Error while Installing BSgenome.Hsapiens.UCSC.hg38
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Entering edit mode
@rohitsatyam102-24390
Last seen 1 day 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
BSgenome.Hsapiens.UCSC.hg38 • 1.5k views
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Entering edit mode
@rohitsatyam102-24390
Last seen 1 day 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.

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Entering edit mode

I was getting the same error when trying to innstall hg38: BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

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")

This is what i did too fix it.

  1. as rohitsatyam102 mentioned, BiocManager::valid() suggested some updates for me to install for other bioconductoor packages so i did
  2. I also installed the new version of Bioconductor with BiocManager::install(version = "3.12")
  3. Then, i adjusted the download timeout with options(timeout = 300) because it seemed whenever id try to downlood hg38, it would stop too soon.
  4. Then i ran BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") to download again. This time the download coompleted without an error.
  5. Then i had to restart the R session. I was getting an error that the lazy-load database was corrupt and the fix for that was to start a new R session. I closed Rstudio and reopened it to a fresh console.
  6. I loaded the library(BSgenome.Hsapiens.UCSC.hg38) and ran BSgenome.Hsapiens.UCSC.hg38 without and error.

I would have posted my sessionInfo() but these steps required me to refresh the session (see step 5). The sessionInfo() below is after I performed step 6: running library(BSgenome.Hsapiens.UCSC.hg38) and BSgenome.Hsapiens.UCSC.hg38

tl;dr - If I had to do this again, id suggest doing steps 3-6 only.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0                   rtracklayer_1.50.0               
 [4] Biostrings_2.58.0                 XVector_0.30.0                    GenomicRanges_1.42.0             
 [7] GenomeInfoDb_1.26.2               IRanges_2.24.1                    S4Vectors_0.28.1                 
[10] BiocGenerics_0.36.0              

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13             knitr_1.31                  GenomicAlignments_1.26.0   
 [4] zlibbioc_1.36.0             BiocParallel_1.24.1         lattice_0.20-41            
 [7] rlang_0.4.10                tools_4.0.3                 grid_4.0.3                 
[10] SummarizedExperiment_1.20.0 Biobase_2.50.0              xfun_0.20                  
[13] matrixStats_0.58.0          htmltools_0.5.1.1           yaml_2.2.1                 
[16] digest_0.6.27               crayon_1.3.4                Matrix_1.3-2               
[19] GenomeInfoDbData_1.2.4      BiocManager_1.30.10         bitops_1.0-6               
[22] RCurl_1.98-1.2              evaluate_0.14               rmarkdown_2.6              
[25] DelayedArray_0.16.1         compiler_4.0.3              MatrixGenerics_1.2.0       
[28] Rsamtools_2.6.0             XML_3.99-0.5
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