[Bioc-devel] ExperimentList Contructor Failing

Dario Strbenac dstr7320 at uni.sydney.edu.au
Tue Sep 12 08:00:56 CEST 2017

Good day,

Although the package seems to build without errors, I can't run the basic examples of MultiAssayExperiment successfully.

> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “NULL” is not valid for slot ‘elementMetadata’ in an object of class “ExperimentList”; is(value, "DataTableORNULL") is not TRUE

Everything seems fine with the package check:

> BiocInstaller::biocValid()

* sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8       
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

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

other attached packages:
[1] MultiAssayExperiment_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               BiocInstaller_1.26.1       compiler_3.4.1            
 [4] GenomeInfoDb_1.12.2        plyr_1.8.4                 XVector_0.16.0            
 [7] bitops_1.0-6               tools_3.4.1                zlibbioc_1.22.0           
[10] digest_0.6.12              tibble_1.3.4               gtable_0.2.0              
[13] lattice_0.20-35            rlang_0.1.2                Matrix_1.2-11             
[16] DelayedArray_0.2.7         shiny_1.0.5                parallel_3.4.1            
[19] GenomeInfoDbData_0.99.0    gridExtra_2.3              stringr_1.2.0             
[22] UpSetR_1.3.3               S4Vectors_0.14.4           IRanges_2.10.3            
[25] stats4_3.4.1               grid_3.4.1                 shinydashboard_0.6.1      
[28] glue_1.1.1                 Biobase_2.36.2             R6_2.2.2                  
[31] purrr_0.2.3                tidyr_0.7.1                magrittr_1.5              
[34] reshape2_1.4.2             ggplot2_2.2.1              scales_0.5.0              
[37] matrixStats_0.52.2         htmltools_0.3.6            BiocGenerics_0.22.0       
[40] GenomicRanges_1.28.5       SummarizedExperiment_1.6.3 mime_0.5                  
[43] xtable_1.8-2               colorspace_1.3-2           httpuv_1.3.5              
[46] stringi_1.1.5              RCurl_1.95-4.8             lazyeval_0.2.0            
[49] munsell_0.4.3             

* Out-of-date packages
      Package LibPath                         Installed Built   ReposVer
rJava "rJava" "/usr/local/lib/R/site-library" "0.9-8"   "3.2.3" "0.9-8" 
rJava "https://cran.rstudio.com/src/contrib"

update with biocLite()

Error: 1 package(s) out of date

The same example works on another computer using Windows operating system. What's the issue with this Linux environment?

Dario Strbenac
University of Sydney
Camperdown NSW 2050

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