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://bioconductor.org/checkResults/release/bioc-LATEST/DMRcate/merida1-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
<https://gimr.garvan.unsw.edu.au/owa/t.pet...@garvan.org.au> | W:
http://www.garvan.org.au<http://www.garvan.org.au/> | P: +612 9295 8325
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