From 45ea3a148396ffe4c6456172c0698df51dbaeb0c Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 14 Oct 2026 14:05:10 +0100 Subject: [PATCH] Updating DESCRIPTION, perf_profile, roxygen2 to version: 8.1.1, plus side effects --- DESCRIPTION | 2 +- docs/404.html | 4 +- docs/LICENSE.html | 4 +- docs/PULL_REQUEST_TEMPLATE.html | 80 +++++++++++++++ docs/PULL_REQUEST_TEMPLATE.md | 38 ++++++++ docs/authors.html | 8 +- docs/authors.md | 4 +- ...=> 109cfdfecabbfbf5e2364aaceece5d12.woff2} | Bin ...=> 5cd426f27cf61d86c207d97f8db6cf8a.woff2} | Bin ...=> a8e2cb7ac3da2c4d38cd7c8c06ca5e46.woff2} | Bin ...=> c0540813382b64c1dde636c1fa0b592a.woff2} | Bin ...=> e0243c1a22ed284bb57c07b3ac886694.woff2} | Bin docs/index.html | 16 +-- docs/llms.txt | 10 +- docs/pkgdown.yml | 6 +- docs/reference/BooleDS.html | 5 +- docs/reference/BooleDS.md | 2 + docs/reference/absDS.html | 5 +- docs/reference/absDS.md | 2 + docs/reference/asCharacterDS.html | 5 +- docs/reference/asCharacterDS.md | 2 + docs/reference/asDataMatrixDS.html | 5 +- docs/reference/asDataMatrixDS.md | 2 + docs/reference/asFactorDS1.html | 8 +- docs/reference/asFactorDS1.md | 4 + docs/reference/asFactorDS2.html | 8 +- docs/reference/asFactorDS2.md | 4 + docs/reference/asFactorSimpleDS.html | 8 +- docs/reference/asFactorSimpleDS.md | 4 + docs/reference/asIntegerDS.html | 5 +- docs/reference/asIntegerDS.md | 2 + docs/reference/asListDS.html | 32 ++---- docs/reference/asListDS.md | 29 ++---- docs/reference/asLogicalDS.html | 15 +-- docs/reference/asLogicalDS.md | 10 +- docs/reference/asMatrixDS.html | 5 +- docs/reference/asMatrixDS.md | 2 + docs/reference/asNumericDS.html | 5 +- docs/reference/asNumericDS.md | 2 + docs/reference/aucDS.html | 5 +- docs/reference/aucDS.md | 2 + docs/reference/blackBoxDS.html | 4 +- docs/reference/blackBoxRanksDS.html | 4 +- docs/reference/boxPlotGGDS.html | 14 ++- docs/reference/boxPlotGGDS.md | 12 ++- .../reference/boxPlotGG_data_TreatmentDS.html | 14 ++- docs/reference/boxPlotGG_data_TreatmentDS.md | 11 ++- .../boxPlotGG_data_Treatment_numericDS.html | 16 +-- .../boxPlotGG_data_Treatment_numericDS.md | 13 ++- docs/reference/bp_standardsDS.html | 5 +- docs/reference/bp_standardsDS.md | 2 + docs/reference/cDS.html | 11 ++- docs/reference/cDS.md | 8 +- docs/reference/cbindDS.html | 5 +- docs/reference/cbindDS.md | 2 + docs/reference/changeRefGroupDS.html | 13 +-- docs/reference/changeRefGroupDS.md | 10 +- docs/reference/checkNegValueDS.html | 4 +- .../checkPermissivePrivacyControlLevel.html | 4 +- docs/reference/classDS.html | 5 +- docs/reference/classDS.md | 2 + docs/reference/colnamesDS.html | 4 +- docs/reference/completeCasesDS.html | 5 +- docs/reference/completeCasesDS.md | 2 + docs/reference/corDS.html | 8 +- docs/reference/corDS.md | 5 +- docs/reference/corTestDS.html | 8 +- docs/reference/corTestDS.md | 5 +- docs/reference/covDS.html | 8 +- docs/reference/covDS.md | 6 +- docs/reference/dataFrameDS.html | 5 +- docs/reference/dataFrameDS.md | 2 + docs/reference/dataFrameFillDS.html | 5 +- docs/reference/dataFrameFillDS.md | 2 + docs/reference/dataFrameSortDS.html | 5 +- docs/reference/dataFrameSortDS.md | 2 + docs/reference/dataFrameSubsetDS1.html | 5 +- docs/reference/dataFrameSubsetDS1.md | 2 + docs/reference/dataFrameSubsetDS2.html | 5 +- docs/reference/dataFrameSubsetDS2.md | 2 + docs/reference/densityGridDS.html | 22 +++-- docs/reference/densityGridDS.md | 25 +++-- docs/reference/dimDS.html | 8 +- docs/reference/dimDS.md | 6 +- docs/reference/dmtC2SDS.html | 4 +- docs/reference/dsBase-package.html | 4 +- docs/reference/elsplineDS.html | 5 +- docs/reference/elsplineDS.md | 2 + docs/reference/expDS.html | 87 +++++++++++++++++ docs/reference/expDS.md | 32 ++++++ docs/reference/extractQuantilesDS1.html | 4 +- docs/reference/extractQuantilesDS2.html | 4 +- docs/reference/fixClassDS.html | 4 +- docs/reference/fixColsDS.html | 4 +- docs/reference/fixLevelsDS.html | 4 +- docs/reference/gamlssDS.html | 5 +- docs/reference/gamlssDS.md | 2 + docs/reference/getAllLevelsDS.html | 4 +- docs/reference/getClassAllColsDS.html | 4 +- docs/reference/getWGSRDS.html | 5 +- docs/reference/getWGSRDS.md | 2 + docs/reference/glmDS1.html | 5 +- docs/reference/glmDS1.md | 2 + docs/reference/glmDS2.html | 5 +- docs/reference/glmDS2.md | 2 + docs/reference/glmPredictDS.ag.html | 5 +- docs/reference/glmPredictDS.ag.md | 2 + docs/reference/glmPredictDS.as.html | 5 +- docs/reference/glmPredictDS.as.md | 2 + docs/reference/glmSLMADS.assign.html | 4 +- docs/reference/glmSLMADS1.html | 5 +- docs/reference/glmSLMADS1.md | 2 + docs/reference/glmSLMADS2.html | 5 +- docs/reference/glmSLMADS2.md | 2 + docs/reference/glmSummaryDS.ag.html | 5 +- docs/reference/glmSummaryDS.ag.md | 2 + docs/reference/glmSummaryDS.as.html | 5 +- docs/reference/glmSummaryDS.as.md | 2 + docs/reference/glmerSLMADS.assign.html | 5 +- docs/reference/glmerSLMADS.assign.md | 2 + docs/reference/glmerSLMADS2.html | 5 +- docs/reference/glmerSLMADS2.md | 2 + docs/reference/heatmapPlotDS.html | 18 ++-- docs/reference/heatmapPlotDS.md | 17 ++-- docs/reference/hetcorDS.html | 5 +- docs/reference/hetcorDS.md | 2 + docs/reference/histogramDS1.html | 14 +-- docs/reference/histogramDS1.md | 14 ++- docs/reference/histogramDS2.html | 11 ++- docs/reference/histogramDS2.md | 9 +- docs/reference/igb_standardsDS.html | 5 +- docs/reference/igb_standardsDS.md | 2 + docs/reference/index.html | 22 ++++- docs/reference/index.md | 10 +- docs/reference/isNaDS.html | 15 +-- docs/reference/isNaDS.md | 12 ++- docs/reference/isValidDS.html | 16 +-- docs/reference/isValidDS.md | 13 ++- docs/reference/kurtosisDS1.html | 7 +- docs/reference/kurtosisDS1.md | 5 +- docs/reference/kurtosisDS2.html | 10 +- docs/reference/kurtosisDS2.md | 7 +- docs/reference/lengthDS.html | 9 +- docs/reference/lengthDS.md | 6 +- docs/reference/levelsDS.html | 10 +- docs/reference/levelsDS.md | 7 +- docs/reference/lexisDS1.html | 5 +- docs/reference/lexisDS1.md | 2 + docs/reference/lexisDS2.html | 5 +- docs/reference/lexisDS2.md | 2 + docs/reference/lexisDS3.html | 4 +- docs/reference/listDS.html | 13 +-- docs/reference/listDS.md | 10 +- docs/reference/listDisclosureSettingsDS.html | 4 +- docs/reference/lmerSLMADS.assign.html | 5 +- docs/reference/lmerSLMADS.assign.md | 2 + docs/reference/lmerSLMADS2.html | 5 +- docs/reference/lmerSLMADS2.md | 2 + docs/reference/logDS.html | 92 ++++++++++++++++++ docs/reference/logDS.md | 37 +++++++ docs/reference/lsDS.html | 4 +- docs/reference/lsplineDS.html | 5 +- docs/reference/lsplineDS.md | 2 + docs/reference/matrixDS.html | 5 +- docs/reference/matrixDS.md | 2 + docs/reference/matrixDetDS1.html | 5 +- docs/reference/matrixDetDS1.md | 2 + docs/reference/matrixDetDS2.html | 5 +- docs/reference/matrixDetDS2.md | 2 + docs/reference/matrixDiagDS.html | 5 +- docs/reference/matrixDiagDS.md | 2 + docs/reference/matrixDimnamesDS.html | 5 +- docs/reference/matrixDimnamesDS.md | 2 + docs/reference/matrixInvertDS.html | 5 +- docs/reference/matrixInvertDS.md | 2 + docs/reference/matrixMultDS.html | 5 +- docs/reference/matrixMultDS.md | 2 + docs/reference/matrixTransposeDS.html | 5 +- docs/reference/matrixTransposeDS.md | 2 + docs/reference/mdPatternDS.html | 8 +- docs/reference/mdPatternDS.md | 6 ++ docs/reference/meanDS.html | 15 +-- docs/reference/meanDS.md | 12 ++- docs/reference/meanSdGpDS.html | 11 ++- docs/reference/meanSdGpDS.md | 8 +- docs/reference/mergeDS.html | 5 +- docs/reference/mergeDS.md | 2 + docs/reference/messageDS.html | 4 +- docs/reference/metadataDS.html | 5 +- docs/reference/metadataDS.md | 2 + docs/reference/miceDS.html | 5 +- docs/reference/miceDS.md | 2 + docs/reference/minMaxRandDS.html | 4 +- docs/reference/namesDS.html | 5 +- docs/reference/namesDS.md | 2 + docs/reference/nsDS.html | 5 +- docs/reference/nsDS.md | 2 + docs/reference/numNaDS.html | 15 +-- docs/reference/numNaDS.md | 12 ++- docs/reference/qlsplineDS.html | 5 +- docs/reference/qlsplineDS.md | 2 + docs/reference/quantileMeanDS.html | 15 +-- docs/reference/quantileMeanDS.md | 12 ++- docs/reference/rBinomDS.html | 16 ++- docs/reference/rBinomDS.md | 13 +-- docs/reference/rNormDS.html | 17 ++-- docs/reference/rNormDS.md | 14 ++- docs/reference/rPoisDS.html | 16 ++- docs/reference/rPoisDS.md | 13 +-- docs/reference/rUnifDS.html | 17 ++-- docs/reference/rUnifDS.md | 14 ++- docs/reference/rangeDS.html | 11 ++- docs/reference/rangeDS.md | 8 +- docs/reference/ranksSecureDS1.html | 4 +- docs/reference/ranksSecureDS2.html | 4 +- docs/reference/ranksSecureDS3.html | 4 +- docs/reference/ranksSecureDS4.html | 4 +- docs/reference/ranksSecureDS5.html | 4 +- docs/reference/rbindDS.html | 5 +- docs/reference/rbindDS.md | 2 + docs/reference/reShapeDS.html | 10 +- docs/reference/reShapeDS.md | 7 +- docs/reference/recodeLevelsDS.html | 4 +- docs/reference/recodeValuesDS.html | 5 +- docs/reference/recodeValuesDS.md | 2 + docs/reference/repDS.html | 5 +- docs/reference/repDS.md | 2 + docs/reference/replaceNaDS.html | 9 +- docs/reference/replaceNaDS.md | 6 +- docs/reference/rmDS.html | 4 +- docs/reference/rowColCalcDS.html | 11 ++- docs/reference/rowColCalcDS.md | 9 +- docs/reference/sampleDS.html | 5 +- docs/reference/sampleDS.md | 2 + docs/reference/scatterPlotDS.html | 18 ++-- docs/reference/scatterPlotDS.md | 17 ++-- docs/reference/seqDS.html | 5 +- docs/reference/seqDS.md | 2 + docs/reference/setSeedDS.html | 5 +- docs/reference/setSeedDS.md | 2 + docs/reference/skewnessDS1.html | 7 +- docs/reference/skewnessDS1.md | 5 +- docs/reference/skewnessDS2.html | 10 +- docs/reference/skewnessDS2.md | 7 +- docs/reference/sqrtDS.html | 5 +- docs/reference/sqrtDS.md | 2 + docs/reference/subsetByClassDS.html | 4 +- docs/reference/subsetDS.html | 4 +- docs/reference/table1DDS.html | 4 +- docs/reference/table2DDS.html | 4 +- docs/reference/tableDS.assign.html | 5 +- docs/reference/tableDS.assign.md | 2 + docs/reference/tableDS.html | 5 +- docs/reference/tableDS.md | 2 + docs/reference/tableDS2.html | 5 +- docs/reference/tableDS2.md | 2 + docs/reference/tapplyDS.assign.html | 5 +- docs/reference/tapplyDS.assign.md | 2 + docs/reference/tapplyDS.html | 5 +- docs/reference/tapplyDS.md | 2 + docs/reference/testObjExistsDS.html | 4 +- docs/reference/unListDS.html | 5 +- docs/reference/unListDS.md | 2 + docs/reference/uniqueDS.html | 5 +- docs/reference/uniqueDS.md | 2 + docs/reference/varDS.html | 15 +-- docs/reference/varDS.md | 13 +-- docs/reference/vectorDS.html | 4 +- docs/search.json | 2 +- docs/sitemap.xml | 3 + .../hp-laptop-quay_perf-profile.csv | 8 +- 271 files changed, 1378 insertions(+), 639 deletions(-) create mode 100644 docs/PULL_REQUEST_TEMPLATE.html create mode 100644 docs/PULL_REQUEST_TEMPLATE.md rename docs/deps/bootstrap-5.3.8/fonts/{ee91700cdbf7ce16c054c2bb8946c736.woff2 => 109cfdfecabbfbf5e2364aaceece5d12.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 => 5cd426f27cf61d86c207d97f8db6cf8a.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{07d40e985ad7c747025dabb9f22142c4.woff2 => a8e2cb7ac3da2c4d38cd7c8c06ca5e46.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{1f5e011d6aae0d98fc0518e1a303e99a.woff2 => c0540813382b64c1dde636c1fa0b592a.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{626330658504e338ee86aec8e957426b.woff2 => e0243c1a22ed284bb57c07b3ac886694.woff2} (100%) create mode 100644 docs/reference/expDS.html create mode 100644 docs/reference/expDS.md create mode 100644 docs/reference/logDS.html create mode 100644 docs/reference/logDS.md diff --git a/DESCRIPTION b/DESCRIPTION index d733e042..f3411680 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -82,4 +82,4 @@ Suggests: Encoding: UTF-8 Language: en-GB Config/testthat/edition: 3 -Config/roxygen2/version: 8.1.0 +Config/roxygen2/version: 8.1.1 diff --git a/docs/404.html b/docs/404.html index 17940f30..1ad5f6a8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -20,7 +20,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 + + + + + +
+
+
+ +

NA

+ +
+ + +
+

Instructions & checklist for PR author

+
+

Description of changes

+

[Add descriptions of changes made]

+
+
+

Refactor instructions

+
    • +
    • +
+
+

Testing instructions

+
    • +
    • +
    • +
    • +
+
+
+

Instructions & checklist for PR reviewers

+
    • +
    • +
    • +
+ + +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.1.

+
+ +
+ + + + + + + diff --git a/docs/PULL_REQUEST_TEMPLATE.md b/docs/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 00000000..35a1ccdf --- /dev/null +++ b/docs/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,38 @@ +# NA + +## Instructions & checklist for PR author + +### Description of changes + +\[Add descriptions of changes made\] + +### Refactor instructions + +Replaced `x <- eval(parse(text = x.name), envir = parent.frame())` with +`x <- .loadServersideObject(x)` + +If necessary, check the class of the object using `.checkClass()` + +### Testing instructions + +Writen server-side unit tests for unhappy flow + +Run `devtools::test(filter = "smk-|disc|arg")` and check it passes + +Run `devtools::check(args = '--no-tests')` and check it passes (we run +tests separately to skip performance checks) + +Run +[`devtools::build()`](https://devtools.r-lib.org/reference/build.html) +and check it builds without errors + +## Instructions & checklist for PR reviewers + +Run `devtools::test(filter = "smk-|disc|arg")` and check it passes + +Run `devtools::check(args = '--no-tests')` and check it passes (we run +tests separately to skip performance checks) + +Run +[`devtools::build()`](https://devtools.r-lib.org/reference/build.html) +and check it builds without errors diff --git a/docs/authors.html b/docs/authors.html index dc47fb0e..26299dab 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -7,7 +7,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 + + + + + +
+
+
+ +

Computes the exponential values of the input variable

+ +
expDS.Rd
+
+ +
+

This function is similar to R function exp.

+
+ +
+

Usage

+ 
expDS(x)
+
+ +
+

Arguments

+ + +
x
+

a string character, the name of a numeric or integer vector

+ +
+
+

Value

+

the object specified by the newobj argument +of ds.exp (or default name exp.newobj) +which is written to the serverside. The output object is of class numeric.

+
+
+

Details

+

The function computes the exponential values of an input numeric +or integer vector.

+
+
+

Author

+

DataSHIELD Development Team

+

Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands

+
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.1.

+
+ +
+ + + + + + + diff --git a/docs/reference/expDS.md b/docs/reference/expDS.md new file mode 100644 index 00000000..ae216f74 --- /dev/null +++ b/docs/reference/expDS.md @@ -0,0 +1,32 @@ +# Computes the exponential values of the input variable + +This function is similar to R function `exp`. + +## Usage + +``` r +expDS(x) +``` + +## Arguments + +- x: + + a string character, the name of a numeric or integer vector + +## Value + +the object specified by the `newobj` argument of `ds.exp` (or default +name `exp.newobj`) which is written to the serverside. The output object +is of class numeric. + +## Details + +The function computes the exponential values of an input numeric or +integer vector. + +## Author + +DataSHIELD Development Team + +Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands diff --git a/docs/reference/extractQuantilesDS1.html b/docs/reference/extractQuantilesDS1.html index 757856e3..8d6107dc 100644 --- a/docs/reference/extractQuantilesDS1.html +++ b/docs/reference/extractQuantilesDS1.html @@ -9,7 +9,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 + + + + + +
+
+
+ +

Computes the logarithm values of the input variable

+ +
logDS.Rd
+
+ +
+

This function is similar to R function log.

+
+ +
+

Usage

+ 
logDS(x, base = exp(1))
+
+ +
+

Arguments

+ + +
x
+

a string character, the name of a numeric or integer vector

+ + +
base
+

a positive number, the base for which logarithms are computed. +Default exp(1).

+ +
+
+

Value

+

the object specified by the newobj argument +of ds.log (or default name log.newobj) +which is written to the serverside. The output object is of class numeric.

+
+
+

Details

+

The function computes the logarithm values of an input numeric +or integer vector. By default natural logarithms are computed.

+
+
+

Author

+

DataSHIELD Development Team

+

Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands

+
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.1.

+
+ +
+ + + + + + + diff --git a/docs/reference/logDS.md b/docs/reference/logDS.md new file mode 100644 index 00000000..570e548a --- /dev/null +++ b/docs/reference/logDS.md @@ -0,0 +1,37 @@ +# Computes the logarithm values of the input variable + +This function is similar to R function `log`. + +## Usage + +``` r +logDS(x, base = exp(1)) +``` + +## Arguments + +- x: + + a string character, the name of a numeric or integer vector + +- base: + + a positive number, the base for which logarithms are computed. Default + `exp(1)`. + +## Value + +the object specified by the `newobj` argument of `ds.log` (or default +name `log.newobj`) which is written to the serverside. The output object +is of class numeric. + +## Details + +The function computes the logarithm values of an input numeric or +integer vector. By default natural logarithms are computed. + +## Author + +DataSHIELD Development Team + +Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands diff --git a/docs/reference/lsDS.html b/docs/reference/lsDS.html index 8fdea6b9..04957006 100644 --- a/docs/reference/lsDS.html +++ b/docs/reference/lsDS.html @@ -9,7 +9,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000