Question: Problem in installing Bioconductor packages due to "IRanges"
gravatar for topijush
6 months ago by
topijush10 wrote:

I have been trying since few days to install a package named methyAnalysis. Firstly it says to update my older version R. I have then updated the in to update the R version 3.4.3 (2017-11-30 and the latest RStudio in my windows 64 bit PC. Then I face a problem due to the package named  IRanges regarding some dependency error. Someone suggest me in Biostear to update recent bioconductor version. I did that. After that I have updated all the packages it suggested. But facing the same error . Then I try to see the other packages which are previously install in my pc then I also find that they are not being able to make library. Some kind of error shown below.

"No methods found in package ‘IRanges’ for requests: ‘%in%’, ‘elementLengths’, ‘elementMetadata’, ‘ifelse’, ‘queryHits’, ‘Rle’, ‘subjectHits’, ‘t’ when loading ‘bumphunter’ "

Then I try to install the packages after downloading it manually. That time also it is showing error.

"No methods found in package ‘IRanges’ for requests: ‘%in%’, ‘elementLengths’, ‘elementMetadata’, ‘ifelse’, ‘queryHits’, ‘Rle’, ‘subjectHits’, ‘t’ when loading ‘bumphunter’
Error: package or namespace load failed for ‘lumi’:
 objects ‘.__T__split:base’, ‘split’ are not exported by 'namespace:IRanges'
In addition: Warning message:
replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘methylumi’ "  

Please help me for solving such problem.

Thank you very much.





ADD COMMENTlink written 6 months ago by topijush10

What is the output of `sessionInfo()` after you load IRanges? 

ADD REPLYlink written 6 months ago by Sean Davis21k

Also BiocInstaller::biocValid(), which may flag some packages that are not correct for your version of R and Bioconductor.

ADD REPLYlink written 6 months ago by Martin Morgan ♦♦ 22k
> library(wateRmelon)
Loading required package: methylumi
Loading required package: minfi
Loading required package: bumphunter
Error: package or namespace load failed for ‘bumphunter’:
 objects ‘metadata’, ‘isTRUEorFALSE’, ‘isSingleString’, ‘elementLengths’ are not exported by 'namespace:IRanges'
Error: package ‘bumphunter’ could not be loaded
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] locfit_1.5-9.1       iterators_1.0.9      foreach_1.4.4        Biostrings_2.45.3    XVector_0.18.0       GenomicRanges_1.30.0
 [7] GenomeInfoDb_1.14.0  lattice_0.20-35      ggplot2_2.2.1        reshape2_1.4.3       scales_0.5.0         matrixStats_0.52.2  
[13] limma_3.20.9         Biobase_2.24.0       IRanges_2.12.0       S4Vectors_0.16.0     BiocInstaller_1.14.3 BiocGenerics_0.24.0 

loaded via a namespace (and not attached):
 [1] colorspace_1.3-2       yaml_2.1.16            blob_1.1.0             XML_3.98-1.9           rlang_0.1.6            pillar_1.0.1          
 [7] DBI_0.7                bit64_0.9-7            registry_0.5           rngtools_1.2.4         doRNG_1.6.6            GenomeInfoDbData_1.0.0
[13] plyr_1.8.4             pkgmaker_0.22          stringr_1.2.0          zlibbioc_1.10.0        munsell_0.4.3          gtable_0.2.0          
[19] codetools_0.2-15       memoise_1.1.0          Rcpp_0.12.14           xtable_1.8-2           bit_1.1-12             digest_0.6.13         
[25] stringi_1.1.6          grid_3.4.3             tools_3.4.3            bitops_1.0-6           magrittr_1.5           lazyeval_0.2.1        
[31] RCurl_1.95-4.10        tibble_1.4.1           RSQLite_2.0            compiler_3.4.3        
ADD REPLYlink modified 6 months ago by Martin Morgan ♦♦ 22k • written 6 months ago by topijush10

And packageVersion("bumphunter") ? It should be 1.20.0.

ADD REPLYlink written 6 months ago by Martin Morgan ♦♦ 22k
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