Question

error: namespace Loading DESeq2

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jpcourneya • 0

@jpcourneya-18930

Last seen 4.6 years ago

Hello Community, I am trying to load DESeq2 and have been receiving a namespace error :

library("DESeq2")

Loading required package: SummarizedExperiment

Loading required package: Biobase

Error: package or namespace load failed for ‘Biobase’:

&nbsp;object ‘dims’ is not exported by 'namespace:BiocGenerics'

Error: package ‘Biobase’ could not be loaded

.libpaths()

> .libPaths()
[1] "/home/hshslgalaxy/R/x86_64-pc-linux-gnu-library/3.5" "/usr/local/lib/R/site-library"                      
[3] "/usr/lib/R/site-library"

sessionInfo()

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] tibble_1.4.2         tidyr_0.8.2          stringr_1.3.1        readr_1.3.0          GenomicRanges_1.34.0
[6] GenomeInfoDb_1.18.1  IRanges_2.16.0       S4Vectors_0.20.1     BiocGenerics_0.28.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0             rstudioapi_0.8         XVector_0.22.0         magrittr_1.5          
 [5] hms_0.4.2              zlibbioc_1.28.0        tidyselect_0.2.5       R6_2.3.0              
 [9] rlang_0.3.0.1          tools_3.5.1            yaml_2.2.0             crayon_1.3.4          
[13] GenomeInfoDbData_1.2.0 purrr_0.2.5            BiocManager_1.30.4     bitops_1.0-6          
[17] RCurl_1.95-4.11        glue_1.3.0             stringi_1.2.4          compiler_3.5.1        
[21] pillar_1.3.1           pkgconfig_2.0.2

Any guidance on how to resolve this would be much appreciated!

JP

deseq2 error namespace biobase • 2.8k views

ADD COMMENT • link updated 5.9 years ago by James W. MacDonald 67k • written 5.9 years ago by jpcourneya • 0

James W. MacDonald · Answer 1 · 2018-12-18

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 19 hours ago

United States

To start you should do

BiocManager::valid()

and do what you are told. The current version of BiocGenerics does export dims, and the current version of Biobase does import that. Another possibility is that you have a borked BiocGenerics, so you could try re-installing that as well.

ADD COMMENT • link 5.9 years ago James W. MacDonald 67k

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Hi James, Thanks for the response. i have run

> BiocManager::valid() 
[1] TRUE

Upon reinstalling BiocGenerics and attempting to load DESEq library i am receiving the following error.

 library("DESeq2")

Loading required package: SummarizedExperiment

Loading required package: Biobase

Error: package or namespace load failed for ‘Biobase’: object ‘dims’ is not exported by 'namespace:BiocGenerics'

Error: package ‘Biobase’ could not be loaded

i would like to add when i detached Biobase i received this notice:

detach("package:Biobase", unload=TRUE)

Error in detach("package:Biobase", unload = TRUE) : invalid 'name' argument

Thanks for your answer

ADD REPLY • link updated 5.9 years ago by James W. MacDonald 67k • written 5.9 years ago by jpcourneya • 0

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Right. And I gave two suggestions. What happens when (you restart R) and then do

library(BiocManager)

BiocManager::install(c("Biobase","BiocGenerics"))

and then try to load DESeq2?

ADD REPLY • link 5.9 years ago James W. MacDonald 67k

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my dreams come true and i can move forward! That works James! Thanks so much!

ADD REPLY • link 5.9 years ago jpcourneya • 0