AnnotationHub::display() giving incorrect output

[MattBrauer]

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:

> 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]

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]

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]

Hi,

Getting same issue. Any update on this?

Brian

[lshep]

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]

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]

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]

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]

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]

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]

Thanks! Will do :)

On Mon, Jun 1, 2020 at 10:26 PM Marcel Ramos notifications@github.com wrote:

Hi Chloé @Chloe-Girard https://github.com/Chloe-Girard and others, @MattBrauer https://github.com/MattBrauer @BJWiley233 https://github.com/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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/AnnotationHub/issues/10#issuecomment-637083666, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMKJ435K4Z44YNTSD7IKYH3RUQFFRANCNFSM4JAUCANA .

-- Chloé

[lshep]

Thank you @LiNk-NY

[Chloe-Girard]

So... still doesn't work in my hands.

What I did was: using R studio with R version 4.0.0 (2020-04-24) -- "Arbor Day" macOS Mojave Version 10.14.6

ahub <- AnnotationHub() snapshotDate(): 2020-04-27

qh <- query(ahub, "Scerevisiae")) qh AnnotationHub with 19 records

snapshotDate(): 2020-04-27

$dataprovider: Ensembl, FungiDB, UCSC

$species: Saccharomyces cerevisiae, Saccharomyces cerevisiae S288C

$rdataclass: EnsDb, TxDb, GRanges

additional mcols(): taxonomyid, genome, description, coordinate_1_based,

maintainer,

rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype

retrieve records with, e.g., 'object[["AH52271"]]'

        title

AH52271 | TxDb.Scerevisiae.UCSC.sacCer2.sgdGene.sqlite AH52272 | TxDb.Scerevisiae.UCSC.sacCer3.sgdGene.sqlite AH53241 | Ensembl 87 EnsDb for Saccharomyces Cerevisiae AH53745 | Ensembl 88 EnsDb for Saccharomyces Cerevisiae AH56711 | Ensembl 89 EnsDb for Saccharomyces Cerevisiae ... ... AH74136 | Transcript information for Saccharomyces cerevisiae S288c AH74775 | Transcript information for Saccharomyces cerevisiae S288c AH75092 | Ensembl 98 EnsDb for Saccharomyces cerevisiae AH78877 | Ensembl 99 EnsDb for Saccharomyces cerevisiae AH79782 | Ensembl 100 EnsDb for Saccharomyces cerevisiae

Then I tried to install your package

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("LiNk-NY/interactiveDisplayBase") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24) Installing github package(s) 'LiNk-NY/interactiveDisplayBase'

[...] #it installed the package ` At the end, it prompted me to update some packages, and I got an error (not finding Xcode...)

Do you want to install from sources the package which needs compilation?

(Yes/no/cancel) yes installing the source package ‘rtracklayer’

essai de l'URL ' https://bioconductor.org/packages/3.11/bioc/src/contrib/rtracklayer_1.48.0.tar.gz ' Content type 'application/x-gzip' length 4012631 bytes (3.8 MB)

downloaded 3.8 MB

• installing source package ‘rtracklayer’ ... using staged installation checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... no configure: creating ./config.status config.status: creating src/Makevars libs dyld: Library not loaded: @rpath/DVTFoundation.framework/Versions/A/DVTFoundation Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild Reason: no suitable image found. Did find: /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation: cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation' because Objective-C garbage collection is not supported xcrun: error: unable to locate xcodebuild, please make sure the path to the Xcode folder is set correctly! xcrun: error: You can set the path to the Xcode folder using /usr/bin/xcode-select -switch ERROR: compilation failed for package ‘rtracklayer’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rtracklayer’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rtracklayer’

The downloaded source packages are in

‘/private/var/folders/2b/hjdl8syn5153mdbpn0fpb8k00000gn/T/RtmpTz5abz/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘rtracklayer’ had non-zero exit status

Then I tried to display my query

d <- display(qh)

Listening on http://127.0.0.1:5399 Warning in checkDT9(options) : shiny (>= 0.10.2) has upgraded DataTables from 1.9.4 to 1.10.2, and DataTables 1.10.x uses different parameter names with 1.9.x. Please follow the upgrade guide https://datatables.net/upgrade/1.10-convert to change your DataTables parameter names:

• bSortClasses
• aLengthMenu
• iDisplayLength
• sDom

I got a window prompting the following message:

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

Here is a picture of the viewer:

Thanks for all you do

Chloé

[LiNk-NY]

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]

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