[Bioc-devel] AnnotationHub failing to load on Mac
What is interesting is the resource can load fine on its own when accessed from AnnotationHub so it might be related to the way it is being access/loaded in DMRcate.
ah = AnnotationHub()
snapshotDate(): 2024-04-30
temp = ah[["AH116484"]]
loading from cache
head(temp)
IlmnID Name AddressA_ID cg00000029_TC21 cg00000029_TC21 cg00000029 41791408 cg00000109_TC21 cg00000109_TC21 cg00000109 66725308 cg00000155_BC21 cg00000155_BC21 cg00000155 87669537 cg00000158_BC21 cg00000158_BC21 cg00000158 47668938 cg00000165_TC21 cg00000165_TC21 cg00000165 45649248 cg00000221_BC21 cg00000221_BC21 cg00000221 82633489 .... You can try to have members force redownload the annotation resource however this is not recommended for daily use or subsequent calls as Bioconductor will pay an egress cost each time a resource is redownloaded. So this should be avoided whenever possible and made very clear that the extra argument should only be used once and not in subsequent R sessions or code runs and if the problem reappears or persists should be addressed in the DMRcate code itself.
temp = ah[["AH116484", force=TRUE]]
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 at r-project.org> on behalf of Tim Peters <t.peters at garvan.org.au>
Sent: Monday, June 24, 2024 3:10 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Cc: Braydon Meyer <B.Meyer at garvan.org.au>
Subject: [Bioc-devel] AnnotationHub failing to load on Mac
Sent: Monday, June 24, 2024 3:10 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Cc: Braydon Meyer <B.Meyer at garvan.org.au>
Subject: [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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/18oYaFak8NOjryu58woeWoygvoCOCfQtZh2l2bMZE2CGrjO1ccV8JfGpzkbMvNXAwXsrUeqKtyAngzdoEDl3ntx5pOX-I7i2Gw_35bcVjc4ABGxjYhkHQ7Z_aku_5UiNFZXp-kOJtXMps6g5Bre_8Oo_dlvM1NMLdFOHeWhMIe2e6YSPQOGD8N7QBK8J4zxMVvC4yI9kuHia5F1vn8IeI2fCtV4WjHQbXCRrfnbVGjhK8xSdCGPMzJh0jmvvxWUo0LD2zQ2C3gH_96i_oIvcjZ0VenqLbvI6fNUCLAcSU835iFV1dU-McjLNg5EdWMiow/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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