Question

BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR

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shepherl 4.1k

@lshep

Last seen 2 days ago

United States

There was a bug reported relating to BiocFileCache compatibility with the new version dbplyr. This affected BiocFileCache, ExperimentHub, and AnnotationHub. This has already been corrected in BiocFileCache versions 2.10.1 (Release_3_18) and 2.11.1 (devel/3.19) respectively. These versions were pushed up this morning and should be available after tomorrow's daily build. You can install from BiocFileCache github as a temporary workaround for the next 24 hours. Sorry for the inconvenience.

BiocFileCache AnnotationHub ExperimentHub • 6.9k views

ADD COMMENT • link 13 months ago • updated 7 months ago shepherl 4.1k

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Kindly help:

I am getting this error when I try to run this code: ah <- AnnotationHub()

Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect()

Do you have any suggestions?

Note that I have R version 4.3.1 and 2023.09.1 Build 494

ADD REPLY • link 13 months ago BS • 0

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I was getting a similar error when running hub <- AnnotationHub() on one machine but not another.

On an RStudio Server running R version 4.3.0 (2023-04-21) [platform: x86_64-pc-linux-gnu], the above command works, returning snapshotDate(): 2023-04-25.

On RStudio on my Mac running R version 4.3.1 (2023-06-16) [platform: x86_64-apple-darwin20], the above command returned:

Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. Problematic argument: ..1 = Inf Did you misspell an argument name? Run rlang::last_trace() to see where the error occurred.

I noticed that I had BiocFileCache 2.8.0 in both implementations, so I tried to update the package to 2.11.0 in RStudio on my Mac by running BiocManager::install(pkgs = c("BiocFileCache"), update = TRUE), but that didn't update the package, responding that I already had the most update package. However, when I ran BiocManager::install("Bioconductor/BiocFileCache"), the package did update to 2.11.0.

After restarting RStudio, I found that the above command does work now, returning snapshotDate(): 2023-04-25.

ADD REPLY • link 12 months ago wmorgan ▴ 10

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Would this work for R version 4.2.1? I am afraid upgrading R might cause a whole lot of dependency issues with other packages in my ongoing project.

ADD REPLY • link 11 months ago Mansi • 0

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Installing the package manually should work with the latest BiocFileCache BiocManager::install("Bioconductor/BiocFileCache"), but you will not be able to get it using just BiocManager("BiocFileCache") since R/Bioc/packages are closely tied to an R release the default will always make it appropriate for your version of R; it is not guaranteed to work correctly if not running on the current R with the appropriately tested package dependencies but it should.

ADD REPLY • link 11 months ago shepherl 4.1k

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update BiocFileCache and then restarting Rstudio, it did work! Thanks for your solution!

ADD REPLY • link 10 months ago pyhu • 0

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Thank you so much for these comment! I had the same issue and downloaded the source file to update and also needed to restart RStudio even though it appeared to update the package, still needed to restart.

ADD REPLY • link 8 months ago Melissa • 0

score 1 · Answer 1 · 2023-10-27

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shepherl 4.1k

@lshep

Last seen 2 days ago

United States

You commented in this issue as well Annotation hub and clusterProfiler errors where you still have the original version of the package. As mentioned here and there, this is corrected in versions 2.10.1 and 2.11.1 respectively for release and devel. You can either wait the 24 (48 hr max) for it to propagate on the build system and use BiocManager::install("BiocFileCache") or you can install from github temporarily BiocManager::install("Bioconductor/BiocFileCache")

ADD COMMENT • link 13 months ago shepherl 4.1k

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Neither of these solutions work for me, I get stuck with this error:

ERROR: configuration failed for package lwgeom

ADD REPLY • link 12 months ago christopherjamessteel1990 • 0

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We cannot help you if you do not show the full code you tried and output.

ADD REPLY • link 12 months ago shepherl 4.1k

score 0 · Answer 2 · 2024-04-21

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CP • 0

@a2a7fc75

Last seen 5 months ago

United States

Hi!

I tried the solution. They did not work for me either.

> ah <- AnnotationHub()

Error in collect(): Failed to collect lazy table. Caused by error in db_collect() Arguments in ... must be used. Problematic argument:1 = Inf Did you misspell an argument name? Run rlang::last_trace() to see where the error occurred.

ADD COMMENT • link 7 months ago CP • 0

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Hi

I got to solve it by installing BiocFileCache from github.This library influences AnnotationHub and others. It did not work by reinstalling using BiocManager.

devtools::install_github('https://github.com/Bioconductor/BiocFileCache.git')

ADD REPLY • link 7 months ago CP • 0

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Likely you are using a version of R and Bioconductor that occurred after the fix was introduced in the BiocFileCache code base. This has to do with dplyr/dbplyr updates that occurred.
The recommended fix is using BiocArchive that will match the versions of CRAN and Bioconductor package appropriately for the version of R you have installed

install.packages(c("devtools", "lubridate"))
devtools::install_github("Bioconductor/BiocArchive")
BiocArchive::install("AnnotationHub")
ah <- AnnotationHub::AnnotationHub()

ADD REPLY • link 7 months ago shepherl 4.1k