Question: error installing ""
gravatar for lavanya.kannan
3.3 years ago by
lavanya.kannan10 wrote:

I am getting the following error while installing the "" package. I installed vis biocLite and still get the same error. How can I troubleshoot this error?

Thanks, Lavanya

> install.packages("", repos="")
Installing package into ‘/Users/kannal01/Library/R/3.4/library’
(as ‘lib’ is unspecified)
trying URL ''
Content type 'application/x-gzip' length 69557350 bytes (66.3 MB)
downloaded 66.3 MB

* installing *source* package ‘’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (

The downloaded source packages are in
> library(
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

[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 • 3.2k views
ADD COMMENTlink modified 3.3 years ago by Devon Ryan98k • written 3.3 years ago by lavanya.kannan10

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

ADD REPLYlink written 3.3 years ago by Devon Ryan98k

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

ADD REPLYlink written 3.3 years ago by WouterDeCoster45k

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

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by cpad011215k
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