updated to 2.5.8

3 files changed, 8 insertions, 46 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 7f6f030cf301..5a6be7b4ccdc 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,8 +1,6 @@
-# Generated by mksrcinfo v8
-# Fri Jan 29 22:49:02 UTC 2016
 pkgbase = ncbi-vdb
 	pkgdesc = The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
-	pkgver = 2.5.7
+	pkgver = 2.5.8
 	pkgrel = 1
 	url = https://github.com/ncbi/ncbi-vdb
 	arch = x86_64
@@ -11,10 +9,8 @@ pkgbase = ncbi-vdb
 	depends = ngs
 	depends = hdf5
 	provides = ncbi-vdb
-	source = https://github.com/ncbi/ncbi-vdb/archive/2.5.7.tar.gz
-	source = ncbi-vdb.patch
-	sha256sums = e088717270a48f070d5aeb633558e778081c70e5c42e5e621d6a5b8f3c2c5e41
-	sha256sums = 19f09b19cad2ebd4df4185022e711f9bc32898926168d234833e56d70c2d2029
+	source = https://github.com/ncbi/ncbi-vdb/archive/2.5.8.tar.gz
+	sha256sums = 7a0ccc3434220e5288a016e4a9e24d4a1deae2a7d5de594fc94b2442172b3229
 
 pkgname = ncbi-vdb
 
diff --git a/PKGBUILD b/PKGBUILD
index 71eb250b9c54..dbbd5eb9b784 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,7 +2,7 @@
 # Maintainer: Aaron Baker <aa{last name}99{at}gmail{dt}org>
 
 pkgname=ncbi-vdb
-pkgver=2.5.7
+pkgver=2.5.8
 pkgrel=1
 pkgdesc="The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives."
 arch=('x86_64')
@@ -10,14 +10,11 @@ url="https://github.com/ncbi/ncbi-vdb"
 depends=('libxml2' 'ngs' 'hdf5')
 provides=('ncbi-vdb')
 license=('custom:PublicDomain')
-source=("https://github.com/ncbi/ncbi-vdb/archive/$pkgver.tar.gz" "$pkgname.patch")
-sha256sums=('e088717270a48f070d5aeb633558e778081c70e5c42e5e621d6a5b8f3c2c5e41' '19f09b19cad2ebd4df4185022e711f9bc32898926168d234833e56d70c2d2029')
+source=("https://github.com/ncbi/ncbi-vdb/archive/$pkgver.tar.gz")
+sha256sums=('7a0ccc3434220e5288a016e4a9e24d4a1deae2a7d5de594fc94b2442172b3229')
 
 prepare(){
   cd "${pkgname}-${pkgver}"
-  # ncbi build process frequently checks if we are root user which interferes 
-  #   with makepkg use of fakeroot
-  patch -p1 -i "$srcdir/$pkgname.patch"
 }
 
 build(){
@@ -50,6 +47,6 @@ package(){
   # TODO without this a link from libncbi-vdb-static.a -> libncbi-vdb.a is dead because 
   #   libncbi-vdb.a gets removed somehow??
   cd "$pkgdir/usr/lib/"
-  ln -sf libncbi-vdb.a.2.5.7 libncbi-vdb-static.a
-  ln -sf libncbi-wvdb.a.2.5.7 libncbi-wvdb-static.a
+  ln -sf "libncbi-vdb.a.$pkgver" libncbi-vdb-static.a
+  ln -sf "libncbi-wvdb.a.$pkgver" libncbi-wvdb-static.a
 }
diff --git a/ncbi-vdb.patch b/ncbi-vdb.patch
deleted file mode 100644
index eccbbc8890a0..000000000000
--- a/ncbi-vdb.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff -aur ncbi-vdb-2.5.7.pristine/build/Makefile.install ncbi-vdb-2.5.7.new/build/Makefile.install
---- ncbi-vdb-2.5.7.pristine/build/Makefile.install	2016-01-26 21:10:12.713909719 +0000
-+++ ncbi-vdb-2.5.7.new/build/Makefile.install	2016-01-26 21:18:28.630558667 +0000
-@@ -66,11 +66,7 @@
- PROFILE_FILE = $(ROOT)/etc/profile.d/ncbi-vdb
- KONFIG_DIR = $(ROOT)/etc/ncbi/
- 
--ifeq (linux, $(OS))
--    ifeq (0, $(shell id -u))
--        LINUX_ROOT = true
--    endif
--endif
-+LINUX_ROOT = false
- 
- install: copylibs copyincludes 
- ifeq (true, $(LINUX_ROOT))
-diff -aur ncbi-vdb-2.5.7.pristine/setup/install.perl ncbi-vdb-2.5.7.new/setup/install.perl
---- ncbi-vdb-2.5.7.pristine/setup/install.perl	2016-01-26 21:10:12.810576379 +0000
-+++ ncbi-vdb-2.5.7.new/setup/install.perl	2016-01-26 21:11:20.967240611 +0000
-@@ -81,11 +81,9 @@
- prepare();
- 
- my $LINUX_ROOT;
--++$LINUX_ROOT if (linux_root());
- my $ROOT = '';
- if ($OPT{root}) {
-     $ROOT = "$OPT{root}/root";
--    ++$LINUX_ROOT;
-     foreach ("$ROOT/usr/include", "$ROOT/etc/profile.d") {
-         unless (-e $_) {
-             print "mkdir -p $_... ";