Version 3.42.0

3 files changed, 89 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..ed086809cfe1
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,27 @@
+pkgbase = r-puma
+	pkgdesc = Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
+	pkgver = 3.42.0
+	pkgrel = 1
+	url = https://bioconductor.org/packages/puma
+	arch = x86_64
+	license = LGPL
+	depends = r-affy
+	depends = r-affyio
+	depends = r-biobase
+	depends = r-mclust
+	depends = r-oligo
+	depends = r-oligoclasses
+	optdepends = r-affydata
+	optdepends = r-annotate
+	optdepends = r-limma
+	optdepends = r-pumadata
+	optdepends = r-rocr
+	optdepends = r-snow
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/puma_3.42.0.tar.gz
+	source = fix-lto.patch
+	md5sums = ec485bb2cd3bc9d97a2badb8b1c0be2d
+	md5sums = 885d25cbb9335808ed144d24c323737c
+	sha256sums = 5b7b32a5b2aa5d6c237870296a1f41927efe3ceb9d1df612559f31f010f6c529
+	sha256sums = f8a3b4534b24c2a2a0d7c607cdac148b8b18706b2bf8fcf69b70142b54241bf7
+
+pkgname = r-puma
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..071cda38668b
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,49 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=puma
+_pkgver=3.42.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(LGPL)
+depends=(
+  r-affy
+  r-affyio
+  r-biobase
+  r-mclust
+  r-oligo
+  r-oligoclasses
+)
+optdepends=(
+  r-affydata
+  r-annotate
+  r-limma
+  r-pumadata
+  r-rocr
+  r-snow
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix-lto.patch")
+md5sums=('ec485bb2cd3bc9d97a2badb8b1c0be2d'
+         '885d25cbb9335808ed144d24c323737c')
+sha256sums=('5b7b32a5b2aa5d6c237870296a1f41927efe3ceb9d1df612559f31f010f6c529'
+            'f8a3b4534b24c2a2a0d7c607cdac148b8b18706b2bf8fcf69b70142b54241bf7')
+
+prepare() {
+  # fix compiling with lto
+  patch -Np1 -i fix-lto.patch
+}
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}
diff --git a/fix-lto.patch b/fix-lto.patch
new file mode 100644
index 000000000000..23c9124c29f8
--- /dev/null
+++ b/fix-lto.patch
@@ -0,0 +1,13 @@
+diff --git a/puma/src/user_eval.c b/puma/src/user_eval.c
+index f531d0b..ac948ca 100644
+--- a/puma/src/user_eval.c
++++ b/puma/src/user_eval.c
+@@ -66,7 +66,7 @@ void user_eval(DDOUBLE xvar[],IINTEGER mode) {
+     #undef   X
+     #include "o8cons.h"
+     
+-    void    eval_extern(IINTEGER mode);
++    extern void (*eval_extern)(IINTEGER mode);
+     DDOUBLE* d1_malloc(IINTEGER size1, IINTEGER init); 
+ 
+     static DDOUBLE   *fusave,xhelp,xincr,sd1,sd2,sd3,d1,d2,d3;