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neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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Unable to find chain files on `AnnotationHub` #105

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

1. Bug description

liftover_grlist is unable to find the proper chain files on AnnotationHub, but only on certain platforms (or randomly?).

https://github.com/neurogenomics/EpiCompare/runs/7675828861?check_suite_focus=true

Console output

Preparing chain file.
snapshotDate(): 2022-08-04
downloading 1 resources
retrieving 1 resource
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/18245’
  local file path: ‘/github/home/.cache/R/AnnotationHub/1576625c39d6_18245’
  reason: Internal Server Error (HTTP 500).
Warning: bfcadd() failed; resource removed
  rid: BFC3
  fpath: ‘https://annotationhub.bioconductor.org/fetch/18245’
  reason: download failed
Warning: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/18245’
  cache resource: ‘AH14150 : 18245’
  reason: bfcadd() failed; see warnings()
Error: failed to load resource
  name: AH14150
  title: hg19ToHg38.over.chain.gz
  reason: 1 resources failed to download
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [[127](https://github.com/neurogenomics/EpiCompare/runs/7675828861?check_suite_focus=true#step:23:128)s/[134](https://github.com/neurogenomics/EpiCompare/runs/7675828861?check_suite_focus=true#step:23:135)s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. └─EpiCompare::liftover_grlist(...) at test-liftover_grlist.R:10:4
    2.   └─EpiCompare:::get_chain_file(...)
    3.     ├─ah[["AH[141](https://github.com/neurogenomics/EpiCompare/runs/7675828861?check_suite_focus=true#step:23:142)50"]]
    4.     └─ah[["AH14[150](https://github.com/neurogenomics/EpiCompare/runs/7675828861?check_suite_focus=true#step:23:151)"]]
    5.       └─AnnotationHub (local) .local(x, i, j = j, ...)
    6.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
    7.           └─base::tryCatch(...)
    8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.                 └─value[[3L]](cond)

Expected behaviour

AnnotationHub files are accessible regardless of platform.

2. Reproducible example

Code

> grlist <- list("gr1"=GenomicRanges::GRanges("4:1-100000"),
+                "gr2"=GenomicRanges::GRanges("6:1-100000"),
+                "gr3"=GenomicRanges::GRanges("8:1-100000"))
> 
> grlist_lifted <- liftover_grlist(grlist = grlist,
+                                  input_build = "hg19",
+                                  output_build="hg38")

3. Session info

``` Loading required package: sessioninfo ─ Session info ─────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.2.1 (2022-06-23) os macOS Big Sur ... 10.16 system x86_64, darwin17.0 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz UTC date 2022-08-04 pandoc 2.7.3 @ /usr/local/bin/pandoc ─ Packages ─────────────────────────────────────────────────────────────────────────────────────── ! package * version date (UTC) lib source annotate 1.74.0 2022-04-26 [1] Bioconductor AnnotationDbi 1.58.0 2022-04-26 [1] Bioconductor AnnotationHub 3.4.0 2022-04-26 [1] Bioconductor RUnit 0.4.[32](https://github.com/neurogenomics/EpiCompare/runs/7675828999?check_suite_focus=true#step:20:33) 2018-05-18 [1] CRAN (R 4.2.0) rvcheck 0.2.1 2021-10-22 [1] CRAN (R 4.2.0) S4Vectors 0.[34](https://github.com/neurogenomics/EpiCompare/runs/7675828999?check_suite_focus=true#step:20:35).0 2022-04-26 [1] Bioconductor sass 0.4.2 2022-07-16 [1] CRAN (R 4.2.0) scales 1.2.0 2022-04-13 [1] CRAN (R 4.2.0) scatterpie 0.1.7 2021-08-20 [1] CRAN (R 4.2.0) seqPattern 1.28.0 2022-04-26 [1] Bioconductor sessioninfo * 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) shadowtext 0.1.2 2022-04-22 [1] CRAN (R 4.2.0) shiny 1.7.2 2022-07-19 [1] CRAN (R 4.2.0) snow 0.4-4 2021-10-27 [1] CRAN (R 4.2.0) sourcetools 0.1.7 2018-04-25 [1] CRAN (R 4.2.0) spatial 7.3-15 2022-01-16 [2] CRAN (R 4.2.1) splines 4.2.1 2022-06-24 [?] local P stats * 4.2.1 2022-06-24 [2] local stats4 4.2.1 2022-06-24 [?] local stringdist 0.9.8 2021-09-09 [1] CRAN (R 4.2.0) stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0) stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0) SummarizedExperiment 1.26.1 2022-05-01 [1] Bioconductor survival 3.3-1 2022-03-03 [2] CRAN (R 4.2.1) sys 3.4 2020-07-23 [1] CRAN (R 4.2.0) tcltk 4.2.1 2022-06-24 [?] local testthat 3.1.4 2022-04-26 [1] CRAN (R 4.2.0) tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) tidygraph 1.2.1 2022-04-05 [1] CRAN (R 4.2.0) tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.2.0) tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0) tidytree 0.3.9 2022-03-04 [1] CRAN (R 4.2.0) tinytex 0.40 2022-06-15 [1] CRAN (R 4.2.0) P tools 4.2.1 2022-06-24 [2] local treeio 1.20.1 2022-07-14 [1] Bioconductor tweenr 1.0.2 2021-03-23 [1] CRAN (R 4.2.0) TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 2022-08-04 [1] Bioconductor TxDb.Hsapiens.UCSC.hg38.knownGene 3.15.0 2022-08-04 [1] Bioconductor TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0 2022-08-04 [1] Bioconductor TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2 2022-08-04 [1] Bioconductor tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0) UpSetR 1.4.0 2019-05-22 [1] CRAN (R 4.2.0) usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) P utils * 4.2.1 2022-06-24 [2] local vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) viridis 0.6.2 2021-10-13 [1] CRAN (R 4.2.0) viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.2.0) vroom 1.5.7 2021-11-30 [1] CRAN (R 4.2.0) waldo 0.4.0 2022-03-16 [1] CRAN (R 4.2.0) whisker 0.4 2019-08-28 [1] CRAN (R 4.2.0) withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0) XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.2.0) xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0) xopen 1.0.0 2018-09-17 [1] CRAN (R 4.2.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0) XVector 0.[36](https://github.com/neurogenomics/EpiCompare/runs/7675828999?check_suite_focus=true#step:20:37).0 2022-04-26 [1] Bioconductor yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) yulab.utils 0.0.5 2022-06-30 [1] CRAN (R 4.2.0) zip 2.2.0 2021-05-31 [1] CRAN (R 4.2.0) zlibbioc 1.[42](https://github.com/neurogenomics/EpiCompare/runs/7675828999?check_suite_focus=true#step:20:43).0 2022-04-26 [1] Bioconductor [1] /Users/runner/work/_temp/Library [2] /Library/Frameworks/R.framework/Versions/4.2/Resources/library P ── Loaded and on-disk path mismatch. ```
bschilder commented 2 years ago

Turns out this was a temporary issue due to problems with the Bioc server internet connection. This caused similar issues in other packages: https://github.com/rikenbit/meshr/issues/1

Now seems to be running fine: https://github.com/neurogenomics/EpiCompare/runs/8018488988?check_suite_focus=true