GenomicFeatures load problem : "namespaceExport(ns, exports): undefined exports: %>%"
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Entering edit mode
shipy3 • 0
@shipy3-23666
Last seen 3.9 years ago

Hi everyone. I try to load GenomicFeatures package but fail.

> library(GenomicFeatures)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Error: package or namespace load failed for 'GenomicFeatures' in namespaceExport(ns, exports):
 undefined exports: %>%

Here is the information of my R session:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
[1] C

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

other attached packages:
[1] AnnotationDbi_1.48.0 Biobase_2.46.0       GenomicRanges_1.38.0
[4] GenomeInfoDb_1.22.1  IRanges_2.20.2       S4Vectors_0.24.4    
[7] BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3             pillar_1.4.2           compiler_3.6.0        
 [4] XVector_0.26.0         prettyunits_1.0.2      bitops_1.0-6          
 [7] tools_3.6.0            zlibbioc_1.32.0        progress_1.2.2        
[10] digest_0.6.23          bit_1.1-15.2           lifecycle_0.2.0       
[13] tibble_2.1.3           RSQLite_2.2.0          memoise_1.1.0         
[16] pkgconfig_2.0.3        rlang_0.4.6            DBI_1.1.0             
[19] GenomeInfoDbData_1.2.2 dplyr_1.0.0            stringr_1.4.0         
[22] httr_1.4.1             generics_0.0.2         Biostrings_2.54.0     
[25] vctrs_0.3.1            askpass_1.1            hms_0.5.3             
[28] tidyselect_1.1.0       bit64_0.9-7            glue_1.4.1            
[31] R6_2.4.1               XML_3.99-0.3           purrr_0.3.3           
[34] blob_1.2.1             magrittr_1.5           assertthat_0.2.1      
[37] stringi_1.4.3          RCurl_1.95-4.12        openssl_1.4.1         
[40] crayon_1.3.4          

Could anyone please tell me how to fix it ? Thanks a lot!

software error • 949 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

Upgrade to R-4.0.0 and Bioconductor version 3.11 and see if you still have the problem.

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0
Entering edit mode
@martin-morgan-1513
Last seen 13 days ago
United States

This seems like a version mismatch issue; have you tried

BiocManager::valid()
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