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* Out-of-date packages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Error: 1 package(s) out of date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
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