.dna file does not load into R

[MarleneKammerer]

Hi Afer successfully installing rDNA, I now have a problem loading my DNA file into R. I tested loading the sample file, but I have the same problem as with my own file. This is the code I ran:

library("rDNA") set.seed (12345)

dna_init ("dna-2.0-beta22.jar") dna_gui("Level3_CH_2017.dna") conn <- dna_connection("Level3_CH_2017.dna")

The DNA Software opens in a new window, but then RStudies does nothing. I tried both, the sample file and my own file.

This is my sessionInfo():

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252 LC_MONETARY=German_Switzerland.1252 [4] LC_NUMERIC=C LC_TIME=German_Switzerland.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] rDNA_2.1.9 rJava_0.9-10 cluster_2.0.7-1 igraph_1.2.2 xergm_1.8.3 GERGM_0.13.0
[7] rem_1.3.1 tnam_1.6.5 btergm_1.9.3 ggplot2_3.1.0 xergm.common_1.7.7 statnet_2018.10
[13] tsna_0.2.0 sna_2.4 ergm.count_3.3.0 statnet.common_4.1.4 tergm_3.5.2 networkDynamic_0.9.0 [19] ergm_3.9.4 network_1.13.0.1

loaded via a namespace (and not attached): [1] mcmc_0.9-5 nlme_3.1-137 bitops_1.0-6 doParallel_1.0.14 tools_3.5.1 R6_2.3.0
[7] vegan_2.5-3 KernSmooth_2.23-15 splitstackshape_1.4.6 lazyeval_0.2.1 mgcv_1.8-24 colorspace_1.3-2
[13] permute_0.9-4 withr_2.1.2 tidyselect_0.2.5 gridExtra_2.3 compiler_3.5.1 quantreg_5.36
[19] SparseM_1.77 caTools_1.17.1.1 scales_1.0.0 DEoptimR_1.0-8 robustbase_0.93-3 speedglm_0.3-2
[25] stringr_1.3.1 digest_0.6.18 minqa_1.2.4 MCMCpack_1.4-4 pkgconfig_2.0.2 lme4_1.1-18-1
[31] rlang_0.3.0.1 rstudioapi_0.8 bindr_0.1.1 farver_1.0 gtools_3.8.1 dplyr_0.7.7
[37] magrittr_1.5 texreg_1.36.23 Matrix_1.2-14 Rcpp_1.0.0 munsell_0.5.0 viridis_0.5.1
[43] stringi_1.2.4 ggraph_1.0.2 MASS_7.3-50 gplots_3.0.1 plyr_1.8.4 grid_3.5.1
[49] parallel_3.5.1 gdata_2.18.0 ggrepel_0.8.0 crayon_1.3.4 lattice_0.20-35 cowplot_0.9.3
[55] splines_3.5.1 pillar_1.3.0 tcltk_3.5.1 boot_1.3-20 reshape2_1.4.3 codetools_0.2-15
[61] lpSolve_5.6.13 stats4_3.5.1 glue_1.3.0 trust_0.1-7 data.table_1.11.8 RcppParallel_4.4.1
[67] RSiena_1.2-12 nloptr_1.2.1 tweenr_1.0.0 foreach_1.4.4 MatrixModels_0.4-1 gtable_0.2.0
[73] purrr_0.2.5 assertthat_0.2.0 ggforce_0.1.3 coda_0.19-2 viridisLite_0.3.0 tibble_1.4.2
[79] iterators_1.0.10 units_0.6-1 bindrcpp_0.2.2 ROCR_1.0-7

[leifeld]

See here: https://github.com/leifeld/dna/issues/133#issuecomment-388112253

[MarleneKammerer]

Thanks. And sorry for asking the same question again. I really did not understand (even though I have seen the other comment before I posted the issue) that I need NOT to run the dna_gui() command. My bad. I should have read the comment more carfully. Now it worked super quickly. However, maybe you could still add a respective comment to the manual - would make it easier ;-) ? Best Marlene

[JBGruber]

Hi @MarleneKammerer, thanks for the suggestion. I meant to do this for a while but haven't had the chance in the last few weeks. You can download the new PDF now if you like. But the description of dna_gui() is really all that has changed.