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2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: dsBaseClient
Title: 'DataSHIELD' Client Side Base Functions
Version: 6.3.5
Version: 6.3.6.9000
Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows
you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
been designed to only share non disclosive summary statistics, with built in automated output
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2 changes: 2 additions & 0 deletions armadillo_azure-pipelines.yml
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
PERF_PROFILE: 'azure-pipeline'


#########################################################################################
Expand Down Expand Up @@ -274,6 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)

sudo R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
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6 changes: 4 additions & 2 deletions azure-pipelines.yml
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
PERF_PROFILE: 'azure-pipeline'


#########################################################################################
Expand Down Expand Up @@ -214,7 +215,7 @@ jobs:
# Install dsBase.
# If previous steps have failed then don't run.
- bash: |
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"

Expand Down Expand Up @@ -253,6 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)

sudo R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
Expand Down Expand Up @@ -342,7 +344,7 @@ jobs:
# If previous steps have failed then don't run
- bash: |

R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

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5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:5.12.2
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All @@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock-quebrada-lamda-permissive:latest
environment:
DEBUG: "FALSE"
4 changes: 3 additions & 1 deletion opal_azure-pipelines.yml
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
PERF_PROFILE: 'azure-pipeline'


#########################################################################################
Expand Down Expand Up @@ -272,6 +273,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)

sudo R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
Expand Down Expand Up @@ -361,7 +363,7 @@ jobs:
# If previous steps have failed then don't run
- bash: |

R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

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14 changes: 0 additions & 14 deletions tests/testthat/perf_files/default_perf_profile.csv

This file was deleted.

14 changes: 14 additions & 0 deletions tests/testthat/perf_files/opal_default_perf-profile.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
"refer_name","rate","lower_tolerance","upper_tolerance"
"conndisconn::perf::simple0","0.2725","0.5","2"
"ds.abs::perf::0","2.677","0.5","2"
"ds.asInteger::perf:0","2.294","0.5","2"
"ds.asList::perf:0","4.587","0.5","2"
"ds.asNumeric::perf:0","2.185","0.5","2"
"ds.assign::perf::0","5.490","0.5","2"
"ds.class::perf::combine:0","4.760","0.5","2"
"ds.colnames::perf:0","9.079","0.5","2"
"ds.exists::perf::combine:0","11.09","0.5","2"
"ds.length::perf::combine:0","9.479","0.5","2"
"ds.mean::perf::combine:0","9.650","0.5","2"
"ds.mean::perf::split:0","11.26","0.5","2"
"void::perf::void::0","46250.0","0.5","2"
14 changes: 14 additions & 0 deletions tests/testthat/perf_files/unknown_default_perf-profile.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
"refer_name","rate","lower_tolerance","upper_tolerance"
"conndisconn::perf::simple0","0.2725","0.5","2"
"ds.abs::perf::0","2.677","0.5","2"
"ds.asInteger::perf:0","2.294","0.5","2"
"ds.asList::perf:0","4.587","0.5","2"
"ds.asNumeric::perf:0","2.185","0.5","2"
"ds.assign::perf::0","5.490","0.5","2"
"ds.class::perf::combine:0","4.760","0.5","2"
"ds.colnames::perf:0","9.079","0.5","2"
"ds.exists::perf::combine:0","11.09","0.5","2"
"ds.length::perf::combine:0","9.479","0.5","2"
"ds.mean::perf::combine:0","9.650","0.5","2"
"ds.mean::perf::split:0","11.26","0.5","2"
"void::perf::void::0","46250.0","0.5","2"
31 changes: 27 additions & 4 deletions tests/testthat/perf_tests/perf_rate.R
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#-------------------------------------------------------------------------------
# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
#
# This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0.
Expand All @@ -8,13 +8,36 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#-------------------------------------------------------------------------------

.perf.reference.filename <- 'perf_files/default_perf_profile.csv'
.perf.reference.save.filename <- NULL
.perf.reference.filename.base.prefix <- 'perf_files/'
.perf.reference.filename.base.postfix <- '_perf-profile.csv'
.perf.reference.save.filename <- NULL

.perf.reference <- NULL

.load.pref <- function() {
.perf.reference <<- read.csv(.perf.reference.filename, header = TRUE, sep = ",")
if (ds.test_env$driver == "OpalDriver")
perf.reference.filename.driver.infix <- "opal"
else if (ds.test_env$driver == "ArmadilloDriver")
perf.reference.filename.driver.infix <- "armadillo"
else if (ds.test_env$driver == "DSLiteDriver")
perf.reference.filename.driver.infix <- "dslite"
else
{
perf.reference.filename.infix <- "unknown"
warning("Unknown performance profile driver, using 'unknown'")
}

perf.profile <- base::Sys.getenv("PERF_PROFILE")
if (nchar(perf.profile) > 0)
perf.reference.filename.platform.infix <- base::tolower(perf.profile)
else
{
perf.reference.filename.platform.infix <- "default"
warning("Unknown performance profile platform, using 'default'")
}

perf.reference.filename <- paste(.perf.reference.filename.base.prefix, perf.reference.filename.driver.infix, '_', perf.reference.filename.platform.infix, .perf.reference.filename.base.postfix, sep = "")
.perf.reference <<- read.csv(perf.reference.filename, header = TRUE, sep = ",")
}

perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance.upper) {
Expand Down