Question: Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg19.knownGene'
1
gravatar for charlesgwellem
10 weeks ago by
charlesgwellem10 wrote:

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
ADD COMMENTlink modified 10 weeks ago by Martin Morgan ♦♦ 23k • written 10 weeks ago by charlesgwellem10
Answer: Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg
0
gravatar for Martin Morgan
10 weeks ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

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...

ADD COMMENTlink written 10 weeks ago by Martin Morgan ♦♦ 23k

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

ADD REPLYlink written 10 weeks ago by charlesgwellem10

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

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Martin Morgan ♦♦ 23k
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