Isolate conda R from system user library.

recipe/0019-Disable-default-user-libraries.patch

@@ -0,0 +1,27 @@
+From 8c85f70505694dd181ef47a47896007b150f94c3 Mon Sep 17 00:00:00 2001
+From: John Blischak <jdblischak@gmail.com>
+Date: Thu, 13 Dec 2018 14:12:32 -0500
+Subject: [PATCH] Disable default user libraries.
+
+---
+ etc/Renviron.in | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/etc/Renviron.in b/etc/Renviron.in
+index 49604e54c2..38efb63bb9 100644
+--- a/etc/Renviron.in
++++ b/etc/Renviron.in
+@@ -39,8 +39,8 @@ TAR=${TAR-'@TAR@'}
+ ## System and compiler types.
+ R_SYSTEM_ABI='@R_SYSTEM_ABI@'
+
+-@BUILD_AQUA_FALSE@R_LIBS_USER=${R_LIBS_USER-'~/R/@R_PLATFORM@-library/@MAJ_MIN_VERSION@'}
+-@BUILD_AQUA_TRUE@R_LIBS_USER=${R_LIBS_USER-'~/Library/R/@MAJ_MIN_VERSION@/library'}
++#@BUILD_AQUA_FALSE@R_LIBS_USER=${R_LIBS_USER-'~/R/@R_PLATFORM@-library/@MAJ_MIN_VERSION@'}
++#@BUILD_AQUA_TRUE@R_LIBS_USER=${R_LIBS_USER-'~/Library/R/@MAJ_MIN_VERSION@/library'}
+
+ ### Local Variables: ***
+ ### mode: sh ***
+-- 
+2.17.1
+

recipe/activate-r-base.sh

@@ -6,3 +6,15 @@ if [[ ! -z ${RSTUDIO_WHICH_R+x} ]]; then
   export RSTUDIO_WHICH_R_PREV="$RSTUDIO_WHICH_R"
 fi
 export RSTUDIO_WHICH_R="$CONDA_PREFIX/bin/R"
+
+# store existing R_LIBS_USER if the user has not set CONDA_KEEP_R_LIBS_USER
+if [[ ! -z ${R_LIBS_USER+x} && -z ${CONDA_KEEP_R_LIBS_USER+x} ]]; then
+  export R_LIBS_USER_PREV="$R_LIBS_USER"
+fi
+unset R_LIBS_USER
+
+# store existing R_LIBS if the user has not set CONDA_KEEP_R_LIBS
+if [[ ! -z ${R_LIBS+x} && -z ${CONDA_KEEP_R_LIBS+x} ]]; then
+  export R_LIBS_PREV="$R_LIBS"
+fi
+unset R_LIBS

recipe/deactivate-r-base.sh

@@ -7,3 +7,15 @@ if [[ ! -z ${RSTUDIO_WHICH_R_PREV+x} ]]; then
 else
   unset RSTUDIO_WHICH_R
 fi
+
+# restore pre-existing R_LIBS_USER
+if [[ ! -z ${R_LIBS_USER_PREV+x} ]]; then
+  export R_LIBS_USER="$R_LIBS_USER_PREV"
+  unset R_LIBS_USER_PREV
+fi
+
+# restore pre-existing R_LIBS
+if [[ ! -z ${R_LIBS_PREV+x} ]]; then
+  export R_LIBS="$R_LIBS_PREV"
+  unset R_LIBS_PREV
+fi

recipe/meta.yaml

@@ -27,10 +27,11 @@ source:
     - 0015-link-Xt-to-uuid.patch
     - 0017-Check-for-changes-then-forcibly-mv-in-javareconf.in.patch
     - 0018-Use-LAPACK_LDFLAGS-in-Rlapack_la_LIBADD.patch
+    - 0019-Disable-default-user-libraries.patch
 
 build:
   merge_build_host: True  # [win]
-  number: 3
+  number: 4
   rpaths:
     - lib/R/lib/
     - lib/
@@ -177,8 +178,14 @@ test:
     - Rscript -e "stopifnot(capabilities('jpeg'), TRUE)"
     - Rscript -e "stopifnot(capabilities('png'), TRUE)"
     - if not exist %PREFIX%\\Lib\\R\\bin\\x64\\R.lib exit 1  # [win]
+    - Rscript test-isolation-setup.R
+    - Rscript test-isolation.R
+    - Rscript test-isolation-teardown.R
   files:
     - test-svg.R
+    - test-isolation-setup.R
+    - test-isolation.R
+    - test-isolation-teardown.R
 
 about:
   home: http://www.r-project.org/

recipe/test-isolation-setup.R

@@ -0,0 +1,16 @@
+print(.libPaths())
+os <- .Platform$OS.type
+major <- R.version$major
+minor <- substr(1, 1, R.version$minor)
+platform <- R.version$platform
+
+if (os == "unix" || os == "windows") {
+  d <- sprintf("~/R/%s-library/%s.%s", platform, major, minor)
+} else if (os == "darwin") {
+  d <- sprintf("~/Library/R/%s.%s/library/", major, minor)
+}
+
+d_exists <- dir.exists(d)
+if (!d_exists) {
+  dir.create(d, recursive = TRUE)
+}

recipe/test-isolation-teardown.R

@@ -0,0 +1,24 @@
+print(.libPaths())
+os <- .Platform$OS.type
+major <- R.version$major
+minor <- substr(1, 1, R.version$minor)
+platform <- R.version$platform
+
+if (os == "unix" || os == "windows") {
+  d <- sprintf("~/R/%s-library/%s.%s", platform, major, minor)
+} else if (os == "darwin") {
+  d <- sprintf("~/Library/R/%s.%s/library/", major, minor)
+}
+
+# There were 3 nested subdirectories added for every OS. Only remove if empty
+if (length(dir(d)) == 0) {
+  unlink(d)
+}
+d <- dirname(d)
+if (length(dir(d)) == 0) {
+  unlink(d)
+}
+d <- dirname(d)
+if (length(dir(d)) == 0) {
+  unlink(d)
+}

recipe/test-isolation.R

@@ -0,0 +1,2 @@
+# There should only be one library directory for a local conda R installation
+stopifnot(length(.libPaths()) == 1)