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.ne...@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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel