Failed to download IlluminaHumanMethylationEPICv2anno.20a1.hg38

Question

[christine.a.pedersen]

I am currently working on illumina EPIC v1 and v2 data. When trying to annotate the v2 data I am unable to download the annotation package (note: the manifest package works fine). I get the error that the download failed and that 'rhdf5filters' is old. I have tried reinstalling 'rhdf5filters', both through BiocManager and conda, it does not give any errors, but the package download still failes. Does anyone understand why this happens or if there is some other way to annotate my data?

> BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing github package(s) 'jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38'
Downloading GitHub repo jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38/tarball/HEAD' failed
Old packages: 'rhdf5filters'

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS/LAPACK: /mnt/work/workbench/chriap/.conda/envs/r-base/lib/libopenblasp-r0.3.24.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

[Basti]

Did you try to relaunch your R session after updating rhdf5filters ?

[christine.a.pedersen]

yes, but it did not make any difference

Answer 1

[christine.a.pedersen]

Update: solved by cloning the github repo to a local place on my server (have to work on a server due to patient data invloved) and loading the package from there.