Entering edit mode
Hi Everyone!!
This error comes as a surprise to me because the package was working just fine few days ago. I am unable to comprehend what to do about it.
- I uninstalled and reinstalled BSgenome and hg19 and hg38 packages.
- Updated rest of the packages
also tried the following
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", INSTALL_opts = "--no-staged-install")
but no improvement.
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL")
Warning: undefined slot classes in definition of "XInteger": elementMetadata(class "DataTable_OR_NULL")
Warning: undefined slot classes in definition of "XDouble": elementMetadata(class "DataTable_OR_NULL")
Warning: multiple methods tables found for 'which'
Error: package or namespace load failed for 'BSgenome.Hsapiens.UCSC.hg38':
.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
call: validObject(.Object)
error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")
Error: loading failed
Execution halted
*** arch - x64
Warning: undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL")
Warning: undefined slot classes in definition of "XInteger": elementMetadata(class "DataTable_OR_NULL")
Warning: undefined slot classes in definition of "XDouble": elementMetadata(class "DataTable_OR_NULL")
Warning: multiple methods tables found for 'which'
Error: package or namespace load failed for 'BSgenome.Hsapiens.UCSC.hg38':
.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
call: validObject(.Object)
error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Rohit Satyam/Documents/R/win-library/4.0/BSgenome.Hsapiens.UCSC.hg38'
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 cluster_2.1.0 BiocGenerics_0.36.0 IRanges_2.24.1 colorspace_2.0-0
[6] clue_0.3-58 rjson_0.2.20 fansi_0.4.1 tools_4.0.3 parallel_4.0.3
[11] grid_4.0.3 circlize_0.4.12 sessioninfo_1.1.1 png_0.1-7 cli_2.2.0
[16] withr_2.3.0 matrixStats_0.57.0 digest_0.6.27 assertthat_0.2.1 crayon_1.3.4
[21] BiocManager_1.30.10 RColorBrewer_1.1-2 S4Vectors_0.28.1 GlobalOptions_0.1.2 shape_1.4.5
[26] glue_1.4.2 ComplexHeatmap_2.7.4 compiler_4.0.3 stats4_4.0.3 Cairo_1.5-12.2
[31] GetoptLong_1.0.5
> BiocManager::valid()
* sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: 0 packages out-of-date; 5 packages too new
2: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'ComplexHeatmap' is missing or broken