From 15aaa115833600ff6b6bbba6c987b2c641be09e8 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 12 Oct 2026 13:00:02 +0100 Subject: [PATCH 1/3] Fixing line length (over 100) problems/notes --- R/ds.asCharacter.R | 3 ++- R/ds.asDataMatrix.R | 3 ++- R/ds.asInteger.R | 3 ++- R/ds.asNumeric.R | 3 ++- R/ds.completeCases.R | 9 ++++++--- R/ds.dataFrame.R | 3 ++- R/ds.dataFrameSort.R | 3 ++- R/ds.densityGrid.R | 7 ++++--- 8 files changed, 22 insertions(+), 12 deletions(-) diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R index 623e43dbe..dfc68ee52 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -44,7 +44,8 @@ #' # Converting the R object into a class character #' ds.asCharacter(x.name = "D$LAB_TSC", #' newobj = "char.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Opal server +#' #is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R index bdfa9fdd0..a49edce4a 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -43,7 +43,8 @@ #' # Converting the R object into a matrix #' ds.asDataMatrix(x.name = "D", #' newobj = "mat.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Opal server +#' #is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R index 0e9670df0..b2457de7f 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -57,7 +57,8 @@ #' # Converting the R object into an integer #' ds.asInteger(x.name = "D$LAB_TSC", #' newobj = "int.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Opal server +#' #is used ("study1") #' ds.class(x = "int.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index 803a6308d..f24fc76b0 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -57,7 +57,8 @@ #' # Converting the R object into a numeric class #' ds.asNumeric(x.name = "D$LAB_TSC", #' newobj = "num.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Opal server +#' #is used ("study1") #' ds.class(x = "num.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.completeCases.R b/R/ds.completeCases.R index 107f70de6..5cd3b5726 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -55,13 +55,16 @@ #' newobj = "D.completeCases", # name for the output object #' # that is stored in the Opal servers #' datasources = connections) # All Opal servers are used -#' # (see above the connection to the Opal servers) +#' # (see above the connection to +#' # the Opal servers) #' -#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Opal servers +#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in +#' #the Opal servers #' #(see above the connection to the Opal servers) #' newobj = "LAB_TSC.completeCases", #name for the output variable #' #that is stored in the Opal servers -#' datasources = connections[2]) #only the second Opal server is used ("study2") +#' datasources = connections[2]) #only the second Opal server +#' #is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index ccd671c4d..3e222ccc6 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -80,7 +80,8 @@ #' completeCases = TRUE, #only rows with not missing values are selected #' DataSHIELD.checks = FALSE, #' newobj = "df1", -#' datasources = connections[1], #only the first Opal server is used ("study1") +#' datasources = connections[1], #only the first Opal server +#' #is used ("study1") #' notify.of.progress = FALSE) #' #' diff --git a/R/ds.dataFrameSort.R b/R/ds.dataFrameSort.R index f8fc52f77..60a5bbdff 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -70,7 +70,8 @@ #' sort.descending = TRUE, #' sort.method = "numeric", #' newobj = "df.sort", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Opal server +#' #is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index d617dd731..23e886585 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -69,10 +69,11 @@ #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", #' type="split" -#' datasources = connections[1])#only the first Opal server is used ("study1") +#' datasources = connections[1])#only the first Opal server +#' #is used ("study1") #' -#' # Example3: generate a grid density object where the number of intervals is set to 15, for -#' each study separately +#' # Example3: generate a grid density object where the number of intervals is set to 15, +#' # for each study separately #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", #' type="split", From 072c28295be583de364d1fed5eb11491952d59d6 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 12 Oct 2026 16:10:19 +0100 Subject: [PATCH 2/3] Fixed type --- .../perf_files/armadillo_azure-pipeline_perf-profile.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/perf_files/armadillo_azure-pipeline_perf-profile.csv b/tests/testthat/perf_files/armadillo_azure-pipeline_perf-profile.csv index 547bac01d..84d295b95 100644 --- a/tests/testthat/perf_files/armadillo_azure-pipeline_perf-profile.csv +++ b/tests/testthat/perf_files/armadillo_azure-pipeline_perf-profile.csv @@ -51,7 +51,7 @@ "ds.levels::perf::combine:0","23.96","0.5","2" "ds.lexis::perf::0","3.760","0.5","2" "ds.list::perf::0","10.03","0.5","2" -"ds.listDisclosureSettings::perf::0","22.08,"0.5","2" +"ds.listDisclosureSettings::perf::0","22.08","0.5","2" "ds.log::perf::0","17.30","0.5","2" "ds.ls::perf::combine:0","24.35","0.5","2" "ds.lspline::perf::0","14.17","0.5","2" From ec019970b4a9fc74f488465f80d3f9501bf25929 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 12 Oct 2026 17:31:01 +0100 Subject: [PATCH 3/3] Updating roxygen2 to version: 8.1.1, plus side effects --- DESCRIPTION | 2 +- man/ds.asCharacter.Rd | 3 ++- man/ds.asDataMatrix.Rd | 3 ++- man/ds.asInteger.Rd | 3 ++- man/ds.asNumeric.Rd | 3 ++- man/ds.completeCases.Rd | 9 ++++++--- man/ds.dataFrame.Rd | 3 ++- man/ds.dataFrameSort.Rd | 3 ++- man/ds.densityGrid.Rd | 7 ++++--- 9 files changed, 23 insertions(+), 13 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index dd838b8c2..9cb98d931 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -90,4 +90,4 @@ Suggests: DSLite Encoding: UTF-8 Language: en-GB -Config/roxygen2/version: 8.1.0 +Config/roxygen2/version: 8.1.1 diff --git a/man/ds.asCharacter.Rd b/man/ds.asCharacter.Rd index e557c9fc1..7bfdcb5eb 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -58,7 +58,8 @@ Server function called: \code{asCharacterDS} # Converting the R object into a class character ds.asCharacter(x.name = "D$LAB_TSC", newobj = "char.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Opal server + #is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asDataMatrix.Rd b/man/ds.asDataMatrix.Rd index d9e253e6a..dec334475 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -60,7 +60,8 @@ Server function called: \code{asDataMatrixDS}. # Converting the R object into a matrix ds.asDataMatrix(x.name = "D", newobj = "mat.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Opal server + #is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asInteger.Rd b/man/ds.asInteger.Rd index 0bf7ab473..9f44a78e1 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -73,7 +73,8 @@ Server function called: \code{asIntegerDS} # Converting the R object into an integer ds.asInteger(x.name = "D$LAB_TSC", newobj = "int.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Opal server + #is used ("study1") ds.class(x = "int.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index 73f03693f..65876105b 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -72,7 +72,8 @@ Server function called: \code{asNumericDS} # Converting the R object into a numeric class ds.asNumeric(x.name = "D$LAB_TSC", newobj = "num.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Opal server + #is used ("study1") ds.class(x = "num.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.completeCases.Rd b/man/ds.completeCases.Rd index 8a8f4ea4f..d76e26d2c 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -70,13 +70,16 @@ Server function called: \code{completeCasesDS} newobj = "D.completeCases", # name for the output object # that is stored in the Opal servers datasources = connections) # All Opal servers are used - # (see above the connection to the Opal servers) + # (see above the connection to + # the Opal servers) - ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Opal servers + ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in + #the Opal servers #(see above the connection to the Opal servers) newobj = "LAB_TSC.completeCases", #name for the output variable #that is stored in the Opal servers - datasources = connections[2]) #only the second Opal server is used ("study2") + datasources = connections[2]) #only the second Opal server + #is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dataFrame.Rd b/man/ds.dataFrame.Rd index 918a50443..6cbb8d663 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -115,7 +115,8 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} completeCases = TRUE, #only rows with not missing values are selected DataSHIELD.checks = FALSE, newobj = "df1", - datasources = connections[1], #only the first Opal server is used ("study1") + datasources = connections[1], #only the first Opal server + #is used ("study1") notify.of.progress = FALSE) diff --git a/man/ds.dataFrameSort.Rd b/man/ds.dataFrameSort.Rd index af86a99fc..4873f8380 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -95,7 +95,8 @@ Server function called: \code{dataFrameSortDS}. sort.descending = TRUE, sort.method = "numeric", newobj = "df.sort", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Opal server + #is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 00fe1e91f..4d6f612bf 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -93,10 +93,11 @@ Server function called: \code{densityGridDS} ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", type="split" - datasources = connections[1])#only the first Opal server is used ("study1") + datasources = connections[1])#only the first Opal server + #is used ("study1") - # Example3: generate a grid density object where the number of intervals is set to 15, for - each study separately + # Example3: generate a grid density object where the number of intervals is set to 15, + # for each study separately ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", type="split",