rohitsatyam102 • 10

@rohitsatyam102-24390

Last seen 8 days ago

India

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.

1. I uninstalled and reinstalled BSgenome and hg19 and hg38 packages.
2. 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

rohitsatyam102 • 10

@rohitsatyam102-24390

Last seen 8 days ago

India

Seems like the latest version of ComplexHeatmap_2.7.4 that was downloaded from github brought some incompatibilities by upgrading BiocGenerics and other 4 packages. These packages were traced using BiocManager::valid()$too_new. Uninstalling these packages and reinstalling these packages fixed the problem.