From 048f2ca0636292a82fc070faa09e99a2e8c87614 Mon Sep 17 00:00:00 2001
From: Greg Lin <glin@rstudio.com>
Date: Wed, 29 Apr 2020 14:44:16 -0500
Subject: [PATCH 1/3] Remove unnecessary PCRE2 dependency on R 3.x

For more details on PCRE2 usage in R 3.x, see:
https://github.com/wch/r-source/blob/7d25524f8b83d63979cc18f0914a321bfbe9a819/m4/R.m4#L3056-L3058
https://github.com/wch/r-source/blob/7d25524f8b83d63979cc18f0914a321bfbe9a819/m4/R.m4#L3139-L3155
---
 builder/build.sh            | 14 ++++++++++++++
 builder/package.centos-6    |  9 +++++++--
 builder/package.centos-7    |  9 +++++++--
 builder/package.centos-8    |  9 +++++++--
 builder/package.debian-10   |  9 +++++++--
 builder/package.debian-9    |  9 +++++++--
 builder/package.opensuse-15 |  9 +++++++--
 builder/package.opensuse-42 |  9 +++++++--
 builder/package.ubuntu-1604 |  9 +++++++--
 builder/package.ubuntu-1804 |  9 +++++++--
 builder/package.ubuntu-2004 |  9 +++++++--
 11 files changed, 84 insertions(+), 20 deletions(-)

diff --git a/builder/build.sh b/builder/build.sh
index aac683a..01461ef 100755
--- a/builder/build.sh
+++ b/builder/build.sh
@@ -65,6 +65,20 @@ compile_r() {
     build_flag=''
   fi
 
+  # Avoid a PCRE2 dependency for R 3.5 and 3.6. R 3.x uses PCRE1, but R 3.5+
+  # will link against PCRE2 if present, although it is not actually used.
+  # Since there's no way to disable this in the configure script, and we need
+  # PCRE2 for R 4.x, we hide PCRE2 from the configure script by temporarily
+  # removing the pkg-config file and pcre2-config script.
+  if [[ "${1}" =~ ^3 ]] && pkg-config --exists libpcre2-8; then
+    mkdir -p /tmp/pcre2
+    pc_dir=$(pkg-config --variable pcfiledir libpcre2-8)
+    mv ${pc_dir}/libpcre2-8.pc /tmp/pcre2
+    config_bin=$(which pcre2-config)
+    mv ${config_bin} /tmp/pcre2
+    trap "{ mv /tmp/pcre2/libpcre2-8.pc ${pc_dir}; mv /tmp/pcre2/pcre2-config ${config_bin}; }" EXIT
+  fi
+
   # Default configure options. Some Dockerfiles override this with an ENV directive.
   default_configure_options="\
     --enable-R-shlib \
diff --git a/builder/package.centos-6 b/builder/package.centos-6
index 93fadd8..a855002 100644
--- a/builder/package.centos-6
+++ b/builder/package.centos-6
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/centos-6 ]]; then
   mkdir -p /tmp/output/centos-6
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='pcre2-devel'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='pcre-devel'
+fi
+
 # create post-install script required for openblas
 cat <<EOF >> /post-install.sh
 mv /opt/R/${R_VERSION}/lib/R/lib/libRblas.so /opt/R/${R_VERSION}/lib/R/lib/libRblas.so.keep 
@@ -60,8 +66,7 @@ fpm \
   -d make \
   -d openblas-devel \
   -d pango \
-  -d pcre-devel \
-  -d pcre2-devel \
+  -d ${pcre_lib} \
   -d tcl \
   -d tk \
   -d unzip \
diff --git a/builder/package.centos-7 b/builder/package.centos-7
index e927d8f..1623d6a 100644
--- a/builder/package.centos-7
+++ b/builder/package.centos-7
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/centos-7 ]]; then
   mkdir -p /tmp/output/centos-7
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='pcre2-devel'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='pcre-devel'
+fi
+
 # create post-install script required for openblas
 cat <<EOF >> /post-install.sh
 mv /opt/R/${R_VERSION}/lib/R/lib/libRblas.so /opt/R/${R_VERSION}/lib/R/lib/libRblas.so.keep 
@@ -45,8 +51,7 @@ fpm \
   -d make \
   -d openblas-devel \
   -d pango \
-  -d pcre-devel \
-  -d pcre2-devel \
+  -d ${pcre_lib} \
   -d tcl \
   -d tk \
   -d unzip \
diff --git a/builder/package.centos-8 b/builder/package.centos-8
index a873d1d..4568261 100644
--- a/builder/package.centos-8
+++ b/builder/package.centos-8
@@ -2,6 +2,12 @@ if [[ ! -d /tmp/output/centos-8 ]]; then
   mkdir -p /tmp/output/centos-8
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='pcre2-devel'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='pcre-devel'
+fi
+
 # create post-install script required for openblas
 cat <<EOF >> /post-install.sh
 mv /opt/R/${R_VERSION}/lib/R/lib/libRblas.so /opt/R/${R_VERSION}/lib/R/lib/libRblas.so.keep
@@ -43,8 +49,7 @@ fpm \
   -d make \
   -d openblas-threads \
   -d pango \
-  -d pcre-devel \
-  -d pcre2-devel \
+  -d ${pcre_lib} \
   -d tcl \
   -d tk \
   -d unzip \
diff --git a/builder/package.debian-10 b/builder/package.debian-10
index afacab5..5d9dfc9 100644
--- a/builder/package.debian-10
+++ b/builder/package.debian-10
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/debian-10 ]]; then
   mkdir -p /tmp/output/debian-10
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='libpcre2-8-0'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='libpcre3'
+fi
+
 fpm \
   -s dir \
   -t deb \
@@ -33,8 +39,7 @@ fpm \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
   -d libpaper-utils \
-  -d libpcre2-8-0 \
-  -d libpcre3 \
+  -d ${pcre_lib} \
   -d libpng16-16 \
   -d libreadline7 \
   -d libtcl8.6 \
diff --git a/builder/package.debian-9 b/builder/package.debian-9
index ee90933..b60d330 100644
--- a/builder/package.debian-9
+++ b/builder/package.debian-9
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/debian-9 ]]; then
   mkdir -p /tmp/output/debian-9
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='libpcre2-8-0'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='libpcre3'
+fi
+
 fpm \
   -s dir \
   -t deb \
@@ -33,8 +39,7 @@ fpm \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
   -d libpaper-utils \
-  -d libpcre2-8-0 \
-  -d libpcre3 \
+  -d ${pcre_lib} \
   -d libpng16-16 \
   -d libreadline7 \
   -d libtcl8.6 \
diff --git a/builder/package.opensuse-15 b/builder/package.opensuse-15
index 834a8a9..25b7f24 100644
--- a/builder/package.opensuse-15
+++ b/builder/package.opensuse-15
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/opensuse-15 ]]; then
   mkdir -p /tmp/output/opensuse-15
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='pcre2-devel'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='pcre-devel'
+fi
+
 # create post-install script required for openblas
 cat <<EOF >> /post-install.sh
 mv /opt/R/${R_VERSION}/lib/R/lib/libRblas.so /opt/R/${R_VERSION}/lib/R/lib/libRblas.so.keep
@@ -50,8 +56,7 @@ fpm \
   -d libtiff5 \
   -d make \
   -d openblas-devel \
-  -d pcre-devel \
-  -d pcre2-devel \
+  -d ${pcre_lib} \
   -d tar \
   -d tcl \
   -d tk \
diff --git a/builder/package.opensuse-42 b/builder/package.opensuse-42
index 4ee631d..5bb72c9 100644
--- a/builder/package.opensuse-42
+++ b/builder/package.opensuse-42
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/opensuse-42 ]]; then
   mkdir -p /tmp/output/opensuse-42
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='pcre2-devel'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='pcre-devel'
+fi
+
 # create post-install script required for openblas
 cat <<EOF >> /post-install.sh
 mv /opt/R/${R_VERSION}/lib/R/lib/libRblas.so /opt/R/${R_VERSION}/lib/R/lib/libRblas.so.keep
@@ -48,8 +54,7 @@ fpm \
   -d libtiff5 \
   -d make \
   -d openblas-devel \
-  -d pcre-devel \
-  -d pcre2-devel \
+  -d ${pcre_lib} \
   -d tar \
   -d tcl \
   -d tk \
diff --git a/builder/package.ubuntu-1604 b/builder/package.ubuntu-1604
index 27b797b..e9c9034 100644
--- a/builder/package.ubuntu-1604
+++ b/builder/package.ubuntu-1604
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/ubuntu-1604 ]]; then
   mkdir -p /tmp/output/ubuntu-1604
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='libpcre2-8-0'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='libpcre3'
+fi
+
 fpm \
   -s dir \
   -t deb \
@@ -33,8 +39,7 @@ fpm \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
   -d libpaper-utils \
-  -d libpcre2-8-0 \
-  -d libpcre3 \
+  -d ${pcre_lib} \
   -d libpng16-16 \
   -d libreadline6 \
   -d libtcl8.6 \
diff --git a/builder/package.ubuntu-1804 b/builder/package.ubuntu-1804
index e858c1f..2d9d8d5 100644
--- a/builder/package.ubuntu-1804
+++ b/builder/package.ubuntu-1804
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/ubuntu-1804 ]]; then
   mkdir -p /tmp/output/ubuntu-1804
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='libpcre2-8-0'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='libpcre3'
+fi
+
 fpm \
   -s dir \
   -t deb \
@@ -33,8 +39,7 @@ fpm \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
   -d libpaper-utils \
-  -d libpcre2-8-0 \
-  -d libpcre3 \
+  -d ${pcre_lib} \
   -d libpng16-16 \
   -d libreadline7 \
   -d libtcl8.6 \
diff --git a/builder/package.ubuntu-2004 b/builder/package.ubuntu-2004
index 60f8f28..f615651 100644
--- a/builder/package.ubuntu-2004
+++ b/builder/package.ubuntu-2004
@@ -4,6 +4,12 @@ if [[ ! -d /tmp/output/ubuntu-2004 ]]; then
   mkdir -p /tmp/output/ubuntu-2004
 fi
 
+# R 3.x requires PCRE1
+pcre_lib='libpcre2-8-0'
+if [[ "${R_VERSION}" =~ ^3 ]]; then
+  pcre_lib='libpcre3'
+fi
+
 fpm \
   -s dir \
   -t deb \
@@ -34,8 +40,7 @@ fpm \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
   -d libpaper-utils \
-  -d libpcre2-8-0 \
-  -d libpcre3 \
+  -d ${pcre_lib} \
   -d libpng16-16 \
   -d libreadline8 \
   -d libtcl8.6 \

From 650d3650ce13da3a83205d4d57226fecfcf73e14 Mon Sep 17 00:00:00 2001
From: Greg Lin <glin@rstudio.com>
Date: Thu, 14 May 2020 13:56:58 -0500
Subject: [PATCH 2/3] Switch to dev PCRE in Ubuntu/Debian packages

For consistency with CentOS and SUSE, and because packages that
link against libR like rJava need PCRE dev headers to install
from source.
---
 builder/package.debian-10   | 4 ++--
 builder/package.debian-9    | 4 ++--
 builder/package.ubuntu-1604 | 4 ++--
 builder/package.ubuntu-1804 | 4 ++--
 builder/package.ubuntu-2004 | 4 ++--
 5 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/builder/package.debian-10 b/builder/package.debian-10
index 5d9dfc9..c010223 100644
--- a/builder/package.debian-10
+++ b/builder/package.debian-10
@@ -5,9 +5,9 @@ if [[ ! -d /tmp/output/debian-10 ]]; then
 fi
 
 # R 3.x requires PCRE1
-pcre_lib='libpcre2-8-0'
+pcre_lib='libpcre2-dev'
 if [[ "${R_VERSION}" =~ ^3 ]]; then
-  pcre_lib='libpcre3'
+  pcre_lib='libpcre3-dev'
 fi
 
 fpm \
diff --git a/builder/package.debian-9 b/builder/package.debian-9
index b60d330..5842f3d 100644
--- a/builder/package.debian-9
+++ b/builder/package.debian-9
@@ -5,9 +5,9 @@ if [[ ! -d /tmp/output/debian-9 ]]; then
 fi
 
 # R 3.x requires PCRE1
-pcre_lib='libpcre2-8-0'
+pcre_lib='libpcre2-dev'
 if [[ "${R_VERSION}" =~ ^3 ]]; then
-  pcre_lib='libpcre3'
+  pcre_lib='libpcre3-dev'
 fi
 
 fpm \
diff --git a/builder/package.ubuntu-1604 b/builder/package.ubuntu-1604
index e9c9034..e52065e 100644
--- a/builder/package.ubuntu-1604
+++ b/builder/package.ubuntu-1604
@@ -5,9 +5,9 @@ if [[ ! -d /tmp/output/ubuntu-1604 ]]; then
 fi
 
 # R 3.x requires PCRE1
-pcre_lib='libpcre2-8-0'
+pcre_lib='libpcre2-dev'
 if [[ "${R_VERSION}" =~ ^3 ]]; then
-  pcre_lib='libpcre3'
+  pcre_lib='libpcre3-dev'
 fi
 
 fpm \
diff --git a/builder/package.ubuntu-1804 b/builder/package.ubuntu-1804
index 2d9d8d5..19eeebc 100644
--- a/builder/package.ubuntu-1804
+++ b/builder/package.ubuntu-1804
@@ -5,9 +5,9 @@ if [[ ! -d /tmp/output/ubuntu-1804 ]]; then
 fi
 
 # R 3.x requires PCRE1
-pcre_lib='libpcre2-8-0'
+pcre_lib='libpcre2-dev'
 if [[ "${R_VERSION}" =~ ^3 ]]; then
-  pcre_lib='libpcre3'
+  pcre_lib='libpcre3-dev'
 fi
 
 fpm \
diff --git a/builder/package.ubuntu-2004 b/builder/package.ubuntu-2004
index f615651..9199b7b 100644
--- a/builder/package.ubuntu-2004
+++ b/builder/package.ubuntu-2004
@@ -5,9 +5,9 @@ if [[ ! -d /tmp/output/ubuntu-2004 ]]; then
 fi
 
 # R 3.x requires PCRE1
-pcre_lib='libpcre2-8-0'
+pcre_lib='libpcre2-dev'
 if [[ "${R_VERSION}" =~ ^3 ]]; then
-  pcre_lib='libpcre3'
+  pcre_lib='libpcre3-dev'
 fi
 
 fpm \

From d49f9104dbdd617ef18e17591f5fac2de7cd2ae1 Mon Sep 17 00:00:00 2001
From: Greg Lin <glin@rstudio.com>
Date: Thu, 14 May 2020 14:53:06 -0500
Subject: [PATCH 3/3] Add -dev libs for R packages that link against libR

For consistency with CentOS and SUSE, and to install packages that
link against libR from source, like rJava. See `R CMD config --ldflags` and
https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Compiling-against-the-R-library
---
 builder/package.debian-10   | 8 ++++----
 builder/package.debian-9    | 8 ++++----
 builder/package.ubuntu-1604 | 8 ++++----
 builder/package.ubuntu-1804 | 8 ++++----
 builder/package.ubuntu-2004 | 8 ++++----
 5 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/builder/package.debian-10 b/builder/package.debian-10
index c010223..f1319fc 100644
--- a/builder/package.debian-10
+++ b/builder/package.debian-10
@@ -27,14 +27,14 @@ fpm \
   -d g++ \
   -d gcc \
   -d gfortran \
-  -d libbz2-1.0 \
+  -d libbz2-dev \
   -d libc6 \
   -d libcairo2 \
   -d libcurl4-openssl-dev \
   -d libglib2.0-0 \
   -d libgomp1 \
-  -d libicu63 \
-  -d liblzma5 \
+  -d libicu-dev \
+  -d liblzma-dev \
   -d libopenblas-dev \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
@@ -51,7 +51,7 @@ fpm \
   -d ucf \
   -d unzip \
   -d zip \
-  -d zlib1g \
+  -d zlib1g-dev \
   /opt/R/${R_VERSION}
 
 shopt -s extglob
diff --git a/builder/package.debian-9 b/builder/package.debian-9
index 5842f3d..508a15d 100644
--- a/builder/package.debian-9
+++ b/builder/package.debian-9
@@ -27,14 +27,14 @@ fpm \
   -d g++ \
   -d gcc \
   -d gfortran \
-  -d libbz2-1.0 \
+  -d libbz2-dev \
   -d libc6 \
   -d libcairo2 \
   -d libcurl4-openssl-dev \
   -d libglib2.0-0 \
   -d libgomp1 \
-  -d libicu57 \
-  -d liblzma5 \
+  -d libicu-dev \
+  -d liblzma-dev \
   -d libopenblas-dev \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
@@ -51,7 +51,7 @@ fpm \
   -d ucf \
   -d unzip \
   -d zip \
-  -d zlib1g \
+  -d zlib1g-dev \
   /opt/R/${R_VERSION}
 
 shopt -s extglob
diff --git a/builder/package.ubuntu-1604 b/builder/package.ubuntu-1604
index e52065e..eb4b281 100644
--- a/builder/package.ubuntu-1604
+++ b/builder/package.ubuntu-1604
@@ -26,15 +26,15 @@ fpm \
   -d g++ \
   -d gcc \
   -d gfortran \
-  -d libbz2-1.0 \
+  -d libbz2-dev \
   -d libc6 \
   -d libcairo2 \
   -d libcurl3 \
   -d libglib2.0-0 \
   -d libgomp1 \
-  -d libicu55 \
+  -d libicu-dev \
   -d libjpeg8 \
-  -d liblzma5 \
+  -d liblzma-dev \
   -d libopenblas-dev \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
@@ -51,7 +51,7 @@ fpm \
   -d ucf \
   -d unzip \
   -d zip \
-  -d zlib1g \
+  -d zlib1g-dev \
   /opt/R/${R_VERSION}
 
 shopt -s extglob
diff --git a/builder/package.ubuntu-1804 b/builder/package.ubuntu-1804
index 19eeebc..123d9ed 100644
--- a/builder/package.ubuntu-1804
+++ b/builder/package.ubuntu-1804
@@ -26,15 +26,15 @@ fpm \
   -d g++ \
   -d gcc \
   -d gfortran \
-  -d libbz2-1.0 \
+  -d libbz2-dev \
   -d libc6 \
   -d libcairo2 \
   -d libcurl4 \
   -d libglib2.0-0 \
   -d libgomp1 \
-  -d libicu60 \
+  -d libicu-dev \
   -d libjpeg8 \
-  -d liblzma5 \
+  -d liblzma-dev \
   -d libopenblas-dev \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
@@ -51,7 +51,7 @@ fpm \
   -d ucf \
   -d unzip \
   -d zip \
-  -d zlib1g \
+  -d zlib1g-dev \
   /opt/R/${R_VERSION}
 
 shopt -s extglob
diff --git a/builder/package.ubuntu-2004 b/builder/package.ubuntu-2004
index 9199b7b..191ce89 100644
--- a/builder/package.ubuntu-2004
+++ b/builder/package.ubuntu-2004
@@ -26,17 +26,17 @@ fpm \
   -d g++ \
   -d gcc \
   -d gfortran \
-  -d libbz2-1.0 \
+  -d libbz2-dev \
   -d libblas-dev \
   -d libc6 \
   -d libcairo2 \
   -d libcurl4 \
   -d libglib2.0-0 \
   -d libgomp1 \
-  -d libicu66 \
+  -d libicu-dev \
   -d libjpeg8 \
   -d liblapack-dev \
-  -d liblzma5 \
+  -d liblzma-dev \
   -d libpango-1.0-0 \
   -d libpangocairo-1.0-0 \
   -d libpaper-utils \
@@ -52,7 +52,7 @@ fpm \
   -d ucf \
   -d unzip \
   -d zip \
-  -d zlib1g \
+  -d zlib1g-dev \
   /opt/R/${R_VERSION}
 
 shopt -s extglob