[Bioc-devel] ExperimentHub: bad restore file magic number (file may be corrupted)
Neumann, Steffen
@neum@nn @end|ng |rom |pb-h@||e@de
Wed Jan 11 11:20:27 CET 2023
Hi,
On Tue, 2023-01-10 at 14:45 +0000, Kern, Lori wrote:
> It looks like the download got corrupted. I reset the cache for that
> EH number and it should clear up on the next build.
not knowing the EH infrastructure in detail,
are there file checksums which, on failure, should
trigger cache invalidation and (one) re-download attempt ?
Yours,
Steffen
>
>
>
>
> 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.
>
> https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsecure-web.cisco.com%2F12y5s79xt-pmTPP6fzsYkMo0aALvDKgR-cUjxZcIL7QocYem0ml4eV-pkh4oqQlVq8ZteIbXcu42Ee2A76ClYhjiLHejdzRpRUWm2tCUEwNc6KBS1AiYDSfsOBC3dQ5mK3b3HgrhfvfXRVwW9TNr64PoANtPMDKwcwCG6aYF-RqHQHmvHDx5W2NluvaWlSV8u3wLL4iE0yfBocZDajrHg02fNfdqKkIbJF_iMnVNrLL950twq0FdVn9plKReI2-Eb1eI4a4OxMYO82sikXLqQmnE3w6f5KD--82FtxHaPjkXqyQSvQbRXLuH3ZBS2ussl%2Fhttp%253A%252F%252Fbioconductor.org%252FcheckResults%252Frelease%252Fdata-experiment-LATEST%252FalpineData%252Fnebbiolo2-buildsrc.html&data=05%7C01%7C%7C7126a52586d641eff7c808daf31a6b71%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638089592201758765%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=zf7IQJCqSGuWRhkvqO7FebkQZz%2FhLkFkZl96HTxjanA%3D&reserved=0
>
> ...
> --- 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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