[Bioc-devel] AnnotationHub failing to load on Mac

Hi Bioc,

A couple of Macx86_64 users have contacted me with this error when using DMRcate::rmPosReps(), which looks like it's propagating from a failure to load AnnotationHub:

Error: failed to load resource
  name: AH116484
  title: EPICv2manifest
  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

Here is the sessionInfo() from one of them.

> sessionInfo()
R Under development (unstable) (2024-03-10 r86088)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Australia/Sydney
tzcode source: internal

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] DMRcatedata_2.22.0   RColorBrewer_1.1-3   Gviz_1.48.0          patchwork_1.2.0      ggrepel_0.9.5        data.table_1.15.4    plyr_1.8.9           DMRcate_3.0.2
 [9] ggthemes_5.1.0       GEOquery_2.72.0      Biobase_2.64.0       limma_3.60.3         lubridate_1.9.3      forcats_1.0.0        stringr_1.5.1        dplyr_1.1.4
[17] purrr_1.0.2          readr_2.1.5          tidyr_1.3.1          tibble_3.2.1         ggplot2_3.5.1        tidyverse_2.0.0      sesame_1.22.1        sesameData_1.22.0
[25] ExperimentHub_2.12.0 AnnotationHub_3.12.0 BiocFileCache_2.12.0 dbplyr_2.5.0         GenomicRanges_1.56.1 GenomeInfoDb_1.40.1  IRanges_2.38.0       S4Vectors_0.42.0
[33] BiocGenerics_0.50.0  BiocManager_1.30.23

loaded via a namespace (and not attached):
  [1] splines_4.4.0                                       BiocIO_1.14.0                                       bitops_1.0-7
  [4] filelock_1.0.3                                      cellranger_1.1.0                                    R.oo_1.26.0
  [7] preprocessCore_1.66.0                               XML_3.99-0.16.1                                     rpart_4.1.23
 [10] lifecycle_1.0.4                                     httr2_1.0.1                                         edgeR_4.2.0
 [13] base64_2.0.1                                        MASS_7.3-61                                         lattice_0.22-6
 [16] ensembldb_2.28.0                                    scrime_1.3.5                                        backports_1.5.0
 [19] magrittr_2.0.3                                      minfi_1.50.0                                        Hmisc_5.1-3
 [22] rmarkdown_2.27                                      yaml_2.3.8                                          doRNG_1.8.6
 [25] askpass_1.2.0                                       DBI_1.2.3                                           abind_1.4-5
 [28] zlibbioc_1.50.0                                     quadprog_1.5-8                                      R.utils_2.12.3
 [31] AnnotationFilter_1.28.0                             biovizBase_1.52.0                                   RCurl_1.98-1.14
 [34] nnet_7.3-19                                         VariantAnnotation_1.50.0                            rappdirs_0.3.3
 [37] GenomeInfoDbData_1.2.12                             genefilter_1.86.0                                   annotate_1.82.0
 [40] permute_0.9-7                                       DelayedMatrixStats_1.26.0                           codetools_0.2-20
 [43] DelayedArray_0.30.1                                 xml2_1.3.6                                          tidyselect_1.2.1
 [46] UCSC.utils_1.0.0                                    beanplot_1.3.1                                      matrixStats_1.3.0
 [49] base64enc_0.1-3                                     illuminaio_0.46.0                                   GenomicAlignments_1.40.0
 [52] jsonlite_1.8.8                                      multtest_2.60.0                                     wheatmap_0.2.0
 [55] Formula_1.2-5                                       iterators_1.0.14                                    survival_3.7-0
 [58] foreach_1.5.2                                       missMethyl_1.38.0                                   tools_4.4.0
 [61] progress_1.2.3                                      Rcpp_1.0.12                                         glue_1.7.0
 [64] gridExtra_2.3                                       SparseArray_1.4.8                                   xfun_0.45
 [67] MatrixGenerics_1.16.0                               HDF5Array_1.32.0                                    IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
 [70] withr_3.0.0                                         fastmap_1.2.0                                       latticeExtra_0.6-30
 [73] rhdf5filters_1.16.0                                 fansi_1.0.6                                         openssl_2.2.0
 [76] digest_0.6.35                                       mime_0.12                                           timechange_0.3.0
 [79] R6_2.5.1                                            colorspace_2.1-0                                    gtools_3.9.5
 [82] jpeg_0.1-10                                         dichromat_2.0-0.1                                   biomaRt_2.60.0
 [85] RSQLite_2.3.7                                       R.methodsS3_1.8.2                                   utf8_1.2.4
 [88] generics_0.1.3                                      rtracklayer_1.64.0                                  prettyunits_1.2.0
 [91] httr_1.4.7                                          htmlwidgets_1.6.4                                   S4Arrays_1.4.1
 [94] pkgconfig_2.0.3                                     IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 gtable_0.3.5
 [97] blob_1.2.4                                          siggenes_1.78.0                                     XVector_0.44.0
[100] htmltools_0.5.8.1                                   ProtGenerics_1.36.0                                 scales_1.3.0
[103] png_0.1-8                                           knitr_1.47                                          rstudioapi_0.16.0
[106] tzdb_0.4.0                                          reshape2_1.4.4                                      rjson_0.2.21
[109] nlme_3.1-165                                        checkmate_2.3.1                                     curl_5.2.1
[112] org.Hs.eg.db_3.19.1                                 bumphunter_1.46.0                                   cachem_1.1.0
[115] rhdf5_2.48.0                                        BiocVersion_3.19.1                                  parallel_4.4.0
[118] foreign_0.8-86                                      AnnotationDbi_1.66.0                                restfulr_0.0.15
[121] reshape_0.8.9                                       pillar_1.9.0                                        vctrs_0.6.5
[124] xtable_1.8-4                                        cluster_2.1.6                                       htmlTable_2.4.2
[127] evaluate_0.24.0                                     bsseq_1.40.0                                        GenomicFeatures_1.56.0
[130] cli_3.6.3                                           locfit_1.5-9.9                                      compiler_4.4.0
[133] Rsamtools_2.20.0                                    rngtools_1.5.2                                      rlang_1.1.4
[136] crayon_1.5.3                                        nor1mix_1.3-3                                       mclust_6.1.1
[139] interp_1.1-6                                        stringi_1.8.4                                       deldir_2.0-4
[142] BiocParallel_1.38.0                                 munsell_0.5.1                                       Biostrings_2.72.1
[145] lazyeval_0.2.2                                      pacman_0.5.1                                        Matrix_1.7-0
[148] BSgenome_1.72.0                                     hms_1.1.3                                           sparseMatrixStats_1.16.0
[151] bit64_4.0.5                                         Rhdf5lib_1.26.0                                     KEGGREST_1.44.1
[154] statmod_1.5.0                                       SummarizedExperiment_1.34.0                         memoise_2.0.1
[157] bit_4.0.5                                           readxl_1.4.3

I notice that the same error happens on merida1 as well: https://secure-web.cisco.com/139QEj96XtFE0crtaFlihorOOWhNEjDfb7A1DHAgpv9IJ5QbAVRKThNWfcUjwXhMfhejU-6DJvc9zFt44cvvNwtMIEX4nsf5ffJGOih-NBq0dv1cZbQ3dHmGgNwJf6rq1D3vcVSCd2TN4eta2-a7llF6As6sSdrmn_mhX3UW8ls9t74KA4KdUg3vmWDYRIJeBLcyI3I6-aG3G7LZcNvSelq96HCBMdg7cFzea0gUzOE8hlI5W-FnkmT-854Ocky0BxNX_ALZ_aH_rXjygx3QpvbS6mV_o7vZBkQFqqQXmLW5Uubyh0XQRWka7bLHa3vga/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FDMRcate%2Fmerida1-checksrc.html

Any suggestions or workarounds?

Best wishes,
Tim


===================

Tim Peters, PhD

Computational Scientist - Immunogenomics Laboratory
Conjoint Lecturer, St Vincent's Healthcare Clinical Campus
Garvan Institute of Medical Research
384 Victoria St., Darlinghurst, NSW, Australia 2010

E: t.peters at garvan.org.au <https://secure-web.cisco.com/1xueKfZ17LeFxjO2W2LJn5fEjhb4T63HPGOJvdVLaNM_vhPi4WPlFYQALHNMrEFYWAzFwNj6SPk0wuA-pLTqZB92aFX96B4PfkYG6q95mcCc2msCSR6-HJ82MCVezT3SLcvBjisZDEuFkbBNlW4gVUhQUgiaFie7LrI6y8wIUy0qrnuCBxBXlDJ-IgflMyitTfEAWsice0c8PW83qtewSrI8ACIISMqj2Q0lJXv2wI1x54MninCipde-TaO0SJ-2JQ1aG2RYeDqupVynGas_Ui0A-BUnaaQofvU-FhafpKD2IiBLR-ZK3bQGVI37sC6mm/https%3A%2F%2Fgimr.garvan.unsw.edu.au%2Fowa%2Ft.peters%40garvan.org.au> | W: http://secure-web.cisco.com/1JMNd-w_7dqVbZLzVJvwsYWwOcyAisEsSQg-M4KZDJj034aLdPbwT7giue0dDtgWiCOrR5z4Woz-rO78Obn_W1d59B4AXYCGiBxcWEJVXyDMX-2uZ_eEhiEZ5JzGTuJ2lak51MPbw9KLg6-ve0x2_Mw7dPARUqN_afqAQxh0wjckzfRwCqXtSLBi3kv9PItys_geRJ_sir6uTZHQyPCckAkf4MRlAtBBiisf_dI0-JD0I9nUzYVp9dn070iKXIO8rMbqrAIe3dyg04liCCRWtJamcLQGiV9qrU_LwUEqNKsSHRF9e0rhLVkMavC4kiNsY/http%3A%2F%2Fwww.garvan.org.au<http://secure-web.cisco.com/1LtYTVkNfTXbH-QxUw_WU9sr3R9OVSc83rt7U5CxR2ZL27-QBfpmq0TLyHtCpLV2_clWj4CHWgjbFCkkgLPs8nZDjPafUhodMLInqOLIJ5Qz6IYVBhJGQ6n8gYN6189f8vnPzYDpcAtP6aL63iCDzzitvhhBobF_zjjTUAkSTUdS-WzxxBdO5g5BmBUuh-GDNOBt3cu652tY4xarRS2DU1w8PZb580MlJ_ukZys6ySvaSm73Sg6ontZ_QQjOnr2IIy9ViqyoWetCMLZaM38_D4Xvh4Sw73L3ijf_zDE5GxPhMoMZ6wH2qu7t_Bs3oZAE9/http%3A%2F%2Fwww.garvan.org.au%2F> | P: +612 9295 8325

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