GeneNet method usage from netbenchmark package sometimes results in error:
> library(netbenchmark) > top20 <- netbenchmark(datasources.names = "syntren300", datasets.num=1, experiments = 280) datasource: syntren300 dataset: 1 aracne.wrap c3net.wrap clr.wrap GeneNet.wrap Estimate (local) false discovery rates (partial correlations): Error in .local(object, from, to, ...) : unknown nodes in 'from': ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA’, ‘NA
I'm not sure weather the error is inside GeneNet package or has smth to do with how netbenchmark handles the data subsetting. However, the bug is hard to catch, the same line above produces error only in 15% of cases.
> sessionInfo() R version 3.4.3 (2017-11-30) 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_US.UTF-8 LC_NUMERIC=C LC_TIME=uk_UA.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=uk_UA.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=uk_UA.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=uk_UA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] netbenchmark_1.8.0 grndata_1.8.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.14 lattice_0.20-35 randomForest_4.6-12 longitudinal_1.1.12 [5] corpcor_1.6.9 grid_3.4.3 stats4_3.4.3 magrittr_1.5 [9] pracma_2.1.1 graph_1.54.0 minet_3.34.0 GeneNet_1.2.13 [13] fdrtool_1.2.15 Matrix_1.2-11 c3net_1.1.1 tools_3.4.3 [17] igraph_1.1.2 parallel_3.4.3 compiler_3.4.3 BiocGenerics_0.22.1 [21] pkgconfig_2.0.1 PCIT_1.5-3
P.S.
https://github.com/Bioconductor/support.bioconductor.org/issues/33
I need to add some dummy sentence to bypass Language "X" is not one of the supported languages ['en']!
To thine own self be true, and it must follow, as the night the day, thou canst not then be false to any man.
To thine own self be true, and it must follow, as the night the day, thou canst not then be false to any man.
To thine own self be true, and it must follow, as the night the day, thou canst not then be false to any man.
To thine own self be true, and it must follow, as the night the day, thou canst not then be false to any man.