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AnnotationHub::display() giving incorrect output #10

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MattBrauer opened this issue Oct 14, 2019 · 14 comments
Closed

AnnotationHub::display() giving incorrect output #10

MattBrauer opened this issue Oct 14, 2019 · 14 comments
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@lshep

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@MattBrauer
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Running on up-to-date installation:

library(AnnotationHub)
ah <- AnnotationHub()
d <- display(ah)

Results in pop-up with error:

DataTables warning: table id=DataTables_Table_0 - Requested unknown parameter '6' for row 0. For more information about this error, please see http://datatables.net/tn/4

and the table displayed is completely garbled:
ah_display

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

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  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] shiny_1.4.0           AnnotationHub_2.17.10 BiocFileCache_1.9.1
[4] dbplyr_1.4.2          BiocGenerics_0.31.6

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2                    pillar_1.4.2
 [3] compiler_3.6.1                BiocManager_1.30.7
 [5] later_1.0.0                   tools_3.6.1
 [7] zeallot_0.1.0                 digest_0.6.21
 [9] bit_1.1-14                    jsonlite_1.6
[11] RSQLite_2.1.2                 memoise_1.1.0
[13] tibble_2.1.3                  pkgconfig_2.0.3
[15] rlang_0.4.0                   DBI_1.0.0
[17] curl_4.2                      yaml_2.2.0
[19] fastmap_1.0.1                 dplyr_0.8.3
[21] httr_1.4.1                    IRanges_2.19.17
[23] vctrs_0.2.0                   S4Vectors_0.23.25
[25] rappdirs_0.3.1                stats4_3.6.1
[27] bit64_0.9-7                   tidyselect_0.2.5
[29] Biobase_2.45.1                glue_1.3.1
[31] R6_2.4.0                      AnnotationDbi_1.47.1
[33] purrr_0.3.2                   blob_1.2.0
[35] magrittr_1.5                  backports_1.1.5
[37] promises_1.1.0                htmltools_0.4.0
[39] assertthat_0.2.1              xtable_1.8-4
[41] mime_0.7                      interactiveDisplayBase_1.23.0
[43] httpuv_1.5.2                  crayon_1.3.4
@lshep
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lshep commented Oct 15, 2019

Thank you for bringing this to our attention. I am able to reproduce and I will look into the issue to see if it is directly in annotationhub or the underlying dependency.

In the meantime you might also try querying through the web app:
https://annotationhub.bioconductor.org/

@lshep lshep self-assigned this Oct 15, 2019
@lshep
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lshep commented Oct 15, 2019

It seems like this is an underlying problem with InteractiveDisplayBase as it is reproducible also with their example
interactiveDisplayBase::display(mtcars) I will send an issue to the interactiveDisplayBase package maintainers.

@BJWiley233
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Hi,

Getting same issue. Any update on this?

Brian

@lshep
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lshep commented Mar 2, 2020

Again - This is not an issue with AnnotationHub , it is actually stemming from the interactiveDisplayBase package - I have reached out to the maintainers and they have been unresponsive. I suggest also reaching out to the InteractiveDisplayBase maintainer too. Once the issue is fixed in that package I would assume it would clear up in AnnotationHub. This ERROR occurs with their example interactiveDisplayBase::display(mtcars) as well.

@lshep
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lshep commented Mar 2, 2020

In the meantime there is a user interface at https://annotationhub.bioconductor.org ; it is not quite as convenient as doing it directly in R and having the shiny app but a temporary solution until the underlying functionality is fixed.

@Chloe-Girard
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Hello!
The problem still occurs for me. Any updates? Thanks for your help!
In the meantime, I've been using the web browser interface, but as noted, it's not as convenient :)

Thanks for your help!

@LiNk-NY
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LiNk-NY commented May 27, 2020 •
edited

Hi Chloé @Chloe-Girard, Matt @MattBrauer, Brian @BJWiley233 ,

What is the main use of this function? I ask because I am reworking it and
I'd like to know what it is being used for.

Is it to select rows and get them back into an R session?

Are there any other features that you need from the package?
Sorry for the delay in getting this fixed.

Thank you,
Marcel

@Chloe-Girard
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Hello Marcel,
Yes, it would be to have a look at the different titles and see the different columns to make sure I'm selecting the right data sets. So mostly looking, being able to see what titles I'm querying (when <50-ish), and clicking is a bonus for me (I query anyway).

Let me know if this is useful,
Thanks!
Chloé

@LiNk-NY
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LiNk-NY commented Jun 1, 2020

Hi Chloé @Chloe-Girard and others, @MattBrauer @BJWiley233

I've sent a fix to Bioconductor. Let me know if you encounter any issues.
I tried to keep the changes minimal but simple to run. I reduced the shiny app
in complexity by updating it with the newer API. You can test drive if you download
from GitHub at BiocManager::install("LiNk-NY/interactiveDisplayBase") OR you
can wait until the changes are propagated in the build system (most likely tomorrow).

Thank you for your patience.

Best,
Marcel

@Chloe-Girard
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Chloe-Girard commented Jun 2, 2020 via email

@lshep
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lshep commented Jun 2, 2020

Thank you @LiNk-NY

@Chloe-Girard
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Chloe-Girard commented Jun 2, 2020 via email •
edited

@LiNk-NY
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LiNk-NY commented Jun 2, 2020

Hi Chloé, @Chloe-Girard

Can you provide the sessionInfo and a reproducible example?

Please make sure that you are not installing an older version of the package on top of the GitHub installation.

Also, I just updated the RELEASE_3_11 version of the package. If you are using release,
wait a day for the updates to propagate to the Bioconductor repository.

Best,
Marcel

@lshep
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lshep commented Jun 5, 2020

This seems to be fixed in release Bioc 3.11 and devel Bioc 3.12. Must use interactiveDisplayBase version 1.27.5 in devel 3.12 and version 1.26.3 in release 3.11. Cheers. Thanks @LiNk-NY

@lshep lshep closed this as completed Jun 5, 2020
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5 participants
@MattBrauer @LiNk-NY @lshep @BJWiley233 @Chloe-Girard