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🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
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'Error in stopAndCache(title) : File EPIC.address needs to be cached to be used in sesame' - but file is listed in sesameDataList #85

Open jhawe opened 2 years ago

jhawe commented 2 years ago

While the other issues is fixed for me (#84 ) I now receive a different one:

After updating the two sesame packages to the latest version on github, I deleted the old cache files and ran again sesameDataCache.

Now I want to run the pipeline but get the following error for some test data:

> betas <- openSesame(idat_directory)
Error in stopAndCache(title) :
| File EPIC.address needs to be cached to be used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache()
| to retrieve and cache needed sesame data.

When I check sesameDataList("EPIC") it gives the following result, with EPIC.address being listed:

> sesameDataList("EPIC")
# A tibble: 19 × 2
   EHID   Title
   <chr>  <chr>
 1 TBD    EPICv2.address
 2 EH7322 EPIC.1.SigDF
 3 EH6841 EPIC.5.SigDF.normal
 4 EH7323 EPIC.address
 5 EH7327 EPIC.addressSpecies
 6 EH3676 EPIC.probeInfo
 7 EH7334 EPIC.publicQC
 8 EH7339 EPIC.tissueSignature
 9 EH6809 KYCG.EPIC.CGI.20210713
10 EH7346 KYCG.EPIC.chromHMM.20211020
11 EH6810 KYCG.EPIC.chromosome.hg19.20210630
12 EH6811 KYCG.EPIC.chromosome.hg38.20210630
13 EH7348 KYCG.EPIC.HMconsensus.20211013
14 EH7318 KYCG.EPIC.mask.20220123
15 EH7313 KYCG.EPIC.metagene.20220126
16 EH7349 KYCG.EPIC.probeType.20211013
17 EH6817 KYCG.EPIC.seqContext.20210713
18 EH7350 KYCG.EPIC.TFBSconsensus.20211013
19 EH7340 KYCG.EPIC.tissueSignature.20211211

What could be the issue here?

Thanks and best j

EDIT: add the sessionInfo:

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] 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
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] sesame_1.15.12      sesameData_1.17.2   ExperimentHub_2.2.1
[4] AnnotationHub_3.2.2 BiocFileCache_2.2.1 dbplyr_2.2.1
[7] BiocGenerics_0.40.0 readr_2.1.3
[...]
arvinhm commented 1 year ago

I had the same problem, but once I deleted all related files to ExperimentHub, it resolved. Make sure there is no related file and folder in the ~ Users/Library/Caches; then try again for installing new version. Keep in mind you should use matched versions.