Merge branch 'develop'

.Rbuildignore

@@ -14,3 +14,4 @@
 ^_config.yml$
 ^_pkgdown\.yml$
 ^docs$
+^tmp/.*$

.travis.yml

@@ -1,30 +1,75 @@
 matrix:
   include:
     -  os: linux
-       dist: trusty
+       dist: xenial
+       script: |
+         R CMD build .
+         R CMD INSTALL RMINC*.tar.gz
+         R CMD check --as-cran --no-install RMINC*.tar.gz
+         cat RMINC.Rcheck/00check.log         
+         Rscript -e "\
+         testr <- devtools::test(); \
+         testr <- as.data.frame(testr); \
+         if(any(testr\$error) || any(testr\$warning > 0)) \
+           stop('Found failing tests') \
+         "
+         pass=$?
+         if [[ $pass -ne 0 || $(grep "WARNING\|ERROR" RMINC.Rcheck/00check.log) != "" ]]; then
+           (exit 1)
+         else
+           (exit 0)
+         fi
     -  os: osx
+       script: |
+         R CMD build .
+         R CMD INSTALL RMINC*.tar.gz
+         R CMD check --as-cran --no-install RMINC*.tar.gz
+         cat RMINC.Rcheck/00check.log         
+         Rscript -e "\
+         testr <- devtools::test(); \
+         testr <- as.data.frame(testr); \
+         if(any(testr\$error) || any(testr\$warning > 0)) \
+           stop('Found failing tests') \
+         "
+         pass=$?
+         if [[ $pass -ne 0 || $(grep "WARNING\|ERROR" RMINC.Rcheck/00check.log) != "" ]]; then
+           (exit 1)
+         else
+           (exit 0)
+         fi
 
 language: r
+r_binary_packages:
+  - devtools
+  - roxygen2
+  - tidyverse
+  - lme4
 sudo: required
-
+addons:
+  apt:
+    update: true
+    packages:
+      - libgl1-mesa-dev
+      - libglu1-mesa-dev
+      - freeglut3-dev
+env:
+  MINC_PATH=/opt/minc/1.9.17
+
 before_install: |
    if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      (cd ../ ;
-     wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.16-20180117-Ubuntu_14.04-x86_64.deb )
-     sudo dpkg -i ../minc-toolkit-1.9.16-20180117-Ubuntu_14.04-x86_64.deb
-     source /opt/minc/1.9.16/minc-toolkit-config.sh
+     wget https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.17-20190313-Ubuntu_16.04-x86_64.deb)
+     sudo dpkg -i ../minc-toolkit-1.9.17-20190313-Ubuntu_16.04-x86_64.deb
+     source /opt/minc/1.9.17/minc-toolkit-config.sh
    fi
    
    if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-     ## brew install gcc
-     ## mkdir $HOME/.R/; touch $HOME/.R/Makevars
-     ## echo 'FLIBS=-L/usr/local/Cellar/gcc/5.3.0/lib/gcc/5' > $HOME/.R/Makevars
      (cd ../ ;
      wget http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.16-20180117-Darwin-10.8-x86_64.dmg)
      sudo hdiutil attach ../minc-toolkit-1.9.16-20180117-Darwin-10.8-x86_64.dmg
      sudo installer -package /Volumes/minc-toolkit-1.9.16-20180117-Darwin-x86_64/minc-toolkit-1.9.16-20180117-Darwin-x86_64.pkg -target /
      source /opt/minc/1.9.16/minc-toolkit-config.sh
+     export LDFLAGS="$LDFLAGS -L$(brew --prefix zlib)/lib"
+     Rscript -e "install.packages('digest')"
    fi
    
-repos:
-  bioCsoft: http://bioconductor.org/packages/3.8/bioc

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: RMINC
-Version: 1.5.2.2
+Version: 1.5.2.3
 Date: 2017-05-31
 Title: Statistical Tools for Medical Imaging NetCDF (MINC) Files
 Authors@R: c(person("Jason", "Lerch", role = "aut", email = "jason.lerch@sickkids.ca"), 
@@ -13,7 +13,7 @@ Authors@R: c(person("Jason", "Lerch", role = "aut", email = "jason.lerch@sickkid
              person("Gabriel", "Devenyi", role = "ctb", email = "gdevenyi@gmail.com"))      
 Description: Tools for reading, writing, analyzing, and visualizing Medical
     Imaging NetCDF (MINC) files with R.
-Additional_repositories: http://bioconductor.org/packages/3.6/bioc
+Additional_repositories: http://bioconductor.org/packages/3.10/bioc
 Depends:
     R (>= 3.2)
 Imports:
@@ -40,12 +40,12 @@ Imports:
     visNetwork (>= 2.0.4),
     rjson (>= 0.2.20),
     DT (>= 0.4),
-    rlang (>= 0.2.1)
+    rlang (>= 0.2.1),
+    bigstatsr
 Suggests:
     rgl,
     plotrix,
     lmerTest,
-    BiocInstaller,
     qvalue,
     testthat,
     igraph
@@ -62,4 +62,4 @@ OS_type: unix
 BugReports: https://github.com/Mouse-Imaging-Centre/RMINC/issues
 URL: https://github.com/Mouse-Imaging-Centre/RMINC,
     https://wiki.mouseimaging.ca/display/MICePub/RMINC
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1

INSTALL

@@ -59,11 +59,12 @@ you can use homebrew to install the Gnu Compiler Collection which
 comes with gfortran
 
 ```
-brew install gcc
+brew install gcc libssh2 libgit2 libomp libz
 ```
 
 Regardless of how you install gfortran you will need to tell
-R where to find it. If you installed via brew you can run
+R where to find it. If you installed via brew you can run the
+following in terminal 
 
 ```
 mkdir $HOME/.R/ ## Ignore the error if this directory already exists
@@ -79,6 +80,15 @@ library path. My best guess is
 echo 'FLIBS=-L/usr/local/gfortran/lib" >> $HOME/.R/Makevars'
 ```
 
+Additionally, recent mac versions have struggled to link libz in
+to RMINC. You will probably need to run the following in the terminal
+before opening R
+
+```
+export LDFLAGS="$LDFLAGS -L$(brew --prefix zlib)/lib"
+```
+
+
 If that works or doesn't let me know in the issues!
 
 

NAMESPACE

@@ -179,6 +179,7 @@ export(mincSelectRandomVoxels)
 export(mincSum)
 export(mincSummary)
 export(mincTFCE)
+export(mincTable)
 export(mincTriplanarSlicePlot)
 export(mincTtest)
 export(mincVar)

NEWS

@@ -1,5 +1,24 @@
 New in Version 1.5.*.*
 =======================
+2.3
+--
+- Fixed mincLmer reinit (formula out of scope bug)
+- Improved mac install notes (issue #261)
+- Defaults RMINC_LABEL_DEFINITIONS to null instead of empty string
+  (issue #259)
+- anatGetAll fails faster if the label defs are broken (issue #260)
+- civet.readCBrain now supports `columnsToKeep` to pass to flattening
+  code
+- Add environment variable to configure where test data is located, useful
+  for systems where internet isn't available.
+- Improvement to FDR threshold selection in launch_shiny_RMINC
+- Code for reading in a matrix of minc files `mincTable`. Supports
+  file backed matrices for when your files are too big for your computers
+  memory.
+- Fixed reading QC for CIVET 1.1.12 experiments
+- Fixed and streamlined the continuous integration (travis) build scripts
+- Fixed all outstanding R CMD check and test issues
+
 2.2
 --
 - Improvements to vertex code (thanks @vfonov), now can

R/RMINC.R

@@ -77,6 +77,9 @@ NULL
 ### Package initialization function, syncs environment vars and defines defaults
 .onLoad <-
   function(libname, pkgname){
+    empty_to_null <- function(x){
+      `if`(x == "", NULL, x)
+    }
 
     #Set default options taken from Hadley's r-packages book
     op <- options()
@@ -85,11 +88,13 @@ NULL
       RMINC_MASKED_VALUE = 
         structure(0, class = "RMINC_MASKED_VALUE")
     , RMINC_LABEL_DEFINITIONS =
-        Sys.getenv("RMINC_LABEL_DEFINITIONS")
+        empty_to_null(Sys.getenv("RMINC_LABEL_DEFINITIONS"))          
     , RMINC_BATCH_CONF =
         `if`(Sys.getenv("RMINC_BATCH_CONF") == ""
            , system.file("parallel/pbs_batchtools.R", package = "RMINC")
            , Sys.getenv("RMINC_BATCH_CONF"))
+    , RMINC_DATA_DIR =
+        empty_to_null(Sys.getenv("RMINC_DATA_DIR"))           
     )
 
     toset <- !(names(op.RMINC) %in% names(op))