[Bioc-devel] ExperimentHub: bad restore file magic number (file may be corrupted)

[Kern, Lori]

It looks like the download got corrupted.  I reset the cache for that EH number and it should clear up on the next build.




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Michael Love <michaelisaiahlove using gmail.com>
Sent: Tuesday, January 10, 2023 9:40 AM
To: bioc-devel <bioc-devel using r-project.org>
Subject: [Bioc-devel] ExperimentHub: bad restore file magic number (file may be corrupted)

In the latest release, one of my files in ExperimentHub is giving the
following error on Bioc machines. I haven't touched these files since
they were submitted many years ago to EHub.

http://secure-web.cisco.com/12y5s79xt-pmTPP6fzsYkMo0aALvDKgR-cUjxZcIL7QocYem0ml4eV-pkh4oqQlVq8ZteIbXcu42Ee2A76ClYhjiLHejdzRpRUWm2tCUEwNc6KBS1AiYDSfsOBC3dQ5mK3b3HgrhfvfXRVwW9TNr64PoANtPMDKwcwCG6aYF-RqHQHmvHDx5W2NluvaWlSV8u3wLL4iE0yfBocZDajrHg02fNfdqKkIbJF_iMnVNrLL950twq0FdVn9plKReI2-Eb1eI4a4OxMYO82sikXLqQmnE3w6f5KD--82FtxHaPjkXqyQSvQbRXLuH3ZBS2ussl/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fdata-experiment-LATEST%2FalpineData%2Fnebbiolo2-buildsrc.html

...
--- re-building �alpineData.Rmd� using knitr
Quitting from lines 18-22 (alpineData.Rmd)
Error: processing vignette 'alpineData.Rmd' failed with diagnostics:
failed to load resource
  name: EH167
  title: ERR188088
  reason: error in evaluating the argument 'x' in selecting a method
for function 'get': bad restore file magic number (file may be
corrupted) -- no data loaded
--- failed re-building �alpineData.Rmd�

On my machine I can load this resource:

 > library(alpineData)
!> ERR188088()
 snapshotDate(): 2022-10-31
 see ?alpineData and browseVignettes('alpineData') for documentation
 loading from cache
 GAlignmentPairs object with 28576 pairs, strandMode=1, and 0 metadata columns:
           seqnames strand   :              ranges  --              ranges
              <Rle>  <Rle>   :           <IRanges>  --           <IRanges>
       [1]        1      -   : 108565979-108566053  -- 108565846-108565920
       [2]        1      -   : 108573341-108573415  -- 108573234-108573308
       [3]        1      +   : 108581087-108581161  -- 108581239-108581313
       [4]        1      +   : 108601105-108601179  -- 108601196-108601270
       [5]        1      -   : 108603628-108603701  -- 108603540-108603614
       ...      ...    ... ...                 ... ...                 ...
   [28572]        X      -   : 119791266-119791340  -- 119791130-119791204
   [28573]        X      -   : 119791431-119791505  -- 119791358-119791432
   [28574]        X      -   : 119791593-119791667  -- 119786691-119789940
   [28575]        X      -   : 119791629-119791703  -- 119789951-119791587
   [28576]        X      -   : 119791637-119791711  -- 119789976-119791612
   -------
   seqinfo: 194 sequences from an unspecified genome

> eh <- ExperimentHub()

!> eh[["EH167"]]
 see ?alpineData and browseVignettes('alpineData') for documentation
 loading from cache
 GAlignmentPairs object with 28576 pairs, strandMode=1, and 0 metadata columns:
           seqnames strand   :              ranges  --              ranges
              <Rle>  <Rle>   :           <IRanges>  --           <IRanges>
       [1]        1      -   : 108565979-108566053  -- 108565846-108565920
       [2]        1      -   : 108573341-108573415  -- 108573234-108573308
       [3]        1      +   : 108581087-108581161  -- 108581239-108581313
       [4]        1      +   : 108601105-108601179  -- 108601196-108601270
       [5]        1      -   : 108603628-108603701  -- 108603540-108603614
       ...      ...    ... ...                 ... ...                 ...
   [28572]        X      -   : 119791266-119791340  -- 119791130-119791204
   [28573]        X      -   : 119791431-119791505  -- 119791358-119791432
   [28574]        X      -   : 119791593-119791667  -- 119786691-119789940
   [28575]        X      -   : 119791629-119791703  -- 119789951-119791587
   [28576]        X      -   : 119791637-119791711  -- 119789976-119791612
   -------
   seqinfo: 194 sequences from an unspecified genome

!> sessionInfo()
 R version 4.2.2 (2022-10-31)
 Platform: aarch64-apple-darwin20 (64-bit)
 Running under: macOS Ventura 13.0.1

 Matrix products: default
 BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
 LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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] stats4    stats     graphics  grDevices datasets  utils     methods   base

 other attached packages:
  [1] rtracklayer_1.58.0          alpineData_1.24.0
GenomicAlignments_1.34.0
  [4] Rsamtools_2.14.0            Biostrings_2.66.0           XVector_0.38.0
  [7] SummarizedExperiment_1.28.0 Biobase_2.58.0
MatrixGenerics_1.10.0
 [10] matrixStats_0.63.0          GenomicRanges_1.50.1
GenomeInfoDb_1.34.4
 [13] IRanges_2.32.0              S4Vectors_0.36.0
ExperimentHub_2.6.0
 [16] AnnotationHub_3.6.0         BiocFileCache_2.6.0         dbplyr_2.2.1
 [19] BiocGenerics_0.44.0         pkgdown_2.0.6               testthat_3.1.5
 [22] rmarkdown_2.18              devtools_2.4.5              usethis_2.1.6

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