[Bioc-devel] ExperimentList Contructor Failing

[Marcel Ramos]

Hi Dario,

I wasn't able to reproduce this error on my version of Ubuntu. (see below)

Please kindly post any future package inquiries at
support.bioconductor.org.


Best,

Marcel

---


> ExperimentList()
ExperimentList class object of length 0: 

> BiocInstaller::biocValid()

* sessionInfo()

R version 3.4.1 Patched (2017-07-19 r72930)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/libf77blas.so.3.0
LAPACK: /usr/lib/openblas-base/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      

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

other attached packages:
[1] MultiAssayExperiment_1.2.1


On 09/12/2017 02:00 AM, Dario Strbenac wrote:
> Good day,
>
> Although the package seems to build without errors, I can't run the basic examples of MultiAssayExperiment successfully.
>
> library(MultiAssayExperiment)
>> 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
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8       
>  [4] LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=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" 
>       Repository                            
> 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
> Australia
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
Marcel Ramos
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics


This email message may contain legally privileged and/or...{{dropped:4}}