Merge branch 'devel' into feature/cleanup-and-refactor

ipb-halle · Jan 30, 2025 · 698091c · 698091c
2 parents eac46fc + 0a349b9
commit 698091c
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Showing 6 changed files with 32 additions and 24 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,11 @@
 Package: MetFamily
 Type: Package
 Title: MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
-Version: 0.99.4
-Date: 2024-08-22
-Author: c( person("Hendrik", "Treutler, role = c("aut"), email = "[email protected]"),
-           person("Khabat", "Vahabi", role = c("aut"), email = "[email protected]"),
-           person("Norman", "Storz", role = c("aut"), email = "[email protected]"),
+Version: 0.99.5
+Date: 2024-11-07
+Author: c( person(given = "Hendrik", family = "Treutler", role = c("aut"), email = "[email protected]"),
+           person(given = "Khabat", family = "Vahabi", role = c("ctb"), email = "[email protected]"),
+           person(given = "Norman", family = "Storz", role = c("ctb"), email = "[email protected]"),
            person(given = "Steffen", family = "Neumann", email = "[email protected]",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7899-7192")) )
 Depends:
@@ -32,7 +32,8 @@ Depends:
     matrixStats,
     plotrix,
     slam,
-    plotly
+    plotly,
+    xcms
 Imports:
     egg,
     graphics,

diff --git a/Dockerfile-base b/Dockerfile-base
@@ -1,5 +1,6 @@
 # syntax=docker/dockerfile:1.3-labs
 FROM rocker/shiny:4.4
+#FROM rocker/shiny:4.4
 
 LABEL maintainer="Steffen Neumann <[email protected]>"
 LABEL Description="MetFamily Base Image with dependencies."
@@ -28,8 +29,11 @@ RUN echo 'sanitize_errors off;disable_protocols xdr-streaming xhr-streaming ifra
 ## })
 ## EOF
 
+## Temporarily disable gcc choking on "error: format not a string literal and no format arguments"
+#RUN sed -i -e 's/-Werror=format-security//g' /usr/local/lib/R/etc/Makeconf
+
 ADD DESCRIPTION /tmp/MetFamily/DESCRIPTION
-RUN R -e 'options(warn=2) ; install.packages("devtools")'
-RUN R -e 'library(devtools); options(warn=2) ; install_deps("/tmp/MetFamily")'
+RUN R -e 'options(warn=2) ; install.packages(c("devtools", "BiocManager"))'
+RUN R -e 'library(devtools); options(warn=2) ; install_deps("/tmp/MetFamily", repos=BiocManager::repositories())'
 
 WORKDIR /srv/shiny-server
diff --git a/R/parsePeakAbundanceMatrixQF.R b/R/parsePeakAbundanceMatrixQF.R
@@ -191,6 +191,8 @@ parsePeakAbundanceMatrixQF <- function(qfeatures,
 #' @param siriusID 
 #'
 #' @return
+#' @importFrom SummarizedExperiment rowData
+#' @importFrom SummarizedExperiment rowData<- 
 #' @export
 #' @importFrom SummarizedExperiment rowData<-
 #'

diff --git a/inst/MetFamily/server.R b/inst/MetFamily/server.R
@@ -1,34 +1,35 @@
 
-options(shiny.sanitize.errors = FALSE)
-
 #########################################################################################
 #########################################################################################
 ## libraries and functions
 
 sourceFolder <- getwd()
 isDevelopment <- FALSE
-errorHunting <- FALSE
+errorHunting <- TRUE
+hcaHeatMapNew <- TRUE
+
+##
+## Load dependency libraries. Formerly in sourceTheCode()
+##
+library(MetFamily)
+load_metfamily_dependencies()
 
 #####################################################################################################
 ## handling of errors and warnings
 if(errorHunting){
   options(warn = 2, shiny.error = recover)
-  options(shiny.trace=TRUE)
+  #options(shiny.trace=TRUE)
+  options(shiny.trace=FALSE)
   options(shiny.fullstacktrace=TRUE)
   options(shiny.testmode=TRUE)
+  options(shiny.sanitize.errors = FALSE)
 } else {
   options(warn = 1, shiny.error = NULL)
   options(shiny.trace=FALSE)
   options(shiny.fullstacktrace=FALSE)
   options(shiny.testmode=FALSE)
 }
 
-##
-## Load dependency libraries. Formerly in sourceTheCode()
-##
-library(MetFamily)
-load_metfamily_dependencies()
-
 #########################################################################################
 #########################################################################################
 ## server-side logic of the Shiny app

diff --git a/inst/MetFamily/version.R b/inst/MetFamily/version.R
@@ -2,7 +2,7 @@
 
 toolName       <- "MetFamily"
 toolVersion    <- "1.0"    
-metFamilyAppVersion <- "1.3.4"
+metFamilyAppVersion <- "1.3.5"
 
 packageVersion <- package.version("MetFamily")
 

diff --git a/vignettes/discoveringregulatedmetabolitefamilies.Rmd b/vignettes/discoveringregulatedmetabolitefamilies.Rmd
@@ -97,7 +97,7 @@ pcaDimensionTwo <<- 2
 
   resultObj <- calcPlotPCAscores(
     pcaObj = pca, 
-    dataList = project, 
+    dataList = dataList, #project, 
     filterObj = filterObj,
     pcaDimensionOne = pcaDimensionOne, 
     pcaDimensionTwo = pcaDimensionTwo, 
@@ -108,7 +108,7 @@ pcaDimensionTwo <<- 2
 
   resultObj <- calcPlotPCAloadings(
     pcaObj = pca, 
-    dataList = project, 
+    dataList = dataList, #project, 
     filter = filterObj, 
     pcaDimensionOne = pcaDimensionOne, 
     pcaDimensionTwo = pcaDimensionTwo, 
@@ -136,9 +136,9 @@ HCA on MS2 in Figure \@ref(fig:hca).
 ```{r hca, fig.cap="HCA on MS2.", echo=FALSE}
 
 if (FALSE) {
-p <- calcPlotDendrogram_plotly(dataList=project, 
+p <- calcPlotDendrogram_plotly(dataList=dataList, #project, 
                                filterObj=filterObj, 
-                               clusterDataList=project, 
+                               clusterDataList=dataList, #project, 
   distanceMeasure = "Jaccard", 
   showClusterLabels=FALSE, 
   hcaPrecursorLabels="m/z / RT", 
@@ -156,7 +156,7 @@ load(fileName)
 fileName <- system.file("extdata/testdata/hcaFilter.Rdata", package = "MetFamily")
 load(fileName) 
 
-returnObj <- calcPlotDendrogram(dataList=project, 
+returnObj <- calcPlotDendrogram(dataList=dataList, #project, 
                                 filter=filter, 
                                 clusterDataList=clusterDataList, 
                                 annoPresentAnnotationsList = annoPresentAnnotationsList ,