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@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
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