Question: error installing "org.Hs.eg.db"
0
gravatar for lavanya.kannan
21 months ago by
lavanya.kannan0 wrote:

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
bioconductor • 1.2k views
ADD COMMENTlink modified 21 months ago by Devon Ryan91k • written 21 months ago by lavanya.kannan0
1

Have you tried closing and restarting R? I suspect that'll do the trick.

ADD REPLYlink written 21 months ago by Devon Ryan91k
1

The good ol' turning it off and on again :)

ADD REPLYlink written 21 months ago by WouterDeCoster40k
1

try unloading all libraries (copy/pasted from here) and reload the library again:

lapply(paste('package:',names(sessionInfo()$otherPkgs),sep=""),detach,character.only=TRUE,unload=TRUE)
ADD REPLYlink modified 21 months ago • written 21 months ago by cpad011211k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1440 users visited in the last hour