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-boun...@r-project.org> on behalf of Michael Love <michaelisaiahl...@gmail.com> Sent: Tuesday, January 10, 2023 9:40 AM To: bioc-devel <bioc-devel@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1Tei72T7gV40RjM6ISSISNoNEBBvQvt7jf11MmxhywT3KYHM8TYfKjmPLJgmrj6djgMWNX-TfFuprLHkhyLfd2ixdw6yM_2sSU5XYqRdjn6kb7wRHHQstz_IxbqI2RUQsMe16ZeaI6bOPpFlt8ZEHaVAmhaAi_luwe2gMfRt-32Tz_p7tCMVObcF2RO3jxBfC3ARLT66SmpQwOevoWBFL6J-wZ9QerjHLmGPSxBe55yG0tfxt2_8l5rmxR6agz1x4FtFOuReie8nLLv_WXqW2OBddSosKRNyr3glDKfxlTKZru-YkMtC8QgJB5ysk-jVk/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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