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New DataSHIELD analysis packages profiles #17

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3315876
Addition of 'lemon-donkey-permissive', 'omicron-karma-permissive' and…
StuartWheater Aug 8, 2025
42a6a53
Package additions and updates
StuartWheater Nov 13, 2025
efee3a7
Merge branch 'datashield:main' into main
StuartWheater Nov 17, 2025
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2 changes: 1 addition & 1 deletion lemon-donkey-permissive/Dockerfile
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Expand Up @@ -6,7 +6,7 @@

FROM datashield/rock-lemon-donkey:draft

ENV DSBASE_VERSION=v6.3.1-permissive
ENV DSBASE_VERSION=6.3.4-RC5-permissive
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Copilot AI Nov 17, 2025

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Inconsistent version format: DSBASE_VERSION uses 6.3.4-RC5-permissive without the v prefix. While the base version in lemon-donkey also lacks the prefix, consider adding v for consistency with other DataSHIELD version patterns (e.g., v6.3.4-RC5-permissive).

Suggested change
ENV DSBASE_VERSION=6.3.4-RC5-permissive
ENV DSBASE_VERSION=v6.3.4-RC5-permissive

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ENV ROCK_LIB=/var/lib/rock/R/library

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8 changes: 4 additions & 4 deletions lemon-donkey/Dockerfile
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Expand Up @@ -4,16 +4,16 @@
# https://github.com/datashield/docker-rock
#

# R 4.4.2, Rock 2.1.1
FROM datashield/rock-base:6.3.1-R4.4.2
# R 4.5.0, Rock 2.1.4
FROM datashield/rock-base:6.3.3

ENV DSMEDIATION_VERSION=0.0.3
ENV DSEXPOSOME_VERSION=2.0.9
ENV DSTIDYVERSE_VERSION=v1.0.1
ENV DSTIDYVERSE_VERSION=v1.0.4
ENV DSOMICS_VERSION=v1.0.18-2
ENV DSMTL_VERSION=0.9.9
ENV DSSURVIVAL_VERSION=v2.1.3
ENV DSBASE_VERSION=6.3.1
ENV DSBASE_VERSION=6.3.4-RC5
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Copilot AI Nov 17, 2025

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Inconsistent version format: DSBASE_VERSION uses 6.3.4-RC5 without the v prefix, while other version variables in the file use the v prefix (e.g., v2.1.3, v1.0.18-2, v1.0.4). Consider using v6.3.4-RC5 for consistency.

Suggested change
ENV DSBASE_VERSION=6.3.4-RC5
ENV DSBASE_VERSION=v6.3.4-RC5

Copilot uses AI. Check for mistakes.

ENV ROCK_LIB=/var/lib/rock/R/library

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4 changes: 2 additions & 2 deletions margin-idiom-persistent/Dockerfile
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Expand Up @@ -5,9 +5,9 @@
#

# R 4.5.0, Rock 2.1.4
FROM datashield/rock-margin-idiom:1.2.6
FROM datashield/rock-margin-idiom:2.1.1

ENV DSBASE_VERSION=v6.3.2-permissive
ENV DSBASE_VERSION=v6.3.5-dev-permissive

ENV ROCK_LIB=/var/lib/rock/R/library

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2 changes: 1 addition & 1 deletion margin-idiom-persistent/Makefile
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Expand Up @@ -5,7 +5,7 @@
docker_compose_file=docker-compose.yml
no_cache=true
name=datashield/rock-margin-idiom-permissive
tag=1.2.6
tag=2.1.1

# Build Docker image
build-image:
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2 changes: 1 addition & 1 deletion margin-idiom-persistent/docker-compose.yml
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@@ -1,7 +1,7 @@
version: '3'
services:
rock-margin-idiom-permissive:
image: datashield/rock-margin-idiom-permissive:1.2.6
image: datashield/rock-margin-idiom-permissive:2.1.1
#build: .
ports:
- ${PORT}:8085
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17 changes: 10 additions & 7 deletions margin-idiom/Dockerfile
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Expand Up @@ -5,11 +5,12 @@
#

# R 4.5.0, Rock 2.1.4
FROM datashield/rock-base:6.3.2-R4.5.0
FROM datashield/rock-base:6.3.4

ENV DSSURVIVAL_VERSION=v2.3.0-dev
ENV DSTIDYVERSE_VERSION=v1.0.4
ENV DSBASE_VERSION=6.3.2
ENV DSCODA_VERSION=v0.1.0-dev
ENV DSSURVIVAL_VERSION=v2.3.0-dev
ENV DSBASE_VERSION=v6.3.5-dev

ENV ROCK_LIB=/var/lib/rock/R/library

Expand All @@ -18,10 +19,12 @@ RUN apt-get update -y; apt-get upgrade -y; apt-get autoremove -y
RUN R -q -e "install.packages('ranger')"; R -q -e "update.packages()"

# Install new R packages
# dsTidyverse
RUN Rscript -e "remotes::install_github('molgenis/ds-tidyverse', ref = '$DSTIDYVERSE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
# dsBase
RUN Rscript -e "remotes::install_github('datashield/dsBase', ref = '$DSBASE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
# dsCoda
Rscript -e "remotes::install_github('datashield/dsCoda', ref = '$DSCODA_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
# dsSurvival
Rscript -e "remotes::install_github('datashield/dsSurvival', ref = '$DSSURVIVAL_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
# dsBase
Rscript -e "remotes::install_github('datashield/dsBase', ref = '$DSBASE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
# dsTidyverse
Rscript -e "remotes::install_github('molgenis/ds-tidyverse', ref = '$DSTIDYVERSE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
chown -R rock $ROCK_LIB
2 changes: 1 addition & 1 deletion margin-idiom/Makefile
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Expand Up @@ -5,7 +5,7 @@
docker_compose_file=docker-compose.yml
no_cache=true
name=datashield/rock-margin-idiom
tag=1.2.6
tag=2.1.1

# Build Docker image
build-image:
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2 changes: 1 addition & 1 deletion margin-idiom/docker-compose.yml
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@@ -1,7 +1,7 @@
version: '3'
services:
rock-margin-idiom:
image: datashield/rock-margin-idiom:1.2.6
image: datashield/rock-margin-idiom:2.1.1
#build: .
ports:
- ${PORT}:8085
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4 changes: 2 additions & 2 deletions omicron-karma-permissive/Dockerfile
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Expand Up @@ -4,9 +4,9 @@
# https://github.com/datashield/docker-rock
#

FROM datashield/rock-omicron-karma:1.0.0
FROM datashield/rock-omicron-karma:devel

ENV DSBASE_VERSION=v6.3.3-permissive
ENV DSBASE_VERSION=v6.3.4-dev-permissive

ENV ROCK_LIB=/var/lib/rock/R/library

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2 changes: 1 addition & 1 deletion omicron-karma-permissive/Makefile
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docker_compose_file=docker-compose.yml
no_cache=true
name=datashield/rock-omicron-karma-permissive
tag=1.0.0
tag=devel

# Build Docker image
build-image:
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2 changes: 1 addition & 1 deletion omicron-karma-permissive/docker-compose.yml
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version: '3'
services:
rock-omicron-karma-permissive:
image: datashield/rock-omicron-karma-permissive:draft
image: datashield/rock-omicron-karma-permissive:devel
#build: .
ports:
- ${PORT}:8085
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4 changes: 2 additions & 2 deletions omicron-karma/Dockerfile
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Expand Up @@ -5,15 +5,15 @@
#

# R 4.5.0, Rock 2.1.1
FROM datashield/rock-base:6.3.3
FROM datashield/rock-base:6.3.4

ENV DSMEDIATION_VERSION=0.0.3
ENV DSEXPOSOME_VERSION=2.0.9
ENV DSTIDYVERSE_VERSION=v1.0.4
ENV DSOMICS_VERSION=v1.0.18-2
ENV DSMTL_VERSION=0.9.9
ENV DSSURVIVAL_VERSION=v2.1.3
ENV DSBASE_VERSION=6.3.3
ENV DSBASE_VERSION=v6.3.4
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Copilot AI Nov 17, 2025

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Inconsistent version format: DSBASE_VERSION uses 6.3.3 without the v prefix, while other version variables in the file use the v prefix (e.g., v2.1.3, v1.0.18-2). Consider using v6.3.3 for consistency.

Copilot uses AI. Check for mistakes.

ENV ROCK_LIB=/var/lib/rock/R/library

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2 changes: 1 addition & 1 deletion omicron-karma/Makefile
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Expand Up @@ -5,7 +5,7 @@
docker_compose_file=docker-compose.yml
no_cache=true
name=datashield/rock-omicron-karma
tag=1.0.0
tag=devel

# Build Docker image
build-image:
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2 changes: 1 addition & 1 deletion omicron-karma/docker-compose.yml
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@@ -1,7 +1,7 @@
version: '3'
services:
rock-omicron-karma:
image: datashield/rock-omicron-karma:1.0.0
image: datashield/rock-omicron-karma:devel
#build: .
ports:
- ${PORT}:8085
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15 changes: 15 additions & 0 deletions quebrada-lamda-permissive/Dockerfile
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#
# Rock R Server Dockerfile with DataSHIELD Quebrada Lamda permissive profile
#
# https://github.com/datashield/docker-rock
#

FROM datashield/rock-quebrada-lamda:latest

ENV DSBASE_VERSION=v6.3.4-permissive

ENV ROCK_LIB=/var/lib/rock/R/library

# dsBase
RUN Rscript -e "remotes::install_github('datashield/dsBase', ref = '$DSBASE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
chown -R rock $ROCK_LIB
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