[med-svn] [Git][med-team/ncbi-tools6][master] 4 commits: Start work on ncbi-tools6 6.1.20170106+dfsg2-2, mainly for #1066356.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Wed Mar 20 03:28:55 GMT 2024
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
9d56e415 by Aaron M. Ucko at 2024-03-19T23:06:05-04:00
Start work on ncbi-tools6 6.1.20170106+dfsg2-2, mainly for #1066356.
- - - - -
c0e08c15 by Aaron M. Ucko at 2024-03-19T23:24:38-04:00
Don't rely on any implicit function declarations (#1066356)
- api/asn2gnb2.c: Correct the first(!) <asn2gnbi.h> to <ffprint.h>
for PrintDate.
- api/salutil.c: +<alignmgr2.h> for AlnMgr2IndexSingleChildSeqAlign.
- vibrant/shim3d.h: Add a prototype for Nlm_SetOGLContext and
supporting forward declarations. (Some name clashes preclude
reliably including X headers from here.)
- - - - -
19a9b484 by Aaron M. Ucko at 2024-03-19T23:24:38-04:00
debian/control: Apply routine-update.
- List fields in its preferred order.
- Wrap lists to hold one item per line.
- Standards-Version: 4.6.2 (no changes needed).
- Drop ncbi-cn3d's Breaks/Replaces on ancient ncbi-tools-x11.
- - - - -
b2ceceb7 by Aaron M. Ucko at 2024-03-19T23:24:38-04:00
Finalize ncbi-tools6 6.1.20170106+dfsg2-2 for unstable.
- - - - -
6 changed files:
- api/asn2gnb2.c
- api/salutil.c
- debian/changelog
- debian/control
- debian/patches/debian-changes
- vibrant/shim3d.h
Changes:
=====================================
api/asn2gnb2.c
=====================================
@@ -58,7 +58,7 @@
#include <validerr.h>
#include <objvalid.h>
#include <valapi.h>
-#include <asn2gnbi.h>
+#include <ffprint.h>
#include <asn2gnbi.h>
#ifdef WIN_MAC
=====================================
api/salutil.c
=====================================
@@ -51,6 +51,7 @@
#include <edutil.h>
#include <sequtil.h>
#include <sqnutils.h>
+#include <alignmgr2.h>
#ifdef SALSA_DEBUG
#include <simutil.h>
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+ncbi-tools6 (6.1.20170106+dfsg2-2) unstable; urgency=medium
+
+ * Don't rely on any implicit function declarations. (Closes: #1066356.)
+ - api/asn2gnb2.c: Correct the first(!) <asn2gnbi.h> to <ffprint.h>
+ for PrintDate.
+ - api/salutil.c: +<alignmgr2.h> for AlnMgr2IndexSingleChildSeqAlign.
+ - vibrant/shim3d.h: Add a prototype for Nlm_SetOGLContext and
+ supporting forward declarations. (Some name clashes preclude
+ reliably including X headers from here.)
+ * debian/control: Apply routine-update.
+ - List fields in its preferred order.
+ - Wrap lists to hold one item per line.
+ - Standards-Version: 4.6.2 (no changes needed).
+ - Drop ncbi-cn3d's Breaks/Replaces on ancient ncbi-tools-x11.
+
+ -- Aaron M. Ucko <ucko at debian.org> Tue, 19 Mar 2024 23:21:24 -0400
+
ncbi-tools6 (6.1.20170106+dfsg2-1) unstable; urgency=medium
* Incorporate final time64 changes; the previous two uploads used
=====================================
debian/control
=====================================
@@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Aaron M. Ucko <ucko at debian.org>
Section: libdevel
Priority: optional
-Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13)
+Build-Depends: dpkg-dev (>= 1.22.5),
+ debhelper-compat (= 13)
Build-Depends-Arch: csh | c-shell,
libglu1-mesa-dev | libglu-dev,
libgnutls28-dev | gnutls-dev,
@@ -13,16 +14,13 @@ Build-Depends-Arch: csh | c-shell,
libxmu-dev
Build-Depends-Indep: icoutils,
imagemagick
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-tools6
Vcs-Git: https://salsa.debian.org/med-team/ncbi-tools6.git
Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Rules-Requires-Root: no
Package: libncbi6t64
-Provides: ${t64:Provides}
-Replaces: libncbi6
-Breaks: libncbi6 (<< ${source:Version})
Architecture: any
Multi-Arch: same
Section: libs
@@ -30,6 +28,9 @@ Depends: ncbi-data (= ${source:Version}),
${misc:Depends},
${shlibs:Depends}
Pre-Depends: ${misc:Pre-Depends}
+Breaks: libncbi6 (<< ${source:Version})
+Provides: ${t64:Provides}
+Replaces: libncbi6
Description: NCBI libraries for biology applications
The NCBI Software Development Toolkit was developed for the production and
distribution of GenBank, Entrez, BLAST, and related services by NCBI. It
@@ -121,16 +122,11 @@ Depends: libncbi6t64 (<< ${source:Upstream-Version}.1),
${shlibs:Depends}
Suggests: ncbi-tools-bin,
ncbi-tools-x11
-Breaks: ncbi-tools-x11 (<< 6.1.20170106+dfsg1-5~)
-Replaces: ncbi-tools-x11 (<< 6.1.20170106+dfsg1-5~)
Description: 3-dimensional viewer for biological molecules
Cn3D is a helper application for your web browser that allows you to
view 3-dimensional structures from NCBI's Entrez retrieval service.
Package: libvibrant6t64
-Provides: ${t64:Provides}
-X-Time64-Compat: libvibrant6b
-Breaks: libvibrant6b (<< ${source:Version})
Architecture: any
Multi-Arch: same
Section: libs
@@ -140,14 +136,18 @@ Depends: libncbi6t64 (<< ${source:Upstream-Version}.1),
${shlibs:Depends}
Recommends: sensible-utils
Pre-Depends: ${misc:Pre-Depends}
+Breaks: libvibrant6b (<< ${source:Version})
Conflicts: libvibrant6,
libvibrant6a
-Replaces: libvibrant6b, libvibrant6,
+Provides: ${t64:Provides}
+Replaces: libvibrant6b,
+ libvibrant6,
libvibrant6a
Description: NCBI libraries for graphic biology applications
This is the library for those who just want to run Vibrant applications.
It also includes a wrapper (vibrate) that allows many NCBI applications to
provide a GUI for selecting options.
+X-Time64-Compat: libvibrant6b
Package: libvibrant6-dev
Architecture: any
=====================================
debian/patches/debian-changes
=====================================
@@ -19,6 +19,27 @@ Combined patches from git.
}
#ifdef OS_MAC
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/api/asn2gnb2.c
++++ ncbi-tools6-6.1.20170106+dfsg2/api/asn2gnb2.c
+@@ -58,7 +58,7 @@
+ #include <validerr.h>
+ #include <objvalid.h>
+ #include <valapi.h>
+-#include <asn2gnbi.h>
++#include <ffprint.h>
+ #include <asn2gnbi.h>
+
+ #ifdef WIN_MAC
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/api/salutil.c
++++ ncbi-tools6-6.1.20170106+dfsg2/api/salutil.c
+@@ -51,6 +51,7 @@
+ #include <edutil.h>
+ #include <sequtil.h>
+ #include <sqnutils.h>
++#include <alignmgr2.h>
+
+ #ifdef SALSA_DEBUG
+ #include <simutil.h>
--- ncbi-tools6-6.1.20170106+dfsg2.orig/api/sqnutil3.c
+++ ncbi-tools6-6.1.20170106+dfsg2/api/sqnutil3.c
@@ -33198,7 +33198,7 @@ ClickableItemPtr LIBCALL ClickableGlobal
@@ -918,6 +939,23 @@ Combined patches from git.
MemFree(fblock);
}
-
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/vibrant/shim3d.h
++++ ncbi-tools6-6.1.20170106+dfsg2/vibrant/shim3d.h
+@@ -402,6 +402,14 @@ NLM_EXTERN void SetOGLFont(TOGL_Data *OG
+ NLM_EXTERN void Nlm_FindAvailableFonts(Nlm_PopuP pupmenu);
+
+
++#ifdef WIN_MOTIF
++typedef struct _WidgetRec *Widget;
++typedef struct _XDisplay Display;
++
++void Nlm_SetOGLContext(Widget /* Nlm_SlateTool */ a, Nlm_Boolean *im,
++ Display **d, struct XVisualInfo **v);
++#endif
++
+ #ifdef _PNG
+ void Nlm_SaveImagePNG(Nlm_Char *defname); /* for PNG export */
+ #endif /* _PNG */
--- ncbi-tools6-6.1.20170106+dfsg2.orig/vibrant/vibmain.c
+++ ncbi-tools6-6.1.20170106+dfsg2/vibrant/vibmain.c
@@ -44,6 +44,21 @@
=====================================
vibrant/shim3d.h
=====================================
@@ -402,6 +402,14 @@ NLM_EXTERN void SetOGLFont(TOGL_Data *OGL_Data, Nlm_Int2 fontNameIndex, Nlm_Int2
NLM_EXTERN void Nlm_FindAvailableFonts(Nlm_PopuP pupmenu);
+#ifdef WIN_MOTIF
+typedef struct _WidgetRec *Widget;
+typedef struct _XDisplay Display;
+
+void Nlm_SetOGLContext(Widget /* Nlm_SlateTool */ a, Nlm_Boolean *im,
+ Display **d, struct XVisualInfo **v);
+#endif
+
#ifdef _PNG
void Nlm_SaveImagePNG(Nlm_Char *defname); /* for PNG export */
#endif /* _PNG */
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/compare/d7cce688b6be16a5c9db28269eb1c3156ce2ac3c...b2ceceb766083a3efd5cb42c157a058d0577240f
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/compare/d7cce688b6be16a5c9db28269eb1c3156ce2ac3c...b2ceceb766083a3efd5cb42c157a058d0577240f
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