Entering edit mode
Hi, I am running into some issues with installing chromVAR and VariantAnnotation through BioConductor. I am working in R/4.0.1 and BioConductor 3.12. This occurs whether it is installed via the development version from GitHub or through BioConductor and I believe both packages are compatible with this version of BioConductor and R. Any help would be greatly appreciated!
Thanks!
# chromVAR
# installation command:
BiocManager::install('chromVAR')
Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE, :
class “chromVARDeviations” cannot extend class “Vector”: slot in class “chromVARDeviations” must extend corresponding slot in class “Vector”: fails for elementMetadata
Error in setClass("chromVARDeviations", contains = "SummarizedExperiment") :
error in contained classes ("SummarizedExperiment") for class “chromVARDeviations”; class definition removed from ‘chromVAR’
Error: unable to load R code in package ‘chromVAR’
Execution halted
ERROR: lazy loading failed for package ‘chromVAR’
* removing ‘~R-4.0.1-IRkernel/library/chromVAR’
The downloaded source packages are in
‘/tmp/RtmprPOorE/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /n/app/R/4.0.1/lib64/R/library
packages:
boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
Matrix, mgcv, nlme, nnet, spatial, survival
Old packages: 'leiden', 'RJSONIO', 'VariantAnnotation'
#############
# VariantAnnotation
Warning: undefined slot classes in definition of "VcfFileList": elementMetadata(class "DataTable_OR_NULL")
Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE, :
class “VcfFileList” cannot extend class “SimpleList”: slot in class “VcfFileList” must extend corresponding slot in class “SimpleList”: fails for elementMetadata
Error in setClass("VcfFileList", contains = "TabixFileList", prototype = prototype(elementType = "VcfFile")) :
error in contained classes ("TabixFileList") for class “VcfFileList”; class definition removed from ‘VariantAnnotation’
Error: unable to load R code in package ‘VariantAnnotation’
Execution halted
ERROR: lazy loading failed for package ‘VariantAnnotation’
* removing ‘/~/R-4.0.1-IRkernel/library/VariantAnnotation’
* restoring previous ‘~/R-4.0.1-IRkernel/library/VariantAnnotation’
The downloaded source packages are in
‘/tmp/RtmprPOorE/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /n/app/R/4.0.1/lib64/R/library
packages:
boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
Matrix, mgcv, nlme, nnet, spatial, survival
Old packages: 'leiden', 'RJSONIO', 'VariantAnnotation'
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
sessionInfo( )
R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /n/app/openblas/0.2.19/lib/libopenblas_core2p-r0.2.19.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
loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.0.1 tools_4.0.1
You mentioned installing through github and I'm not sure how you mean; if you installed a devel github version that version would not be compatible with the version of Bioc/R you are using. I would recommend running
BiocManager::valid()and doing any recommendations it provides. Also try reinstalling VariantAnnotationBiocManager::install('VariantAnnotation')to ensure you have the correct version.Thanks for the response! What I meant was I initially tried installing through BiocManager and when that failed I attempted to install with devtools install_github() and in both cases ran into the same error with chromVAR when doing lazy loading:
etc...
As for VariantAnnotation, I removed my previous installation of VariantAnnotation and attempted reinstalled it, and again, same error. The error I got in my original post was when trying to upgrade VariantAnnotation (as per recommendation of BiocManager::valid() when previously troubleshooting the chromVAR error).
BiocManager::valid() now reports only one unrelated package being out of date and no packages as too new.
Any suggestions would be greatly appreciated!