Hi,

I am having problems installing several annotation packages from R Bioconductor: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.ensGene, org.Hs.eg.db, GO.db.

They all seem to produce similar error messages (see below) and it seems to be some core dependency packages involved in the installation error, either AnnotationDbi or BiocFileCache. I have tried looking at the respective vignettes but can't see anything special about installing these packages.

Does anyone have any idea what the problem could be?

Cheers,

Alan

I am running this on a Mac with Catalina OS, please see SessionInfo() output below

ERROR: lazy loading failed for package ‘org.Mm.eg.db’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/org.Mm.eg.db’
installation of package ‘org.Mm.eg.db’ had non-zero exit status* installing *source* package ‘TxDb.Mmusculus.UCSC.mm10.ensGene’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘bit’
Error: package ‘AnnotationDbi’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘TxDb.Mmusculus.UCSC.mm10.ensGene’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/TxDb.Mmusculus.UCSC.mm10.ensGene’
installation of package ‘TxDb.Mmusculus.UCSC.mm10.ensGene’ had non-zero exit status* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘bit’
Error: package ‘AnnotationDbi’ could not be loaded
Execution halted

SessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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 
[8] methods   base     

other attached packages:
 [1] Biobase_2.46.0       BiocManager_1.30.10  dbplyr_1.4.2        
 [4] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0  Biostrings_2.54.0   
 [7] XVector_0.26.0       IRanges_2.20.2       S4Vectors_0.24.3    
[10] BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3             compiler_3.6.2         pillar_1.4.3          
 [4] bitops_1.0-6           tools_3.6.2            zlibbioc_1.32.0       
 [7] packrat_0.5.0          tibble_2.1.3           pkgconfig_2.0.3       
[10] rlang_0.4.5            DBI_1.1.0              rstudioapi_0.11       
[13] xfun_0.12              GenomeInfoDbData_1.2.2 dplyr_0.8.4           
[16] knitr_1.28             tidyselect_1.0.0       glue_1.3.1            
[19] R6_2.4.1               purrr_0.3.3            magrittr_1.5          
[22] assertthat_0.2.1       RCurl_1.98-1.1         crayon_1.3.4  

When you post code like that, please highlight the code and click on the 101010 button to make it look like it does now (come back to the support site to see it). Otherwise it's just a great huge bunch of unreadable text and you are relying on others to clean up the mess for you.

Do note that a close reading of the output should have pointed you in the right direction. You got this message multiple times:

there is no package called ‘bit’

Which seems pretty clear? If not, it's saying that R is looking for a package called bit that isn't presently installed (hence the message), and the fix would be to install bit and then try again (obviously using BiocManager::install).

I have never had this problem personally, and I am not sure how one would cause it to happen if using BiocManager for installing all packages, so my suspicion is that you have neglected to do so and somehow borked your installation. In which case you may have other missing dependencies. I don't know if doing

BiocManager::valid()

will tell you about missing dependencies. I do believe it's primarily for finding incorrect versions of installed packages, but you might try running that to see if you are way off.

And you may need to keep installing various dependencies, if for example you install bit and then when trying to install AnnotationDbi you get another message about a missing package. That can be a drag, but you now know how to fix it.