Closed ChristopherEeles closed 3 years ago
I have installed the package in R 3.6.3 and the error goes away. Seems like the package needs to be updated to work with R >= 4.0
Hi Christopher ! Thanks a lot for your investigation. I'm short of time for the coming days, but I'll do my best to make EaCoN compliant with R4 during the winter holidays.
Cheers
Hi
I have the same problem on Affymetrix OncoScan / OncoScan_CNV
data use OS.Process
with R 4.0.3, and I change the original script apt_oncoscan_process.R
#germ[germ %in% c(8,11)] <- 0
#germ[germ !=0 ] <- 1
germ[germ %in% as.raw(c(8, 11))] <- as.raw(0)
germ[germ !=0 ] <- as.raw(1)
and reinstall EaCoN and its working without error, but I don't know the mean of c(8,11)
,although the program works, I don't know if this is the idea of changing the original program, so did I revise it properly?
Hi,
Thanks for your workaround. I'm still a bit short of time right now (and actually just very recently switched from R3 to R4), but in the next 10 days I'll correct this problem thanks to the help of both of you.
Kind regards
Hi,
I added SehnWei-wei's suggestion as a patch in release https://github.com/gustaveroussy/EaCoN/releases/tag/0.3.6 Thanks again :)
Hi, @aoumess the latest fix for R 4.0 is not functioning in R 3.6. I had to install the previous version to get CS.Process working. Also, the link for the wave normalization file for hg38 is not working. Could you please re-upload the file? Thanks in advance!
Hi, @aoumess the latest fix for R 4.0 is not functioning in R 3.6. I had to install the previous version to get CS.Process working. Also, the link for the wave normalization file for hg38 is not working. Could you please re-upload the file? Thanks in advance!
Hi ! Thanks for bringing this problem up. I pushed a fix that evaluate the R major version before applying @ShenWei-wei 's fix. I hope this should do the trick ? Could you confirm, please ? Just use the latest master version (not the latest release tag). As a sidenote, I'm currently checking and renewing the broken dependencies links. Cheers
Hi @aoumess,
Tried to update my current Snakemake pipeline to use R 4.0.5 today, but the installation of the Cytoscan HD design failed, claiming it is unavailable for my R version.
I tried to install using:
install.packages("https://nextcloud.gustaveroussy.fr/s/FHRnT99A2kLJk6p/download", repos = NULL, type = "source")
Thanks for your assistance.
Best, Chris
Hi,
All non-canonical (ie, not on CRAN, Bioconductor, nor github) have been moved to Zenodo.org, which should be reliable enough !
Hello package maintainers,
I have a persistent error in
CS.Process
. I tried to debug it in RStudio, but I actually get a different error inoschp.load
stating the the HDF5 header is not valid in the call torhdf5::h5read
. I have tried running the function on different .CEL files in case it was a data corruption issue, but get the same error each time.sessionInfo:
I have also attached the log file from the function run. I am going to try again with R 3.6 and see if the error persists.
Best, Christopher Eeles Software Developer Benjamin Haibe-Kains Lab Princess Margaret Cancer Centre EaCoN_CS.Process_log_LMS90.txt