Redo container build, adding missing R.utils package

CHANGELOG.md

@@ -6,6 +6,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+- Replace CRAN by https://packagemanager.rstudio.com/cran/__linux__/focal/2023-02-16 as package source.
+- Added missing system deps ``libpoppler-glib-dev``, ``tcl-dev``
+- Install ``R.utils`` enabling reading of .gz files in LAVA
+- Rebuilt container ``f9438a80d50831b4b0e244d455d40d43 magma.sif``
+
 ## [1.0.0] - 2022-11-30
 
 ### Added

src/scripts/R/cran.R

@@ -1,5 +1,10 @@
 require(devtools)
-devtools::install_version('BiocManager', version='1.30.18', repos='https://cloud.r-project.org')
-devtools::install_version('data.table', version='1.14.2', repos='https://cloud.r-project.org')
-devtools::install_version('matrixsampling', version='2.0.0', repos='https://cloud.r-project.org')
+url <- "https://packagemanager.rstudio.com/cran/__linux__/focal/2023-02-16"
+dependencies <- c('Depends', 'Imports', 'LinkingTo')
+upgrade <- 'default'
+devtools::install_version('BiocManager', version='1.30.19', repos=url, dependencies=dependencies, upgrade=upgrade)
+devtools::install_version('BRugs', version='0.9-1', repos=url, dependencies=dependencies, upgrade=upgrade)
+devtools::install_version('data.table', version='1.14.6', repos=url, dependencies=dependencies, upgrade=upgrade)
+devtools::install_version('matrixsampling', version='2.0.0', repos=url, dependencies=dependencies, upgrade=upgrade)
+devtools::install_version('R.utils', version='2.12.2', repos=url, dependencies=dependencies, upgrade=upgrade)
 

src/scripts/apt_get_essential.sh

@@ -21,13 +21,15 @@ apt-get update && apt-get install -y --no-install-recommends \
    libgsl-dev=2.5+dfsg-6build1 \
    libnss3=2:3.49.1-1ubuntu1.8 \
    libpcre2-dev=10.34-7ubuntu0.1 \
+   libpoppler-glib-dev=0.86.1-0ubuntu1.1 \
    libxt-dev=1:1.1.5-1 \
    pandoc=2.5-3build2 \
    pandoc-citeproc=0.15.0.1-1build4 \
    parallel=20161222-1.1 \
    perl=5.30.0-9ubuntu0.3 \
    pkg-config=0.29.1-0ubuntu4 \
    tar=1.30+dfsg-7ubuntu0.20.04.2 \
+   tcl-dev=8.6.9+1 \
    tofrodos=1.7.13+ds-4 \
    unzip=6.0-25ubuntu1.1 \
    vim=2:8.1.2269-1ubuntu5.9 \

tests/extras/check_libraries.R

@@ -0,0 +1,10 @@
+# check that all libraries are installed
+library(BiocGenerics)
+library(BiocManager)
+library(BRugs)
+library(data.table)
+library(LAVA)
+library(matrixsampling)
+library(R.utils)
+library(snpStats)
+library(zlibbioc)

tests/test_magma.py

@@ -64,6 +64,14 @@ def test_R_script():
     assert out.returncode == 0
 
 
+def test_R_libraries():
+    """test that the R libraries are installed"""
+    pwd = os.getcwd() if PREFIX.rfind('docker') >= 0 else '.'
+    call = f'{PREFIX_MOUNT} R {pwd}/tests/extras/check_libraries.R'
+    out = subprocess_run(call)
+    assert out.returncode == 0
+
+
 # py.test tests/test_magma.py  -k test_magma_binary
 def test_magma_binary():
     call=f'{PREFIX} magma --version'