Installation of package 'FDb.InfiniumMethylation.hg19' fails
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Entering edit mode
m.nabais • 0
@mnabais-16887
Last seen 3.2 years ago

I'm trying to install the annotation package 'FDb.InfiniumMethylation.hg19' v2.2.0. I used the following code and an error is produced:

source("https://bioconductor.org/biocLite.R")
biocLite("FDb.InfiniumMethylation.hg19")


BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) 'FDb.InfiniumMethylation.hg19'
trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz'
Content type 'application/x-gzip' length 38996322 bytes (37.2 MB)
==================================================
downloaded 37.2 MB

* installing *source* package 'FDb.InfiniumMethylation.hg19' ...
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : package 'org.Hs.eg.db' required by 'FDb.InfiniumMethylation.hg19' could not be found
Error: loading failed
Execution halted
ERROR: loading failed

However, I do have org.Hs.eg.db installed (v3.6.0), as you can see in the sessionInfo() command:

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)

Matrix products: default
BLAS: /opt/Modules/R/3.5.0/lib64/R/lib/libRblas.so
LAPACK: /opt/Modules/R/3.5.0/lib64/R/lib/libRlapack.so

locale:
[1] C

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

other attached packages:
[1] org.Hs.eg.db_3.6.0   AnnotationDbi_1.42.1 IRanges_2.14.10
[4] S4Vectors_0.18.3     Biobase_2.40.0       BiocGenerics_0.26.0
[7] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18    digest_0.6.15   DBI_1.0.0       RSQLite_2.1.1
 [5] blob_1.1.1      tools_3.5.0     bit64_0.9-7     bit_1.1-14
 [9] compiler_3.5.0  pkgconfig_2.0.1 memoise_1.1.0 

 

Would anyone have any idea why this may be happening? I set the .libPaths() to where my packages are installed...

Thanks in advance.

 

 

bioconductor fdb.infiniummethylation.hg19 edger • 335 views
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If you set the `.libPaths()` is it possible that the org package got installed in a different path before you set it? Could you try reinstalling the org.Hs.eg.db after you set the .libPaths() to make sure it is in the same location.
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