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-boun...@r-project.org> on behalf of Tim Peters
<t.pet...@garvan.org.au>
Sent: Monday, June 24, 2024 3:10 AM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Cc: Braydon Meyer <b.me...@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.pet...@garvan.org.au
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