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Hello: I am having hard time getting AnnotationHub to work. I am using Win10 machine and following the instruction in the Bioconductor landing page of AnnotationHub to download and install AnnotationHub. The following are outputs I got from AnnotationHub. Thank you so much in advance! Charles
> library(AnnotationHub)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter,
Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit,
which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
Error: package or namespace load failed for ‘dbplyr’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘rlang’ 0.4.10 is already loaded, but >= 1.0.0 is required
Error: package ‘dbplyr’ could not be loaded
In addition: Warning messages:
1: package ‘AnnotationHub’ was built under R version 4.0.5
2: package ‘BiocGenerics’ was built under R version 4.0.5
3: package ‘dbplyr’ was built under R version 4.0.5
> ahub <- AnnotationHub()
Error in AnnotationHub() : could not find function "AnnotationHub"
sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
system code page: 65001
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 colorspace_2.0-0 scales_1.1.1
[4] compiler_4.0.3 assertthat_0.2.1 R6_2.5.1
[7] DBI_1.1.2 tools_4.0.3 lifecycle_1.0.1
[10] munsell_0.5.0 rlang_0.4.10
The key message is this:
In other words you will need to update the package
rlang.However, I also notice you are using an old version of R (and thus Bioconductor); R version 4.0.3 (2020-10-10), which has been superseded by multiple R releases. The current version is R-4.1.3, released on 2022-03-10. So, if I were you I would install R-4.1.3 and work with that, and don't spend time on fixing to work with an old version.
Hi, Guido: I installed the R 4.1.3 as you suggested. Then I downloaded BiocManager and AnnotationHub. Now the AnnotationHub is working fine now. Thank you so much for your help! I truly appreciated. Charles Pan
See similar post AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required . The suggestion to update to the current R/Bioc is highly recommended. You could also try BiocManager::valid() to ensure compatibility.
Hi, Shepherl: Yes, BiocManager::valid() is very helpful to me when I try to see whether dependency packages are compatible or updated. When I worked with old version R 4.0.3, I found out that it was two packages that were causing the error: rlang and dbplyr. Thank you so much for sharing! Charles Pan