From 62c9459631141cdea42d0ab91dc59523c333c0ea Mon Sep 17 00:00:00 2001 From: Daniel Claborne Date: Mon, 2 Dec 2024 14:46:04 -0800 Subject: [PATCH 1/2] remove the edata_cname from sample choices when uploading CoreMS data --- Reactive_Variables/upload_revals.R | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Reactive_Variables/upload_revals.R b/Reactive_Variables/upload_revals.R index 2305131..f66ff40 100644 --- a/Reactive_Variables/upload_revals.R +++ b/Reactive_Variables/upload_revals.R @@ -47,7 +47,11 @@ emeta_cnames <- reactive({names(Emeta())}) # Object: Sample names from e_data sample_names <- reactive({ - setdiff(edata_cnames(), input$edata_id_col) + if (!is.null(revals$uploaded_data) & is.null(input$file_edata$datapath)) { + setdiff(edata_cnames(), attr(revals$uploaded_data, "cnames")$edata_cname) + } else { + setdiff(edata_cnames(), input$edata_id_col) + } }) # Create reactive fake f_data (used when action button creates peakData()) From 4091ba4ba8fde5a60c81fcb6da81783674c00692 Mon Sep 17 00:00:00 2001 From: Daniel Claborne Date: Tue, 3 Dec 2024 09:37:54 -0800 Subject: [PATCH 2/2] update ftmsRanalysis to include hotfix in lockfile, version 1.2.4 --- DESCRIPTION | 2 +- renv.lock | 201 +++++++++++++++++++++++++--------------------------- ui.R | 2 +- 3 files changed, 98 insertions(+), 107 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 27ab484..4aa4956 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FREDA Title: An app for the processing and visualization of Fourier-transform mass spectrometry data. -Version: 1.2.3 +Version: 1.2.4 Authors@R: c(person("Lisa", "Bramer", "lisa.bramer@pnnl.gov", role = "aut", "cre"), person("Daniel", "Claborne", "daniel.claborne@pnnl.gov", role = c("aut"))) Description: A frontend application which exposes functionality of the ftmsRanalysis R package. See diff --git a/renv.lock b/renv.lock index 0fca4dd..e34975e 100644 --- a/renv.lock +++ b/renv.lock @@ -139,7 +139,7 @@ }, "ape": { "Package": "ape", - "Version": "5.7-1", + "Version": "5.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -154,17 +154,17 @@ "stats", "utils" ], - "Hash": "10705eec964349f270504754d8fe8ef1" + "Hash": "16b5ff4dff0ead9ea955f62f794b1535" }, "askpass": { "Package": "askpass", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "sys" ], - "Hash": "cad6cf7f1d5f6e906700b9d3e718c796" + "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a" }, "base64enc": { "Package": "base64enc", @@ -178,17 +178,17 @@ }, "bit": { "Package": "bit", - "Version": "4.0.5", + "Version": "4.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "d242abec29412ce988848d0294b208fd" + "Hash": "5dc7b2677d65d0e874fc4aaf0e879987" }, "bit64": { "Package": "bit64", - "Version": "4.0.5", + "Version": "4.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -198,17 +198,18 @@ "stats", "utils" ], - "Hash": "9fe98599ca456d6552421db0d6772d8f" + "Hash": "e84984bf5f12a18628d9a02322128dfd" }, "bslib": { "Package": "bslib", - "Version": "0.6.1", + "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "cachem", + "fastmap", "grDevices", "htmltools", "jquerylib", @@ -219,18 +220,18 @@ "rlang", "sass" ], - "Hash": "c0d8599494bc7fb408cd206bbdd9cab0" + "Hash": "b299c6741ca9746fb227debcb0f9fb6c" }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "callr": { "Package": "callr", @@ -247,14 +248,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.2", + "Version": "3.6.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" + "Hash": "b21916dd77a27642b447374a5d30ecf3" }, "clipr": { "Package": "clipr", @@ -292,7 +293,7 @@ }, "colorspace": { "Package": "colorspace", - "Version": "2.1-0", + "Version": "2.1-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -302,7 +303,7 @@ "methods", "stats" ], - "Hash": "f20c47fd52fae58b4e377c37bb8c335b" + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" }, "commonmark": { "Package": "commonmark", @@ -313,17 +314,17 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.7", + "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "5a295d7d963cc5035284dcdbaf334f4e" + "Hash": "91570bba75d0c9d3f1040c835cee8fba" }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -331,7 +332,7 @@ "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Hash": "859d96e65ef198fd43e82b9628d593ef" }, "crosstalk": { "Package": "crosstalk", @@ -348,24 +349,24 @@ }, "curl": { "Package": "curl", - "Version": "5.2.0", + "Version": "6.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "Hash": "e8ba62486230951fcd2b881c5be23f96" }, "data.table": { "Package": "data.table", - "Version": "1.14.10", + "Version": "1.16.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "6ea17a32294d8ca00455825ab0cf71b9" + "Hash": "2e00b378fc3be69c865120d9f313039a" }, "datadr": { "Package": "datadr", @@ -391,14 +392,14 @@ }, "digest": { "Package": "digest", - "Version": "0.6.34", + "Version": "0.6.37", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a" + "Hash": "33698c4b3127fc9f506654607fb73676" }, "dplyr": { "Package": "dplyr", @@ -423,27 +424,15 @@ ], "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, "evaluate": { "Package": "evaluate", - "Version": "0.23", + "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "R", - "methods" + "R" ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + "Hash": "3fd29944b231036ad67c3edb32e02201" }, "fansi": { "Package": "fansi", @@ -459,21 +448,21 @@ }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fontawesome": { "Package": "fontawesome", - "Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -481,18 +470,18 @@ "htmltools", "rlang" ], - "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" + "Hash": "bd1297f9b5b1fc1372d19e2c4cd82215" }, "fs": { "Package": "fs", - "Version": "1.6.3", + "Version": "1.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "47b5f30c720c23999b913a1a635cf0bb" + "Hash": "7f48af39fa27711ea5fbd183b399920d" }, "ftmsRanalysis": { "Package": "ftmsRanalysis", @@ -503,8 +492,8 @@ "RemoteHost": "api.github.com", "RemoteRepo": "ftmsRanalysis", "RemoteUsername": "EMSL-Computing", - "RemoteRef": "master", - "RemoteSha": "d4c2b9a4ffba2c07126e6732efa62792bc114796", + "RemoteRef": "d8338edbe7df167085b60e7c1b660ad018900028", + "RemoteSha": "d8338edbe7df167085b60e7c1b660ad018900028", "Requirements": [ "R", "RColorBrewer", @@ -525,7 +514,7 @@ "tidyr", "vegan" ], - "Hash": "87885633ec68f669a1fca2b32293c18a" + "Hash": "5043412e26f5d551e620aa688e2eb3aa" }, "generics": { "Package": "generics", @@ -540,7 +529,7 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.4", + "Version": "3.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -561,18 +550,18 @@ "vctrs", "withr" ], - "Hash": "313d31eff2274ecf4c1d3581db7241f9" + "Hash": "44c6a2f8202d5b7e878ea274b1092426" }, "glue": { "Package": "glue", - "Version": "1.7.0", + "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "e0b3a53876554bd45879e596cdb10a52" + "Hash": "5899f1eaa825580172bb56c08266f37c" }, "gridExtra": { "Package": "gridExtra", @@ -590,7 +579,7 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.4", + "Version": "0.3.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -599,9 +588,10 @@ "glue", "grid", "lifecycle", - "rlang" + "rlang", + "stats" ], - "Hash": "b29cf3031f49b04ab9c852c912547eef" + "Hash": "de949855009e2d4d0e52a844e30617ae" }, "here": { "Package": "here", @@ -632,14 +622,14 @@ }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.11", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, "hms": { "Package": "hms", @@ -657,20 +647,19 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.7", + "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -719,7 +708,7 @@ }, "igraph": { "Package": "igraph", - "Version": "1.5.1", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -735,9 +724,10 @@ "pkgconfig", "rlang", "stats", - "utils" + "utils", + "vctrs" ], - "Hash": "80401cb5ec513e8ddc56764d03f63669" + "Hash": "c03878b48737a0e2da3b772d7b2e22da" }, "isoband": { "Package": "isoband", @@ -762,13 +752,13 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.8", + "Version": "1.8.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "e1b9c55281c5adc4dd113652d9e26768" + "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" }, "kableExtra": { "Package": "kableExtra", @@ -800,7 +790,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.45", + "Version": "1.49", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -812,7 +802,7 @@ "xfun", "yaml" ], - "Hash": "1ec462871063897135c1bcbe0fc8f07d" + "Hash": "9fcb189926d93c636dea94fbe4f44480" }, "labeling": { "Package": "labeling", @@ -827,14 +817,14 @@ }, "later": { "Package": "later", - "Version": "1.3.2", + "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Rcpp", "rlang" ], - "Hash": "a3e051d405326b8b0012377434c62b37" + "Hash": "501744395cac0bab0fbcfab9375ae92c" }, "lattice": { "Package": "lattice", @@ -955,14 +945,14 @@ }, "munsell": { "Package": "munsell", - "Version": "0.5.0", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "colorspace", "methods" ], - "Hash": "6dfe8bf774944bd5595785e3229d8771" + "Hash": "4fd8900853b746af55b81fda99da7695" }, "nlme": { "Package": "nlme", @@ -980,13 +970,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.1.1", + "Version": "2.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" + "Hash": "d413e0fef796c9401a4419485f709ca1" }, "pander": { "Package": "pander", @@ -1046,7 +1036,7 @@ }, "plotly": { "Package": "plotly", - "Version": "4.10.3", + "Version": "4.10.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1074,7 +1064,7 @@ "vctrs", "viridisLite" ], - "Hash": "56914cc61df53f2d0283d5498680867e" + "Hash": "a1ac5c03ad5ad12b9d1597e00e23c3dd" }, "plyr": { "Package": "plyr", @@ -1136,7 +1126,7 @@ }, "promises": { "Package": "promises", - "Version": "1.2.1", + "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1148,7 +1138,7 @@ "rlang", "stats" ], - "Hash": "0d8a15c9d000970ada1ab21405387dee" + "Hash": "c84fd4f75ea1f5434735e08b7f50fbca" }, "ps": { "Package": "ps", @@ -1270,18 +1260,18 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.3", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "42548638fae05fd9a9b5f3f437fbbbe2" + "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.26", + "Version": "2.29", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1300,7 +1290,7 @@ "xfun", "yaml" ], - "Hash": "9b148e7f95d33aac01f31282d49e4f44" + "Hash": "df99277f63d01c34e95e3d2f06a79736" }, "rprojroot": { "Package": "rprojroot", @@ -1341,7 +1331,7 @@ }, "sass": { "Package": "sass", - "Version": "0.4.8", + "Version": "0.4.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1351,7 +1341,7 @@ "rappdirs", "rlang" ], - "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035" + "Hash": "d53dbfddf695303ea4ad66f86e99b95d" }, "scales": { "Package": "scales", @@ -1517,7 +1507,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1526,7 +1516,7 @@ "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -1559,10 +1549,10 @@ }, "sys": { "Package": "sys", - "Version": "3.4.2", + "Version": "3.4.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" + "Hash": "de342ebfebdbf40477d0758d05426646" }, "systemfonts": { "Package": "systemfonts", @@ -1596,7 +1586,7 @@ }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1615,11 +1605,11 @@ "utils", "vctrs" ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1631,17 +1621,17 @@ "vctrs", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "tinytex": { "Package": "tinytex", - "Version": "0.49", + "Version": "0.54", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" + "Hash": "3ec7e3ddcacc2d34a9046941222bf94d" }, "tzdb": { "Package": "tzdb", @@ -1690,7 +1680,7 @@ }, "vegan": { "Package": "vegan", - "Version": "2.6-4", + "Version": "2.6-8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1701,7 +1691,7 @@ "mgcv", "permute" ], - "Hash": "659fe7589b8e0b16baa49043a61a0ce0" + "Hash": "1cf04791d6222288c30d3c7d887da1ea" }, "viridis": { "Package": "viridis", @@ -1767,7 +1757,7 @@ }, "withr": { "Package": "withr", - "Version": "3.0.0", + "Version": "3.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1775,19 +1765,20 @@ "grDevices", "graphics" ], - "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + "Hash": "cc2d62c76458d425210d1eb1478b30b4" }, "xfun": { "Package": "xfun", - "Version": "0.43", + "Version": "0.49", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "grDevices", "stats", "tools" ], - "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + "Hash": "8687398773806cfff9401a2feca96298" }, "xml2": { "Package": "xml2", @@ -1816,10 +1807,10 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" } } } diff --git a/ui.R b/ui.R index 97b2df2..36df542 100644 --- a/ui.R +++ b/ui.R @@ -15,7 +15,7 @@ ui <- tagList(useShinyjs(), ), navbarPage( - title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.3")), + title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.4")), windowTitle = 'FREDA', id = "top_page", theme = "yeti.css",