ENH/circleci_rversion

.circleci/config.yml

@@ -2,9 +2,6 @@ version: 2
 
 steps: &steps
   steps:
-    - restore_cache:
-        keys:
-          - cache-{{ .Environment.CIRCLE_JOB }}
     - checkout
     - run:
         name: Install libraries
@@ -13,8 +10,11 @@ steps: &steps
         name: Install libraries for latex
         command: apt-get update && apt-get install -y --no-install-recommends texlive-fonts-recommended
     - run:
-        name: Install package dependencies
-        command: R -e "devtools::install_deps(dep = TRUE)"
+        name: Install package dependencies (via devtools::install_deps)
+        command: R -e "devtools::install_deps(dep = TRUE, upgrade = 'always')"
+    - run:
+        name: Check package version of vctrs
+        command: R -e "packageVersion('vctrs')"
     - run:
         name: Install package dependencies (hdf5r)
         command: R -e "require(hdf5r)" # "lapply(c('hdf5r','HDF5Array','DelayedArray'), require, character.only=TRUE)"
@@ -24,16 +24,16 @@ steps: &steps
     - run:
         name: Check package
         command: R CMD check *tar.gz
-    - save_cache:
-        key: cache-{{ .Environment.CIRCLE_JOB }}
-        paths:
-          - "/usr/local/lib/R/site-library"
 
 jobs:
   releaseR4.1.0:
     docker:
       - image: rocker/verse:4.1.0
     <<: *steps
+  releaseR3.6.3:
+    docker:
+      - image: rocker/verse:3.6.3
+    <<: *steps
   oldR3.5.3:
     docker:
       - image: rocker/verse:3.5.3
@@ -47,10 +47,14 @@ workflows:
   version: 2
   build_test_deploy:
     jobs:
-      #- releaseR4.1.0:   # temporarily comment out as there is error with matrixStats package
+      #- releaseR4.1.0:   
       #    filters:
       #      tags:
       #        only: /.*/
+      - releaseR3.6.3:
+          filters:
+            tags:
+              only: /.*/
       #- oldR3.5.3:
       #    filters:
       #      tags:

DESCRIPTION

@@ -11,14 +11,16 @@ Description: What the package does (one paragraph).
 License: BSD 3-Clause License + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Depends: R (>= 4.1.0)
+Depends: R (>= 3.6.3)
 biocViews:
 Imports: 
-    matrixStats (>= 0.60.1),
+    vctrs (>= 0.3.0),
+    rlang (>= 0.4.6),
+    tidyselect (>= 1.1.0),
     magrittr,
     methods,
     dplyr,
-    tidyr,
+    tidyr (>= 1.1.0),
     tibble,
     stringr,
     glue,
@@ -28,12 +30,11 @@ Imports:
     rhdf5,
     hdf5r,
     mgcv,
-    rlang,
     DelayedArray,
     broom,
     pbmcapply,
     pbapply,
-    crayon,
+    crayon
 RoxygenNote: 7.1.2
 Suggests: 
     rmarkdown,

Dockerfile

@@ -0,0 +1,84 @@
+# Building Docker file for ModelArray (R package) + ConFixel (python package). Core is config.yml for ModelArray's circle.ci.
+# When update this Dockerfile, please update:
+# 1. rocker/verse:<R_version>
+# 2. commitSHA_confixel
+# 3. commitSHA_modelarray - see towards the end of this file
+# 4. ModelArray's dependent R packages - see DESCRIPTION file
+
+## Base image https://hub.docker.com/u/rocker/
+FROM rocker/verse:4.1.2
+
+## versions and parameters:
+# specify the commit SHA:  # e.g. https://github.com/PennLINC/qsiprep/blob/master/Dockerfile#L174
+ENV commitSHA_confixel="eda00bc1c9837b5586a65f24b4c986845f41582c"
+
+
+RUN mkdir /home/data
+# RUN mkdir /home/ModelArray
+
+## Install libraries 
+# ref: .circleci/config.yml from ModelArray:
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libhdf5-dev \
+    texlive-fonts-recommended \
+    git
+
+# # Install libraries
+# RUN apt-get update && apt-get install -y --no-install-recommends libhdf5-dev
+# # Install libraries for latex
+# RUN apt-get update && apt-get install -y --no-install-recommends texlive-fonts-recommended
+# Install git:   # ref a bit from: https://github.com/PennLINC/qsiprep_build/blob/main/Dockerfile_DSIStudio
+# RUN apt-get update && apt-get install -y --no-install-recommends git
+
+# Install python: # ref: https://github.com/PennLINC/flaudit/blob/master/Dockerfile#L23
+RUN apt-get update && apt-get install -y python3-pip python3-dev
+
+
+## Install ConFixel (python package)
+# git clone xxxx.git${commitSHA}
+# cd to directory
+# pip install .
+
+RUN git clone -n https://github.com/PennLINC/ConFixel.git
+WORKDIR ConFixel
+RUN git checkout ${commitSHA_confixel}
+RUN pip install .
+WORKDIR /
+# RUN rm -r ConFixel
+
+
+## Install dependent R packages: 
+# from CRAN:   # removed base packages from the list (otherwise warning in docker build): methods and parallel
+RUN install2.r --error --ncpus -4 \
+    matrixStats \
+    magrittr \
+    dplyr \
+    tidyr \
+    tibble \
+    stringr \
+    glue \
+    doParallel \
+    hdf5r \
+    mgcv \
+    rlang \
+    broom \
+    pbmcapply \
+    pbapply \
+    crayon
+
+# from Bioc: # first, install BiocManager from CRAN:
+RUN install2.r --error BiocManager
+RUN R -e 'BiocManager::install("HDF5Array")'
+RUN R -e 'BiocManager::install("rhdf5")'
+RUN R -e 'BiocManager::install("DelayedArray")'
+
+# # copy necessary files and folders:
+# COPY ./install_packages.R ./install_packages.R
+# # install R-packages:
+# RUN Rscript ./install_packages.R
+
+
+## install ModelArray (R package)
+# please update commit SHA for ModelArray if needed
+RUN R -e 'devtools::install_github("PennLINC/ModelArray@9e735b93f2d6b756f8ef18aadc14e2d10c6cc191")'
+

R/analyse.R

@@ -67,7 +67,7 @@ ModelArray.lm <- function(formula, data, phenotypes, scalar, element.subset = NU
 
   ### sanity check: whether they match: modelarray's source file list and phenotypes' source file list:
   sources.modelarray <- sources(data)[[scalar]]
-  sources.phenotypes <- phenotypes[["source_file"]]
+  sources.phenotypes <- phenotypes[["source_file"]] %>% as.character()
   if (is.null(sources.phenotypes)) {
     stop(paste0("Did not find column 'source_file' in argument 'phenotypes'. Please check!"))
   }
@@ -96,7 +96,7 @@ ModelArray.lm <- function(formula, data, phenotypes, scalar, element.subset = NU
       # apply to phenotypes:
       phenotypes <- phenotypes[reorder_idx, ]
       row.names(phenotypes) <- NULL # reset the row name, just to be safe for later adding scalar values... see ModelArray_paper/notebooks/test_match_sourceFiles.Rmd
-      if (!identical(phenotypes[["source_file"]], sources.modelarray)) {
+      if (!identical(phenotypes[["source_file"]] %>% as.character(), sources.modelarray)) {
         stop("matching source file names were not successful...")
       }
     } else {
@@ -454,7 +454,7 @@ ModelArray.gam <- function(formula, data, phenotypes, scalar, element.subset = N
 
   ### sanity check: whether they match: modelarray's source file list and phenotypes' source file list:
   sources.modelarray <- sources(data)[[scalar]]
-  sources.phenotypes <- phenotypes[["source_file"]]
+  sources.phenotypes <- phenotypes[["source_file"]] %>% as.character()
   if (is.null(sources.phenotypes)) {
     stop(paste0("Did not find column 'source_file' in argument 'phenotypes'. Please check!"))
   }
@@ -483,7 +483,7 @@ ModelArray.gam <- function(formula, data, phenotypes, scalar, element.subset = N
       # apply to phenotypes:
       phenotypes <- phenotypes[reorder_idx, ]
       row.names(phenotypes) <- NULL # reset the row name, just to be safe for later adding scalar values... see ModelArray_paper/notebooks/test_match_sourceFiles.Rmd
-      if (!identical(phenotypes[["source_file"]], sources.modelarray)) {
+      if (!identical(phenotypes[["source_file"]] %>% as.character(), sources.modelarray)) {
         stop("matching source file names were not successful...")
       }
     } else {