openSesame - unused arguments ("KYCG", full = TRUE) error

[jhawe]

Hi,

when trying to run openSesame (latest version from github as of 18Nov2022) I receive the following error:

> betas <- openSesame("<my-idat-prefix>")
Error in sesameDataList("KYCG", full = TRUE) :
  unused arguments ("KYCG", full = TRUE)

It seems the function sesameDataList() does not provide these parameters, when calling it manually I get the following:

> sesameDataList()
# A tibble: 70 × 2
   EHID   Title
   <chr>  <chr>
 1 EH6809 KYCG.EPIC.CGI.20210713
 2 EH6810 KYCG.EPIC.chromosome.hg19.20210630
 3 EH6811 KYCG.EPIC.chromosome.hg38.20210630
 4 EH6812 KYCG.EPIC.gene.20210923
 5 EH6813 KYCG.EPIC.histoneMod.20210819
 6 EH6814 KYCG.EPIC.mask.hg19.20181001
 7 EH6815 KYCG.EPIC.mask.hg38.20181001
 8 EH6816 KYCG.EPIC.probeType.20210630
 9 EH6817 KYCG.EPIC.seqContext.20210713
10 EH6818 KYCG.EPIC.TFBS.20210817
# … with 60 more rows
# ℹ Use `print(n = ...)` to see more rows

It seems that either

1. openSesame uses the wrong parametrization of sesameDataList or 2) sesameDataList is missing the needed parametrization

Could this be fixed?

cheers! j

P.S.: if of relevance, my session info:

> 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_1.12.0   rmarkdown_2.18
[4] ExperimentHub_2.2.1 AnnotationHub_3.2.2 BiocFileCache_2.2.1
[7] dbplyr_2.2.1        BiocGenerics_0.40.0 readr_2.1.3
[...]

[jhawe]

I just realized that this might be a simple issue of the sesameData package not being at the appropriate version. After manually installing sesameData from github, then installing sesame the issue is gone.

So I'd suggest to use a more recent version of sesameData in the dependency list for sesame.