[Bioc-devel] Unable to reproduce OS/X build error for "netDx" package

[Mike Smith]

Hi Shraddha,

I don't know what Java the build system uses, but I can reproduce the error
with Java 13.  It's fine with Java 8 as you say.

I wont copy the whole error message as it's the same as I see on the build
system, but I do notice that in the middle I see:

Java 8 detected

This seems wrong for my system:

> system2('java', '-version')
java version "13.0.2" 2020-01-14
Java(TM) SE Runtime Environment (build 13.0.2+8)
Java HotSpot(TM) 64-Bit Server VM (build 13.0.2+8, mixed mode, sharing)

Perhaps there's an issue with whatever part of the code is detecting the
version of java?

Mike


On Wed, 24 Jun 2020 at 18:10, Shraddha Pai <shraddhapai.neuro using gmail.com>
wrote:

> Hi BioC community,
> My package relies on a Java jar and detects whether the OS has Java 8 or
> 11, to be accordingly compatible. I can't seem to resolve the build error
> on the BioC Mac system; the error message is a symptom of Java 8
> incompatibility.
>
> However, on my 2014 Mac Air which runs Java 8, the offending example
> ("Predict_CaseControl_from_CNV.Rmd") runs through to completion. What is
> the issue here? It would be great to have all operating systems building
> successfully.
>
> Details below. Thanks!
>
> Shraddha
> ---
> Error: This is the error: "WARNING: An illegal reflective access operation
> has occurred
>
> WARNING: Illegal reflective access by net.sf.cglib.core.ReflectUtils$2
>
> (file:/Users/biocbuild/Library/Caches/netDx/763502120e4_genemania-netdx.jar)
> to method
> java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
> WARNING: Please consider reporting this to the maintainers of
> net.sf.cglib.core.ReflectUtils$2"
>
> Mac specs: MacBook Air early 2014; High Sierra 10.13.6
>
> "java -version"  output:
> java version "1.8.0_31"
> Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
> Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)
>
> R: 4.0.2 ; BioC 3.11
>
> sessionInfo output:
> > sessionInfo()
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS High Sierra 10.13.6
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] C/C/C/C/C/en_CA.UTF-8
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] BiocFileCache_1.12.0 dbplyr_1.4.4         GenomicRanges_1.40.0
> [4] GenomeInfoDb_1.24.2  IRanges_2.22.2       S4Vectors_0.26.1
> [7] BiocGenerics_0.34.0  netDx_1.1.1          BiocStyle_2.16.0
>
> loaded via a namespace (and not attached):
>  [1] Biobase_2.48.0              httr_1.4.1
>  [3] splines_4.0.2               bit64_0.9-7
>  [5] foreach_1.5.0               R.utils_2.9.2
>  [7] assertthat_0.2.1            BiocManager_1.30.10
>  [9] blob_1.2.1                  GenomeInfoDbData_1.2.3
> [11] yaml_2.2.1                  pillar_1.4.4
> [13] RSQLite_2.2.0               lattice_0.20-41
> [15] glue_1.4.1                  digest_0.6.25
> [17] RColorBrewer_1.1-2          XVector_0.28.0
> [19] colorspace_1.4-1            plyr_1.8.6
> [21] htmltools_0.5.0             Matrix_1.2-18
> [23] R.oo_1.23.0                 XML_3.99-0.3
> [25] pkgconfig_2.0.3             bookdown_0.20
> [27] zlibbioc_1.34.0             purrr_0.3.4
> [29] scales_1.1.1                MultiAssayExperiment_1.14.0
> [31] pracma_2.2.9                combinat_0.0-8
> [33] tibble_3.0.1                generics_0.0.2
> [35] ggplot2_3.3.2               ellipsis_0.3.1
> [37] SummarizedExperiment_1.18.1 ROCR_1.0-11
> [39] survival_3.1-12             RJSONIO_1.3-1.4
> [41] magrittr_1.5                crayon_1.3.4
> [43] memoise_1.1.0               evaluate_0.14
> [45] R.methodsS3_1.8.0           doParallel_1.0.15
> [47] graph_1.66.0                tools_4.0.2
> [49] lifecycle_0.2.0             matrixStats_0.56.0
> [51] stringr_1.4.0               glmnet_4.0-2
> [53] munsell_0.5.0               DelayedArray_0.14.0
> [55] compiler_4.0.2              rlang_0.4.6
> [57] grid_4.0.2                  RCurl_1.98-1.2
> [59] iterators_1.0.12            rappdirs_0.3.1
> [61] bigmemory.sri_0.1.3         igraph_1.2.5
> [63] bitops_1.0-6                rmarkdown_2.3
> [65] gtable_0.3.0                codetools_0.2-16
> [67] RCy3_2.8.0                  DBI_1.1.0
> [69] curl_4.3                    reshape2_1.4.4
> [71] bigmemory_4.5.36            R6_2.4.1
> [73] knitr_1.29                  dplyr_1.0.0
> [75] bit_1.1-15.2                shape_1.4.4
> [77] stringi_1.4.6               Rcpp_1.0.4.6
> [79] vctrs_0.3.1                 tidyselect_1.1.0
> [81] xfun_0.15
>
>
> --
> Shraddha Pai, PhD
> http://shraddhapai.com ; @spaiglass on Twitter
> Post-doctoral Fellow, http://baderlab.org
> The Donnelly Centre for Cellular and Biomolecular Research
> University of Toronto
>
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>
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