Error attaching GO.db package
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Entering edit mode
@adrianna-christina-7353
Last seen 6.5 years ago
Australia

I want to use ChIPpeakAnno package, but I got an error message:package 'GO.db' could not be loaded. Then I tried to load the GO.db, and I received a loadNamespace error when I tried to attach the package via library(GO.db ). 

Any help would be really appreciated!

> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: VennDiagram
Loading required package: biomaRt
Loading required package: multtest
Loading required package: IRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: BSgenome
Loading required package: GenomicRanges

Attaching package: ‘BSgenome’

The following object is masked from ‘package:AnnotationDbi’:

    species

Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: match.arg(synchronous, c("off", "normal", "full"))
  error: 'arg' must be NULL or a character vector
Error: package ‘GO.db’ could not be loaded

 

> library(GO.db)
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: match.arg(synchronous, c("off", "normal", "full"))
  error: 'arg' must be NULL or a character vector
Error: package or namespace load failed for ‘GO.db’

> traceback()
2: stop(gettextf("package or namespace load failed for %s", sQuote(package)),
       call. = FALSE, domain = NA)
1: library(GO.db)

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

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

other attached packages:
[1] BiocInstaller_1.12.1 RSQLite_1.0.0        DBI_0.3.1            AnnotationDbi_1.24.0 Biobase_2.22.0       BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
[1] IRanges_1.20.7 stats4_3.0.2   tools_3.0.2 

GO.db loadnamespace annotation chippeakanno • 1.2k views
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

You need to either downgrade your RSQLite package to 0.11.4 (and this will require that you have development tools installed), or (recommended) upgrade to the current version of R (3.1.3) and Bioconductor (3.0).

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