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tmuetze / Bioconductor_RCy3_the_new_RCytoscape

Update RCytoscape to work for Cytoscape 3.0 and higher using CyREST
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existing.Cytoscape.Window #8

Closed m-grimes closed 9 years ago

m-grimes commented 9 years ago

Tanja

SessionInfo keeps telling me that RCY 99.2 is installed, though I have installed 99.5 from the terminal command line and within R. Not sure if this is the issue but existing.CytoscapeWindow fails.

Mark

Use RCy3

k2.w <- existing.CytoscapeWindow("Case 2 Pathway", copy=TRUE) Error in function (type, msg, asError = TRUE) : Failed to connect to localhost port 9000: Connection refused getWindowList(cy) [1] "Case 1 Pathway" "Case 3 Pathway" "Case 2 Pathway" "Case 5 Pathway" k2.w <- existing.CytoscapeWindow("Case 2 Pathway", copy=TRUE) Error in function (type, msg, asError = TRUE) : Failed to connect to localhost port 9000: Connection refused sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets [9] methods base

other attached packages: [1] RCy3_0.99.2 RJSONIO_1.3-0 rgl_0.95.1247 RefNet_1.4.0
[5] shiny_0.11.1 RCurl_1.95-4.6 bitops_1.0-6 AnnotationHub_2.0.1 [9] PSICQUIC_1.6.0 plyr_1.8.2 httr_0.6.1 biomaRt_2.24.0
[13] Biostrings_2.36.1 XVector_0.8.0 GOstats_2.34.0 Category_2.34.0
[17] Matrix_1.2-0 GO.db_3.1.2 org.Hs.eg.db_3.1.2 RSQLite_1.0.0
[21] DBI_0.3.1 AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0 IRanges_2.2.1
[25] S4Vectors_0.6.0 Biobase_2.28.0 BiocGenerics_0.14.0 RCytoscape_1.18.0
[29] XMLRPC_0.3-0 graph_1.46.0 igraph_0.7.1 devtools_1.8.0
[33] gplots_2.17.0 Rtsne_0.9 tsne_0.1-2 vegan_2.2-1
[37] permute_0.8-3 RUnit_0.4.28 adegenet_1.4-2 ade4_1.7-2
[41] cluster_2.0.1 Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1
[45] survival_2.38-1 lattice_0.20-31 stringr_1.0.0 sos_1.3-8
[49] brew_1.0-6 fdrtool_1.2.14 qgraph_1.3.1

loaded via a namespace (and not attached): [1] nlme_3.1-120 RColorBrewer_1.1-2
[3] tools_3.2.0 R6_2.0.1
[5] rpart_4.1-9 KernSmooth_2.23-14
[7] d3Network_0.5.2.1 mgcv_1.8-6
[9] colorspace_1.2-6 nnet_7.3-9
[11] gridExtra_0.9.1 mnormt_1.5-2
[13] git2r_0.10.1 caTools_1.17.1
[15] scales_0.2.4 psych_1.5.4
[17] genefilter_1.50.0 quadprog_1.5-5
[19] RBGL_1.44.0 sem_3.1-5
[21] digest_0.6.8 pbivnorm_0.6.0
[23] foreign_0.8-63 AnnotationForge_1.10.1
[25] jpeg_0.1-8 htmltools_0.2.6
[27] huge_1.2.6 BiocInstaller_1.18.1
[29] gtools_3.4.2 acepack_1.3-3.3
[31] magrittr_1.5 Rcpp_0.11.6
[33] munsell_0.4.2 ape_3.2
[35] proto_0.3-10 stringi_0.4-1
[37] whisker_0.3-2 zlibbioc_1.14.0
[39] MASS_7.3-40 matrixcalc_1.0-3
[41] lavaan_0.5-18 gdata_2.16.1
[43] splines_3.2.0 annotate_1.46.0
[45] sna_2.3-2 rjson_0.2.15
[47] corpcor_1.6.7 reshape2_1.4.1
[49] XML_3.98-1.1 latticeExtra_0.6-26
[51] png_0.1-7 httpuv_1.3.2
[53] gtable_0.1.2 mime_0.3
[55] xtable_1.7-4 glasso_1.8
[57] memoise_0.2.1 ggm_2.3
[59] ellipse_0.3-8 rversions_1.0.0
[61] interactiveDisplayBase_1.6.0 GSEABase_1.30.1

library(RCy3) sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets [9] methods base

other attached packages: [1] RCy3_0.99.2 RJSONIO_1.3-0 rgl_0.95.1247 RefNet_1.4.0
[5] shiny_0.11.1 RCurl_1.95-4.6 bitops_1.0-6 AnnotationHub_2.0.1 [9] PSICQUIC_1.6.0 plyr_1.8.2 httr_0.6.1 biomaRt_2.24.0
[13] Biostrings_2.36.1 XVector_0.8.0 GOstats_2.34.0 Category_2.34.0
[17] Matrix_1.2-0 GO.db_3.1.2 org.Hs.eg.db_3.1.2 RSQLite_1.0.0
[21] DBI_0.3.1 AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0 IRanges_2.2.1
[25] S4Vectors_0.6.0 Biobase_2.28.0 BiocGenerics_0.14.0 RCytoscape_1.18.0
[29] XMLRPC_0.3-0 graph_1.46.0 igraph_0.7.1 devtools_1.8.0
[33] gplots_2.17.0 Rtsne_0.9 tsne_0.1-2 vegan_2.2-1
[37] permute_0.8-3 RUnit_0.4.28 adegenet_1.4-2 ade4_1.7-2
[41] cluster_2.0.1 Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1
[45] survival_2.38-1 lattice_0.20-31 stringr_1.0.0 sos_1.3-8
[49] brew_1.0-6 fdrtool_1.2.14 qgraph_1.3.1

loaded via a namespace (and not attached): [1] nlme_3.1-120 RColorBrewer_1.1-2
[3] tools_3.2.0 R6_2.0.1
[5] rpart_4.1-9 KernSmooth_2.23-14
[7] d3Network_0.5.2.1 mgcv_1.8-6
[9] colorspace_1.2-6 nnet_7.3-9
[11] gridExtra_0.9.1 mnormt_1.5-2
[13] git2r_0.10.1 caTools_1.17.1
[15] scales_0.2.4 psych_1.5.4
[17] genefilter_1.50.0 quadprog_1.5-5
[19] RBGL_1.44.0 sem_3.1-5
[21] digest_0.6.8 pbivnorm_0.6.0
[23] foreign_0.8-63 AnnotationForge_1.10.1
[25] jpeg_0.1-8 htmltools_0.2.6
[27] huge_1.2.6 BiocInstaller_1.18.1
[29] gtools_3.4.2 acepack_1.3-3.3
[31] magrittr_1.5 Rcpp_0.11.6
[33] munsell_0.4.2 ape_3.2
[35] proto_0.3-10 stringi_0.4-1
[37] whisker_0.3-2 zlibbioc_1.14.0
[39] MASS_7.3-40 matrixcalc_1.0-3
[41] lavaan_0.5-18 gdata_2.16.1
[43] splines_3.2.0 annotate_1.46.0
[45] sna_2.3-2 rjson_0.2.15
[47] corpcor_1.6.7 reshape2_1.4.1
[49] XML_3.98-1.1 latticeExtra_0.6-26
[51] png_0.1-7 httpuv_1.3.2
[53] gtable_0.1.2 mime_0.3
[55] xtable_1.7-4 glasso_1.8
[57] memoise_0.2.1 ggm_2.3
[59] ellipse_0.3-8 rversions_1.0.0
[61] interactiveDisplayBase_1.6.0 GSEABase_1.30.1

install.packages("/Users/Mark_Grimes/Documents/Work/R/Packages/Rcy3_0.99.5.tar.gz") inferring 'repos = NULL' from 'pkgs'

  • installing source package ‘RCy3’ ... * R * inst * preparing package for lazy loading Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class. * help ** installing help indices * building package indices * installing vignettes * testing if installed package can be loaded Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
  • DONE (RCy3) library("RCy3") sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets [9] methods base

other attached packages: [1] RCy3_0.99.2 RJSONIO_1.3-0 rgl_0.95.1247 RefNet_1.4.0
[5] shiny_0.11.1 RCurl_1.95-4.6 bitops_1.0-6 AnnotationHub_2.0.1 [9] PSICQUIC_1.6.0 plyr_1.8.2 httr_0.6.1 biomaRt_2.24.0
[13] Biostrings_2.36.1 XVector_0.8.0 GOstats_2.34.0 Category_2.34.0
[17] Matrix_1.2-0 GO.db_3.1.2 org.Hs.eg.db_3.1.2 RSQLite_1.0.0
[21] DBI_0.3.1 AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0 IRanges_2.2.1
[25] S4Vectors_0.6.0 Biobase_2.28.0 BiocGenerics_0.14.0 RCytoscape_1.18.0
[29] XMLRPC_0.3-0 graph_1.46.0 igraph_0.7.1 devtools_1.8.0
[33] gplots_2.17.0 Rtsne_0.9 tsne_0.1-2 vegan_2.2-1
[37] permute_0.8-3 RUnit_0.4.28 adegenet_1.4-2 ade4_1.7-2
[41] cluster_2.0.1 Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1
[45] survival_2.38-1 lattice_0.20-31 stringr_1.0.0 sos_1.3-8
[49] brew_1.0-6 fdrtool_1.2.14 qgraph_1.3.1

loaded via a namespace (and not attached): [1] nlme_3.1-120 RColorBrewer_1.1-2
[3] tools_3.2.0 R6_2.0.1
[5] rpart_4.1-9 KernSmooth_2.23-14
[7] d3Network_0.5.2.1 mgcv_1.8-6
[9] colorspace_1.2-6 nnet_7.3-9
[11] gridExtra_0.9.1 mnormt_1.5-2
[13] git2r_0.10.1 caTools_1.17.1
[15] scales_0.2.4 psych_1.5.4
[17] genefilter_1.50.0 quadprog_1.5-5
[19] RBGL_1.44.0 sem_3.1-5
[21] digest_0.6.8 pbivnorm_0.6.0
[23] foreign_0.8-63 AnnotationForge_1.10.1
[25] jpeg_0.1-8 htmltools_0.2.6
[27] huge_1.2.6 BiocInstaller_1.18.1
[29] gtools_3.4.2 acepack_1.3-3.3
[31] magrittr_1.5 Rcpp_0.11.6
[33] munsell_0.4.2 ape_3.2
[35] proto_0.3-10 stringi_0.4-1
[37] whisker_0.3-2 zlibbioc_1.14.0
[39] MASS_7.3-40 matrixcalc_1.0-3
[41] lavaan_0.5-18 gdata_2.16.1
[43] splines_3.2.0 annotate_1.46.0
[45] sna_2.3-2 rjson_0.2.15
[47] corpcor_1.6.7 reshape2_1.4.1
[49] XML_3.98-1.1 latticeExtra_0.6-26
[51] png_0.1-7 httpuv_1.3.2
[53] gtable_0.1.2 mime_0.3
[55] xtable_1.7-4 glasso_1.8
[57] memoise_0.2.1 ggm_2.3
[59] ellipse_0.3-8 rversions_1.0.0
[61] interactiveDisplayBase_1.6.0 GSEABase_1.30.1

k2.w <- existing.CytoscapeWindow("Case 2 Pathway", copy=TRUE) Error in function (type, msg, asError = TRUE) : Failed to connect to localhost port 9000: Connection refused

tmuetze commented 9 years ago

The errors tell me that it is a versioning issue as you correctly assessed as well. It was not able to install v5. I made some changes in the DESCRIPTION file and upgraded the version to v6. Please discard all previous versions.