Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[FEATURE] drawModules documentation: Failed to connect to localhost #9

Open
viallonv opened this issue Oct 2, 2019 · 1 comment
Open
Assignees

Comments

@viallonv
Copy link

viallonv commented Oct 2, 2019

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

@Livia-Rasp Livia-Rasp changed the title [BUG] [BUG] drawModules: Failed to connect to localhost Oct 3, 2019
@Livia-Rasp Livia-Rasp self-assigned this Oct 3, 2019
@Livia-Rasp Livia-Rasp changed the title [BUG] drawModules: Failed to connect to localhost [FEATURE] drawModules documentation: Failed to connect to localhost Oct 3, 2019
@Livia-Rasp
Copy link
Collaborator

Livia-Rasp commented Oct 3, 2019

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants