Cannot Download Bioconductor's "org.Hs.eg.db" package on R 4.0.1

Question

I am trying to install the Bioconductor (Ver. 3.12) package "org.Hs.eg.db" but I keep on receiving the following error:

Error: package or namespace load failed for ‘org.Hs.eg.db’:
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: l$contains
  error: $ operator is invalid for atomic vectors

I've tried to downgrade R to versions 3.6.3, and reinstalling R and RStudio. I've attached my session info below.

Any ideas on how I can upload this package?

Best Santiago

Attempt:

BiocManager::install("BiocManager")
BiocManager::install("org.Hs.eg.db")
library(org.Hs.eg.db)

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0 GO.db_3.12.1                            
 [3] OrganismDbi_1.32.0                       GenomicFeatures_1.42.3                  
 [5] GenomicRanges_1.42.0                     GenomeInfoDb_1.26.7                     
 [7] AnnotationDbi_1.52.0                     IRanges_2.24.1                          
 [9] S4Vectors_0.28.1                         Biobase_2.50.0                          
[11] BiocGenerics_0.36.0                      BiocManager_1.30.12                     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6                  lattice_0.20-41             prettyunits_1.1.1          
 [4] Rsamtools_2.6.0             Biostrings_2.58.0           assertthat_0.2.1           
 [7] utf8_1.2.1                  BiocFileCache_1.14.0        R6_2.5.0                   
[10] RSQLite_2.2.6               httr_1.4.2                  pillar_1.6.0               
[13] zlibbioc_1.36.0             rlang_0.4.10                progress_1.2.2             
[16] curl_4.3                    rstudioapi_0.13             blob_1.2.1                 
[19] Matrix_1.3-2                BiocParallel_1.24.1         stringr_1.4.0              
[22] RCurl_1.98-1.3              bit_4.0.4                   biomaRt_2.46.3             
[25] DelayedArray_0.16.3         compiler_4.0.5              rtracklayer_1.50.0         
[28] pkgconfig_2.0.3             askpass_1.1                 openssl_1.4.3              
[31] tidyselect_1.1.0            SummarizedExperiment_1.20.0 tibble_3.1.0               
[34] GenomeInfoDbData_1.2.4      matrixStats_0.58.0          XML_3.99-0.6               
[37] fansi_0.4.2                 crayon_1.4.1                dplyr_1.0.5                
[40] dbplyr_2.1.1                GenomicAlignments_1.26.0    bitops_1.0-6               
[43] rappdirs_0.3.3              RBGL_1.66.0                 grid_4.0.5                 
[46] lifecycle_1.0.0             DBI_1.1.1                   magrittr_2.0.1             
[49] graph_1.68.0                stringi_1.5.3               cachem_1.0.4               
[52] XVector_0.30.0              xml2_1.3.2                  ellipsis_0.3.1             
[55] generics_0.1.0              vctrs_0.3.7                 tools_4.0.5                
[58] bit64_4.0.5                 glue_1.4.2                  purrr_0.3.4                
[61] hms_1.0.0                   MatrixGenerics_1.2.1        fastmap_1.1.0              
[64] memoise_2.0.0  

Answer 1

I found a solution for this at https://support.bioconductor.org/p/9136239/#9136319:

This appears to be a bug in the communication between the latest release of the RSQLite package and RStudio. In the interim, you can run:

options(connectionsObserver = NULL)

in your RStudio R session before attempting to load these packages (or, use a package that makes a connection via RSQLite). You can also install the previous release of RSQLite using remotes, e.g. with:

remotes::install_version("RSQLite", version = "2.2.5")

It worked for me after I followed this steps and restarted R.