Question: resize functions causes an error - "could not find function "unsafe.update"
gravatar for Assa Yeroslaviz
13 months ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k wrote:

When running the resize function, I keep getting the following error message:

> tAE <- IRanges::resize(tA, 200, fix = "center") 
Error in unsafe.update(object, ...) : 
  could not find function "unsafe.update"


I have read that this might happens when you have older packages conflicted with newer versions of other pacakges. For that reason I have updated to the latest vesion of R (3.4.2) and biocValid() gives me TRUE as a result.

What kind of an error message is it? How can I fix it?

I don't know where to find the conflict.



> R.version
platform       x86_64-apple-darwin15.6.0   
arch           x86_64                      
os             darwin15.6.0                
system         x86_64, darwin15.6.0        
major          3                           
minor          4.2                         
year           2017                        
month          09                          
day            28                          
svn rev        73368                       
language       R                           
version.string R version 3.4.2 (2017-09-28)
nickname       Short Summer

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] BiocInstaller_1.26.1  preprocessCore_1.38.1 GenomicRanges_1.28.6  GenomeInfoDb_1.12.3   ggplot2_2.2.1        
 [6] reshape2_1.4.2        vsn_3.44.0            limma_3.32.10         geneplotter_1.54.0    annotate_1.54.0      
[11] XML_3.98-1.9          AnnotationDbi_1.38.2  IRanges_2.10.5        S4Vectors_0.14.7      lattice_0.20-35      
[16] Biobase_2.36.2        BiocGenerics_0.22.1   gplots_3.0.1          tileHMM_1.0-7         locfdr_1.1-8         
[21] st_1.2.5              sda_1.3.7             fdrtool_1.2.15        corpcor_1.6.9         entropy_1.2.1        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13            GO.db_3.4.1             gtools_3.5.0            digest_0.6.12          
 [5] plyr_1.8.4              RSQLite_2.0             zlibbioc_1.22.0         rlang_0.1.2            
 [9] lazyeval_0.2.0          gdata_2.18.0            SparseM_1.77            blob_1.1.0             
[13] Matrix_1.2-11           splines_3.4.2           stringr_1.2.0           topGO_2.28.0           
[17] RCurl_1.95-4.8          bit_1.1-12              munsell_0.4.3           compiler_3.4.2         
[21] pkgconfig_2.0.1         Ringo_1.40.0            tibble_1.3.4            GenomeInfoDbData_0.99.0
[25] matrixStats_0.52.2      bitops_1.0-6            grid_3.4.2              xtable_1.8-2           
[29] gtable_0.2.0            affy_1.54.0             DBI_0.7                 magrittr_1.5           
[33] scales_0.5.0            graph_1.54.0            KernSmooth_2.23-15      stringi_1.1.5          
[37] XVector_0.16.0          genefilter_1.58.1       affyio_1.46.0           RColorBrewer_1.1-2     
[41] tools_3.4.2             bit64_0.9-7             survival_2.41-3         colorspace_1.3-2       
[45] caTools_1.17.1          memoise_1.1.0           knitr_1.17             



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