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Merged
StuartWheater merged 17 commits into from
Sep 21, 2026
Merged

Refactor/perf batch 10 #513

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a77ac73
Removal of testthat 'skip's
StuartWheater Sep 21, 2026
323e86a
Merge branch 'datashield:refactor/perf-batch-10' into refactor/perf-b…
StuartWheater Sep 21, 2026
648d72b
Update perfence profile
StuartWheater Sep 21, 2026
fd20e4b
Merge branch 'refactor/perf-batch-10' of github.com:StuartWheater/dsB…
StuartWheater Sep 21, 2026
41046bd
Fix setting of PERF.PROFILE env variable
StuartWheater Sep 21, 2026
1923a11
Update to Circle CI code coverage
StuartWheater Sep 21, 2026
f670258
Fixed Comments, I hope
StuartWheater Sep 21, 2026
eec1ebe
Fixed Comments
StuartWheater Sep 21, 2026
c867e6e
Fixed Comments
StuartWheater Sep 21, 2026
824fb5d
Fix CircleCI performance
StuartWheater Sep 21, 2026
4577895
Added debugging output
StuartWheater Sep 21, 2026
cfead15
Added debugging output
StuartWheater Sep 21, 2026
a3540d1
Remove debug code and adjust perf profile
StuartWheater Sep 21, 2026
68f6016
Update logging
StuartWheater Sep 21, 2026
fd3db55
Fix code typo
StuartWheater Sep 21, 2026
59d76de
Fix perf profile
StuartWheater Sep 21, 2026
c3eaedd
Merge branch 'datashield:refactor/perf-batch-10' into refactor/perf-b…
StuartWheater Sep 21, 2026
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18 changes: 2 additions & 16 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,22 +26,8 @@ jobs:
- run:
command: |
echo "options(Ncpus=4)" >> ~/.Rprofile
sudo Rscript -e "install.packages('RANN', dependencies=TRUE)"
sudo Rscript -e "install.packages('stringr', dependencies=TRUE)"
sudo Rscript -e "install.packages('lme4', dependencies=TRUE)"
sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
sudo Rscript -e "install.packages('reshape2', dependencies=TRUE)"
sudo Rscript -e "install.packages('polycor', dependencies=TRUE)"
sudo Rscript -e "install.packages('splines', dependencies=TRUE)"
sudo Rscript -e "install.packages('gamlss', dependencies=TRUE)"
sudo Rscript -e "install.packages('gamlss.dist', dependencies=TRUE)"
sudo Rscript -e "install.packages('mice', dependencies=TRUE)"
sudo Rscript -e "install.packages('childsds', dependencies=TRUE)"
sudo Rscript -e "install.packages('xml2', dependencies=TRUE)"
sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"

sudo R -q -e "options(repos=c(CRAN=paste0('https://packagemanager.posit.co/cran/__linux__/', system('lsb_release -cs', intern=TRUE), '/latest')), HTTPUserAgent=sprintf('R/%s R (%s)', getRversion(), paste(getRversion(), R.version\$platform, R.version\$arch, R.version\$os)), Ncpus=4); install.packages(c('devtools','RANN','stringr','lme4','dplyr','reshape2','polycor','splines','gamlss','gamlss.dist','mice','data.table','childsds'), dependencies=TRUE)"
- run:
command: |
sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'")'
Expand Down
9 changes: 4 additions & 5 deletions azure-pipelines.yml
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Expand Up @@ -27,8 +27,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
PERF_PROFILE: 'azure-pipeline'

perf.profile: 'azure-pipeline'


#########################################################################################
Expand All @@ -50,13 +49,13 @@ schedules:
displayName: Weekly build - latest release
branches:
include:
- 6.3.4
- 6.3.5
always: true
- cron: "0 1 * * *"
displayName: Nightly build - development branchs
branches:
include:
- v6.3.5-dev
- v6.3.6-dev
- v6.4.0-dev
- v7.0.0-dev
always: true
Expand Down Expand Up @@ -184,7 +183,7 @@ jobs:
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml

sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
write.csv(
coverage_to_list(
Expand Down
8 changes: 4 additions & 4 deletions tests/testthat/perf_files/azure-pipeline_perf-profile.csv
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
"refer_name","rate","lower_tolerance","upper_tolerance"
"meanDS::perf::numeric::0","2998.9844","0.5","2"
"meanDS::perf::numberAndNA::0","3027.3963","0.5","2"
"varDS::perf::numeric::0","3124.4088","0.5","2"
"varDS::perf::numberAndNA::0","3146.532","0.5","2"
"meanDS::perf::numeric::0","4497.0","0.5","2"
"meanDS::perf::numberAndNA::0","4542.0","0.5","2"
"varDS::perf::numeric::0","6373.0","0.5","2"
"varDS::perf::numberAndNA::0","4500.0","0.5","2"
12 changes: 6 additions & 6 deletions tests/testthat/test-perf-meanDS.R
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Expand Up @@ -26,7 +26,7 @@ set.standard.disclosure.settings()

# context("meanDS::perf::numeric")
test_that("numeric meanDS - performance", {
skip_on_cran()
# skip_on_cran()

input <- c(0.0, 1.0, 2.0, 3.0, 4.0)

Expand All @@ -45,10 +45,10 @@ test_that("numeric meanDS - performance", {
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
.reference.rate <- perf.reference.rate("meanDS::perf::numeric::0")
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
print(paste("meanDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()))
write(paste("meanDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr())
perf.reference.save("meanDS::perf::numeric::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())
} else {
print(paste("meanDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
write(paste("meanDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr())
}

.reference.rate <- perf.reference.rate("meanDS::perf::numeric::0")
Expand All @@ -61,7 +61,7 @@ test_that("numeric meanDS - performance", {

# context("meanDS::perf::numeric with NA")
test_that("numeric meanDS, with NA - performance", {
skip_on_cran()
# skip_on_cran()

input <- c(0.0, NA, 2.0, NA, 4.0)

Expand All @@ -80,10 +80,10 @@ test_that("numeric meanDS, with NA - performance", {
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
.reference.rate <- perf.reference.rate("meanDS::perf::numberAndNA::0")
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
print(paste("meanDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()))
write(paste("meanDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr())
perf.reference.save("meanDS::perf::numberAndNA::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())
} else {
print(paste("meanDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
write(paste("meanDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr())
}

.reference.rate <- perf.reference.rate("meanDS::perf::numberAndNA::0")
Expand Down
12 changes: 6 additions & 6 deletions tests/testthat/test-perf-varDS.R
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ set.standard.disclosure.settings()

# context("varDS::perf::numeric")
test_that("numeric varDS - performance", {
skip_on_cran()
# skip_on_cran()

input <- c(0.0, 1.0, 2.0, 3.0, 4.0)

Expand All @@ -45,10 +45,10 @@ test_that("numeric varDS - performance", {
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
.reference.rate <- perf.reference.rate("varDS::perf::numeric::0")
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
print(paste("varDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()))
write(paste("varDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr())
perf.reference.save("varDS::perf::numeric::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())
} else {
print(paste("varDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
write(paste("varDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr())
}

.reference.rate <- perf.reference.rate("varDS::perf::numeric::0")
Expand All @@ -61,7 +61,7 @@ test_that("numeric varDS - performance", {

# context("varDS::perf::numeric with NA")
test_that("numeric varDS, with NA - performance", {
skip_on_cran()
# skip_on_cran()

input <- c(0.0, NA, 2.0, NA, 4.0)

Expand All @@ -80,10 +80,10 @@ test_that("numeric varDS, with NA - performance", {
.current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]])
.reference.rate <- perf.reference.rate("varDS::perf::numberAndNA::0")
if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) {
print(paste("varDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()))
write(paste("varDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr())
perf.reference.save("varDS::perf::numberAndNA::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())
} else {
print(paste("varDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''))
write(paste("varDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr())
}

.reference.rate <- perf.reference.rate("varDS::perf::numberAndNA::0")
Expand Down
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