Livia-Rasp
commented
5 years ago To Do Make it clearer in the documentation that Cytoscape has to be openend. for the method to work, i.e. write it in the roxygen documentation and maybe also the README file.
Describe the bug When calling the drawModules function, I get the following message, and error: Cytoscape output could take a few minutes... Error in curl::curl_fetch_memory(url, handle = handle) : Failed to connect to localhost port 1234: Connection refused
Environment (please complete the following information): R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] nlme_3.1-140 hglm_2.2-1 hglm.data_1.0-1 sp_1.3-1
[5] MASS_7.3-51.4 Matrix_1.2-17 reshape2_1.4.3 openxlsx_4.1.0.1
[9] foreach_1.4.4 haven_2.1.1 forcats_0.4.0 stringr_1.4.0
[13] dplyr_0.8.1 purrr_0.3.2 readr_1.3.1 tidyr_0.8.3
[17] tibble_2.1.3 ggplot2_3.2.0 tidyverse_1.2.1 MoDentify_0.99.0
[21] BiocParallel_1.16.6 igraph_1.2.4.1 data.table_1.12.2
loaded via a namespace (and not attached): [1] colorspace_1.4-1 rprojroot_1.3-2 htmlTable_1.13.1 corpcor_1.6.9
[5] base64enc_0.1-3 fs_1.3.1 rstudioapi_0.10 remotes_2.1.0
[9] longitudinal_1.1.12 fansi_0.4.0 lubridate_1.7.4 xml2_1.2.0
[13] codetools_0.2-16 splines_3.5.2 R.methodsS3_1.7.1 knitr_1.23
[17] pkgload_1.0.2 zeallot_0.1.0 Formula_1.2-3 jsonlite_1.6
[21] broom_0.5.2 cluster_2.1.0 R.oo_1.22.0 graph_1.60.0
[25] compiler_3.5.2 httr_1.4.0 backports_1.1.4 assertthat_0.2.1
[29] lazyeval_0.2.2 cli_1.1.0 acepack_1.4.1 htmltools_0.3.6
[33] prettyunits_1.0.2 tools_3.5.2 gtable_0.3.0 glue_1.3.1
[37] Rcpp_1.0.2 cellranger_1.1.0 vctrs_0.2.0 RJSONIO_1.3-1.2
[41] iterators_1.0.10 gbRd_0.4-11 xfun_0.8 RCy3_2.2.9
[45] ps_1.3.0 testthat_2.1.1 rvest_0.3.4 devtools_2.0.2
[49] XML_3.98-1.20 scales_1.0.0 hms_0.5.1 parallel_3.5.2
[53] GeneNet_1.2.13 RColorBrewer_1.1-2 curl_4.0 memoise_1.1.0
[57] gridExtra_2.3 rpart_4.1-15 latticeExtra_0.6-28 stringi_1.4.3
[61] desc_1.2.0 checkmate_1.9.3 BiocGenerics_0.28.0 zip_2.0.4
[65] pkgbuild_1.0.3 bibtex_0.4.2 Rdpack_0.11-0 rlang_0.4.0
[69] pkgconfig_2.0.2 lattice_0.20-38 htmlwidgets_1.3 processx_3.3.1
[73] tidyselect_0.2.5 plyr_1.8.4 magrittr_1.5 R6_2.4.0
[77] generics_0.0.2 Hmisc_4.2-0 pillar_1.4.2 foreign_0.8-71
[81] withr_2.1.2 survival_2.44-1.1 nnet_7.3-12 modelr_0.1.4
[85] crayon_1.3.4 fdrtool_1.2.15 utf8_1.1.4 usethis_1.5.0
[89] grid_3.5.2 readxl_1.3.1 callr_3.2.0 digest_0.6.20
[93] R.utils_2.9.0 stats4_3.5.2 munsell_0.5.0 sessioninfo_1.1.1