Entering edit mode
6.5 years ago
lavanya.kannan
▴
20
I am getting the following error while installing the "org.Hs.eg.db" package. I installed vis biocLite and still get the same error. How can I troubleshoot this error?
Thanks, Lavanya
> install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.4/data/annotation")
Installing package into ‘/Users/kannal01/Library/R/3.4/library’
(as ‘lib’ is unspecified)
trying URL 'http://bioconductor.org/packages/3.4/data/annotation/src/contrib/org.Hs.eg.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 69557350 bytes (66.3 MB)
==================================================
downloaded 66.3 MB
* installing *source* package ‘org.Hs.eg.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (org.Hs.eg.db)
The downloaded source packages are in
‘/private/var/folders/3k/rkpcy0v54wzcqzd00m1nv3_4fb2_sl/T/Rtmptbv6li/downloaded_packages’
> library(org.Hs.eg.db)
Loading required package: AnnotationDbi
Loading required package: BiocGenerics
Error in value[[3L]](cond) :
Package ‘BiocGenerics’ version 0.22.1 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘BiocGenerics’ is imported by ‘geneplotter’, ‘GenomeInfoDb’, ‘AnnotationDbi’, ‘DelayedArray’, ‘S4Vectors’, ‘SummarizedExperiment’, ‘IRanges’, ‘annotate’, ‘DESeq2’, ‘XVector’, ‘GenomicRanges’, ‘Biobase’ so cannot be unloaded
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.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] clusterProfiler_3.6.0 DOSE_3.4.0 BiocInstaller_1.28.0 limma_3.34.0
loaded via a namespace (and not attached):
[1] Biobase_2.38.0 tidyr_0.7.2 bit64_0.9-7 splines_3.4.1 Formula_1.2-2
[6] DO.db_2.9 rvcheck_0.0.9 latticeExtra_0.6-28 blob_1.1.0 GenomeInfoDbData_0.99.1
[11] RSQLite_2.0 backports_1.1.1 lattice_0.20-35 glue_1.2.0 digest_0.6.12
[16] GenomicRanges_1.30.0 RColorBrewer_1.1-2 XVector_0.18.0 checkmate_1.8.5 qvalue_2.10.0
[21] colorspace_1.3-2 htmltools_0.3.6 Matrix_1.2-11 plyr_1.8.4 DESeq2_1.18.0
[26] XML_3.98-1.9 pkgconfig_2.0.1 genefilter_1.60.0 zlibbioc_1.24.0 purrr_0.2.4
[31] xtable_1.8-2 GO.db_3.4.2 scales_0.5.0 BiocParallel_1.12.0 htmlTable_1.9
[36] tibble_1.3.4 annotate_1.56.0 IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.0
[41] nnet_7.3-12 BiocGenerics_0.24.0 lazyeval_0.2.1 survival_2.41-3 magrittr_1.5
[46] memoise_1.1.0 foreign_0.8-69 tools_3.4.1 data.table_1.10.4-3 matrixStats_0.52.2
[51] stringr_1.2.0 S4Vectors_0.16.0 munsell_0.4.3 locfit_1.5-9.1 cluster_2.0.6
[56] DelayedArray_0.4.0 AnnotationDbi_1.40.0 compiler_3.4.1 GenomeInfoDb_1.14.0 rlang_0.1.2
[61] grid_3.4.1 RCurl_1.95-4.8 htmlwidgets_0.9 igraph_1.1.2 bitops_1.0-6
[66] base64enc_0.1-3 gtable_0.2.0 DBI_0.7 reshape2_1.4.2 gridExtra_2.3
[71] knitr_1.17 bit_1.1-12 fastmatch_1.1-0 Hmisc_4.0-3 fgsea_1.4.0
[76] stringi_1.1.5 GOSemSim_2.4.0 Rcpp_0.12.13 geneplotter_1.56.0 rpart_4.1-11
[81] acepack_1.4.1
Have you tried closing and restarting R? I suspect that'll do the trick.
The good ol' turning it off and on again :)
try unloading all libraries (copy/pasted from here) and reload the library again: