Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg19.knownGene'
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@charlesgwellem-16293
Last seen 14 months ago

Hi. I am not able to load the Chipseeker package. I have installed in the following way and I keep having errors while loading and I do not know why.

BiocManager::install("ChIPseeker")
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")

library(ChIPseeker) # produces and error

Error: package or namespace load failed for 'ChIPseeker': 
  'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg19.knownGene'

Thank you in advance for any help on how to go about this.

session info:

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

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

other attached packages:
 [1] BiocInstaller_1.32.1                    TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [3] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 GenomicFeatures_1.34.8                 
 [5] AnnotationDbi_1.44.0                    GenomicRanges_1.34.0                   
 [7] GenomeInfoDb_1.18.2                     IRanges_2.16.0                         
 [9] S4Vectors_0.20.1                        cellrangerRkit_1.1.0                   
[11] Rmisc_1.5                               plyr_1.8.4                             
[13] lattice_0.20-35                         bit64_0.9-7                            
[15] bit_1.1-14                              ggplot2_3.1.1                          
[17] RColorBrewer_1.1-2                      Biobase_2.42.0                         
[19] BiocGenerics_0.28.0                     Matrix_1.2-14                          

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) : DESCRIPTION von Paket 'digest' fehlt oder zerstört
chipseq chipseeker R Bioconductor • 394 views
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@martin-morgan-1513
Last seen 9 weeks ago
United States

I think the problem is that you have incompatible versions of (some) packages installed, with the particular offender in this case indicated in the warning message, digest. I suggest you use remove.packages("digest") perhaps several times, and try again...

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Thank you Martin. After removing the digest package I still have the same error.

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But presumably not the same warning "DESCRIPTION von Paket 'digest' fehlt oder zerstört" in the sessionInfo()?

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