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-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild14
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild13
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild14
3 files changed, 17 insertions, 24 deletions
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index ebc9c33cd..23ff5d869 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -25,8 +25,8 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -35,7 +35,6 @@ KEYWORDS=""
DEPEND="
!sci-biology/sra_sdk
berkdb? ( sys-libs/db:4.3[cxx] )
- ftds? ( dev-db/freetds )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite )
@@ -43,7 +42,7 @@ DEPEND="
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl media-libs/glew )
- mesa? ( media-libs/mesa
+ osmesa? ( media-libs/mesa
media-libs/glew
)
glut? ( media-libs/freeglut )
@@ -70,7 +69,8 @@ DEPEND="
app-arch/bzip2
dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-
+# Intentionally omitted USE flags:
+# ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
@@ -168,7 +168,6 @@ src_configure() {
#--with-ncbi-public ensure compatibility for all in-house platforms
#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
#--with-sybase-new use newer SYBASE install (12.5 rather than 12.0)
- #--without-ftds-renamed do not rename Sybase DBLIB symbols in built-in FTDS
#--without-sp do not use SP libraries
#--without-orbacus do not use ORBacus CORBA libraries
#--with-orbacus=DIR use ORBacus installation in DIR
@@ -228,11 +227,10 @@ src_configure() {
$(use_with lzo lzo "${EPREFIX}/usr")
$(use_with pcre pcre "${EPREFIX}/usr")
$(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with ftds ftds "${EPREFIX}/usr")
$(use_with mysql mysql "${EPREFIX}/usr")
$(usex fltk --with-fltk="${EPREFIX}/usr" "")
$(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with mesa mesa "${EPREFIX}/usr")
+ $(use_with osmesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
$(use_with opengl glew-mx)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 953b011a9..44c444e31 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -26,8 +26,8 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
- glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ glut gnutls hdf5 icu lzo jpeg osmesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -35,7 +35,6 @@ KEYWORDS=""
# sys-libs/db should be compiled with USE=cxx
DEPEND="
berkdb? ( sys-libs/db:4.3[cxx] )
- ftds? ( dev-db/freetds )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite )
@@ -44,7 +43,7 @@ DEPEND="
gnutls? ( net-libs/gnutls )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl )
- mesa? ( media-libs/mesa
+ osmesa? ( media-libs/osmesa
media-libs/glew
)
glut? ( media-libs/freeglut )
@@ -70,6 +69,8 @@ DEPEND="
app-arch/bzip2
dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+# Intentionally omitted USE flags:
+# ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
# seems muParser is required, also glew is required. configure exitss otherwise
@@ -154,7 +155,6 @@ src_configure() {
#--with-ncbi-public ensure compatibility for all in-house platforms
#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
#--with-sybase-new use newer SYBASE install (12.5 rather than 12.0)
- #--without-ftds-renamed do not rename Sybase DBLIB symbols in built-in FTDS
#--without-sp do not use SP libraries
#--without-orbacus do not use ORBacus CORBA libraries
#--with-orbacus=DIR use ORBacus installation in DIR
@@ -224,11 +224,10 @@ src_configure() {
$(use_with lzo lzo "${EPREFIX}/usr")
$(use_with pcre pcre "${EPREFIX}/usr")
$(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with ftds ftds "${EPREFIX}/usr")
$(use_with mysql mysql "${EPREFIX}/usr")
$(use_with fltk fltk "${EPREFIX}/usr")
$(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with mesa mesa "${EPREFIX}/usr")
+ $(use_with osmesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
$(use_with opengl glew-mx)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index b9f804751..89b6a96c7 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -23,13 +23,12 @@ SRC_URI="
LICENSE="public-domain"
SLOT="0"
-IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
# sys-libs/db should be compiled with USE=cxx
DEPEND="berkdb? ( sys-libs/db:4.3 )
- ftds? ( dev-db/freetds )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite )
@@ -38,7 +37,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
gnutls? ( net-libs/gnutls )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl )
- mesa? ( media-libs/mesa )
+ osmesa? ( media-libs/mesa )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
fastcgi? ( www-apache/mod_fastcgi )
@@ -62,6 +61,8 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
app-arch/bzip2
dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+# Intentionally omitted USE flags:
+# ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
# configure options, may want to expose some
# --without-debug build non-debug versions of libs and apps
@@ -171,11 +172,6 @@ src_configure() {
if ! use curl; then
myconf="--without-curl"
fi
- if use ftds; then
- myconf="--with-ftds"
- else
- myconf="--without-ftds"
- fi
if use gnutls; then
myconf="--with-gnutls"
else
@@ -196,7 +192,7 @@ src_configure() {
if ! use opengl; then
myconf="--without-opengl"
fi
- if ! use mesa; then
+ if ! use osmesa; then
myconf="--without-mesa"
fi
if ! use glut; then