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

Shraddha Pai @hr@ddh@p@|@neuro @end|ng |rom gm@||@com
Wed Jun 24 18:09:51 CEST 2020

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

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

Details below. Thanks!

Error: This is the error: "WARNING: An illegal reflective access operation
has occurred

WARNING: Illegal reflective access by net.sf.cglib.core.ReflectUtils$2
to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of

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

[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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