25 BiocGenerics_0.31.6
loaded via a namespace (and not attached):
[1] httr_1.4.1 bit64_0.9-7 assertthat_0.2.1 askpass_1.1 BiocFileCache_1.9.1
[6] blob_1.2.0 BSgenome_1.53.2 GenomeInfoDbData_1.2.1 progress_1.2.2 pillar_1.4.2
[11] RSQLite_2.1.2 backports_1.1.5 lattice_0.20-38 glue_1.3.1 digest_0.6.21
[16] promises_1.1.0 colorspace_1.4-1 Matrix_1.2-17 XML_3.98-1.20 pkgconfig_2.0.3
[21] biomaRt_2.41.9 zlibbioc_1.31.0 purrr_0.3.2 scales_1.0.0 later_1.0.0
[26] Rtsne_0.15 tibble_2.1.3 openssl_1.4.1 GenomicFeatures_1.37.4 randomcoloR_1.1.0
[31] splitstackshape_1.4.8 magrittr_1.5 crayon_1.3.4 memoise_1.1.0 tools_3.6.1
[36] data.table_1.12.2 prettyunits_1.0.2 hms_0.5.1 stringr_1.4.0 V8_2.3
[41] munsell_0.5.0 cluster_2.1.0 AnnotationDbi_1.47.1 compiler_3.6.1 rlang_0.4.0
[46] MotifDb_1.27.0 grid_3.6.1 RCurl_1.95-4.12 VariantAnnotation_1.31.6 rappdirs_0.3.1
[51] bitops_1.0-6 DBI_1.0.0 curl_4.2 R6_2.4.0 dplyr_0.8.3
[56] seqLogo_1.51.0 rtracklayer_1.45.6 bit_1.1-14 zeallot_0.1.0 stringi_1.4.3
[61] Rcpp_1.0.2 vctrs_0.2.0 dbplyr_1.4.2 tidyselect_0.2.5
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duleise commented
hi, Paul. Thanks. I have upgraded to the latest on github.
> getSupportedGenomes(igv)
[1] "hg38" "hg19" "hg18" "mm10" "gorgor4" "pantro4" "panpan2" "susscr11" "bostau8" "canfam3" "rn6"
[12] "danrer11" "danrer10" "dm6" "ce11" "saccer3" "tair10" "pfal3d7"
> setGenome(igv, "hg19")
error, unsupported genome: 'hg19'
> setGenome(igv, "hg38")
error, unsupported genome: 'hg38'
And the sessionInfo is
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] igvR_1.5.37 BrowserViz_2.7.18 httpuv_1.5.2 jsonlite_1.6
[5] GenomicAlignments_1.21.7 Rsamtools_2.1.7 Biostrings_2.53.2 XVector_0.25.0
[9] SummarizedExperiment_1.15.9 DelayedArray_0.11.8 BiocParallel_1.19.4 matrixStats_0.55.0
[13] Biobase_2.45.1 GenomicRanges_1.37.17 GenomeInfoDb_1.21.2 IRanges_2.19.17
[17] S4Vectors_0.23.25 BiocGenerics_0.31.6
loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.3.1 usethis_1.5.1 devtools_2.2.1 bit64_0.9-7
[6] progress_1.2.2 httr_1.4.1 rprojroot_1.3-2 tools_3.6.1 backports_1.1.5
[11] R6_2.4.0 colorspace_1.4-1 seqLogo_1.51.0 DBI_1.0.0 splitstackshape_1.4.8
[16] withr_2.1.2 tidyselect_0.2.5 prettyunits_1.0.2 processx_3.4.1 bit_1.1-14
[21] curl_4.2 compiler_3.6.1 cli_1.1.0 desc_1.2.0 rtracklayer_1.45.6
[26] scales_1.0.0 callr_3.3.2 askpass_1.1 rappdirs_0.3.1 stringr_1.4.0
[31] digest_0.6.21 pkgconfig_2.0.3 sessioninfo_1.1.1 dbplyr_1.4.2 BSgenome_1.53.2
[36] rlang_0.4.0 RSQLite_2.1.2 dplyr_0.8.3 VariantAnnotation_1.31.6 RCurl_1.95-4.12
[41] magrittr_1.5 GenomeInfoDbData_1.2.1 Matrix_1.2-17 munsell_0.5.0 Rcpp_1.0.2
[46] stringi_1.4.3 zlibbioc_1.31.0 Rtsne_0.15 pkgbuild_1.0.6 BiocFileCache_1.9.1
[51] grid_3.6.1 blob_1.2.0 randomcoloR_1.1.0 promises_1.1.0 crayon_1.3.4
[56] lattice_0.20-38 GenomicFeatures_1.37.4 hms_0.5.1 zeallot_0.1.0 ps_1.3.0
[61] pillar_1.4.2 biomaRt_2.41.9 pkgload_1.0.2 XML_3.98-1.20 glue_1.3.1
[66] V8_2.3 data.table_1.12.2 remotes_2.1.0 vctrs_0.2.0 testthat_2.2.1
[71] openssl_1.4.1 purrr_0.3.2 assertthat_0.2.1 later_1.0.0 MotifDb_1.27.0
[76] tibble_2.1.3 AnnotationDbi_1.47.1 memoise_1.1.0 cluster_2.1.0 ellipsis_0.3.0
Let me try to find more symptom.
paul-shannon commented
Thank, Otto. Let’s figure this out.
A clue may come from the Javascript console. After I call
R> setGenome(igv, “hg19”)
the console shows:
…--- igvApp.js, initializeIGV
(index):666 actual genome name we will use: hg19
On Oct 18, 2019, at 6:40 AM, Otto Bergman ***@***.***> wrote:
hi, Paul. Thanks. I have upgraded to the latest on github.
> getSupportedGenomes(igv)
[1] "hg38" "hg19" "hg18" "mm10" "gorgor4" "pantro4" "panpan2" "susscr11" "bostau8" "canfam3" "rn6"
[12] "danrer11" "danrer10" "dm6" "ce11" "saccer3" "tair10" "pfal3d7"
> setGenome(igv, "hg19")
error, unsupported genome: 'hg19'
> setGenome(igv, "hg38")
error, unsupported genome: 'hg38'
And the sessionInfo is
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] igvR_1.5.37 BrowserViz_2.7.18 httpuv_1.5.2 jsonlite_1.6
[5] GenomicAlignments_1.21.7 Rsamtools_2.1.7 Biostrings_2.53.2 XVector_0.25.0
[9] SummarizedExperiment_1.15.9 DelayedArray_0.11.8 BiocParallel_1.19.4 matrixStats_0.55.0
[13] Biobase_2.45.1 GenomicRanges_1.37.17 GenomeInfoDb_1.21.2 IRanges_2.19.17
[17] S4Vectors_0.23.25 BiocGenerics_0.31.6
loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.3.1 usethis_1.5.1 devtools_2.2.1 bit64_0.9-7
[6] progress_1.2.2 httr_1.4.1 rprojroot_1.3-2 tools_3.6.1 backports_1.1.5
[11] R6_2.4.0 colorspace_1.4-1 seqLogo_1.51.0 DBI_1.0.0 splitstackshape_1.4.8
[16] withr_2.1.2 tidyselect_0.2.5 prettyunits_1.0.2 processx_3.4.1 bit_1.1-14
[21] curl_4.2 compiler_3.6.1 cli_1.1.0 desc_1.2.0 rtracklayer_1.45.6
[26] scales_1.0.0 callr_3.3.2 askpass_1.1 rappdirs_0.3.1 stringr_1.4.0
[31] digest_0.6.21 pkgconfig_2.0.3 sessioninfo_1.1.1 dbplyr_1.4.2 BSgenome_1.53.2
[36] rlang_0.4.0 RSQLite_2.1.2 dplyr_0.8.3 VariantAnnotation_1.31.6 RCurl_1.95-4.12
[41] magrittr_1.5 GenomeInfoDbData_1.2.1 Matrix_1.2-17 munsell_0.5.0 Rcpp_1.0.2
[46] stringi_1.4.3 zlibbioc_1.31.0 Rtsne_0.15 pkgbuild_1.0.6 BiocFileCache_1.9.1
[51] grid_3.6.1 blob_1.2.0 randomcoloR_1.1.0 promises_1.1.0 crayon_1.3.4
[56] lattice_0.20-38 GenomicFeatures_1.37.4 hms_0.5.1 zeallot_0.1.0 ps_1.3.0
[61] pillar_1.4.2 biomaRt_2.41.9 pkgload_1.0.2 XML_3.98-1.20 glue_1.3.1
[66] V8_2.3 data.table_1.12.2 remotes_2.1.0 vctrs_0.2.0 testthat_2.2.1
[71] openssl_1.4.1 purrr_0.3.2 assertthat_0.2.1 later_1.0.0 MotifDb_1.27.0
[76] tibble_2.1.3 AnnotationDbi_1.47.1 memoise_1.1.0 cluster_2.1.0 ellipsis_0.3.0
Let me try to find more symptom.
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duleise commented
Thanks Paul. I have little knowledge on Javascript.
I will try it after a system reboot but I am in the middle of something now.
Let me know if there is any test I can do from my end.
paul-shannon commented
Sure - let me help when you have time to pursue this.
Which web browser do you use? Almost all have an easy command, usually available from a menu, which opens the Javascript console. Nothing else is needed: our Javascript code writes messages to the console, and we may be able to figure out what the problem is. I can add more diagnostic code that will appear there.
If you use chrome, you can open the Javascript console like this:
View -> Developer -> Javascript Console
Thanks for your patience!
- Paul
… On Oct 18, 2019, at 6:51 AM, Otto Bergman ***@***.***> wrote:
Thanks Paul. I have little knowledge on Javascript.
I will try it after a system reboot but I am in the middle of something now.
Let me know if there is any test I can do from my end.
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duleise commented
Thanks Paul. This is the contents in my Chrome after I initiated igvR().
== localhost addOnDocumentReadyFunction
(index):198 typeof(func): function
(index):203 == after push, count: 1
(index):393 === starting bv.start, state? loading
(index):379 === starting bv.init
(index):232 browserViz.js, initializeWebSocket, uri: ws://localhost:15003/
(index):387 === concluding bv.init
(index):218 23 jan 1:45p
(index):221 doc ready functions, count: 1
(index):224 browserviz.js, calling on ready function
(index):121 === BrowserViz.js, websocket connection now open.
(index):130 === BrowserViz.js, message received: setWindowTitle
(index):264 === BrowserViz.js, dispatchMessage: setWindowTitle
(index):276 dispatching for setWindowTitle
(index):334 ==== entering browserviz.setWindowTitle, whose notion of this is:
(index):335 Object
(index):336 ==== msg:
(index):337 Object
(index):339 Object
(index):285 === BrowserViz send:
(index):286 Object
DevTools failed to parse SourceMap: http://localhost:15003/igv.min.js.map
DevTools failed to parse SourceMap: http://localhost:15003/igv.css.map
paul-shannon commented
Good! Can you also send me the text which appears in the console when you enter the R command:
R> setGenome(igv, “hg19”)
… On Oct 18, 2019, at 8:01 AM, Otto Bergman ***@***.***> wrote:
Thanks Paul. This is the contents in my Chrome after I initiated igvR().
== localhost addOnDocumentReadyFunction
(index):198 typeof(func): function
(index):203 == after push, count: 1
(index):393 === starting bv.start, state? loading
(index):379 === starting bv.init
(index):232 browserViz.js, initializeWebSocket, uri: ws://localhost:15003/
(index):387 === concluding bv.init
(index):218 23 jan 1:45p
(index):221 doc ready functions, count: 1
(index):224 browserviz.js, calling on ready function
(index):121 === BrowserViz.js, websocket connection now open.
(index):130 === BrowserViz.js, message received: setWindowTitle
(index):264 === BrowserViz.js, dispatchMessage: setWindowTitle
(index):276 dispatching for setWindowTitle
(index):334 ==== entering browserviz.setWindowTitle, whose notion of this is:
(index):335 Object
(index):336 ==== msg:
(index):337 Object
(index):339 Object
(index):285 === BrowserViz send:
(index):286 Object
DevTools failed to parse SourceMap: http://localhost:15003/igv.min.js.map
DevTools failed to parse SourceMap: http://localhost:15003/igv.css.map
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duleise commented
I don't know what to say. It worked! And I definitely did nothing...
paul-shannon commented
@duleise I suppose that's good news! But far better it would be if I could figure out what caused the problem. Will you let me know if it comes up again? Along with any other problems you encounter, requests for features you would like to see?
duleise commented
Thank you so much, Paul. What happened today is unexplainable, at least to me. I will surely report it if it comes again.
I have been constantly using your package since before this summer and will most likely continue using it for quite a while. It's been a pleasure.
I have asked about a trivial feature in another thread and you have answered.
Working on a paper now and will definitely thank you in it.