summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/vmd/files
downloadgentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz
gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2
gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-chemistry/vmd/files')
-rw-r--r--sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch28
-rw-r--r--sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch25
-rw-r--r--sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch16
3 files changed, 69 insertions, 0 deletions
diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
new file mode 100644
index 000000000000..ce842448decf
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
@@ -0,0 +1,28 @@
+ vmd-1.9.1/src/CUDAMarchingCubes.cu | 1 +
+ vmd-1.9.1/src/CUDAQuickSurf.cu | 1 +
+ 2 files changed, 2 insertions(+)
+
+diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu
+index 5bfe7bf..36faaf0 100755
+--- a/vmd-1.9.1/src/CUDAMarchingCubes.cu
++++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu
+@@ -45,6 +45,7 @@
+ #include "CUDAMarchingCubes.h"
+ #include <thrust/scan.h>
+ #include <thrust/functional.h>
++#include <thrust/device_ptr.h>
+
+ // The number of threads to use for triangle generation
+ // (limited by shared memory size)
+diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu
+index a21ebde..56a42c8 100755
+--- a/vmd-1.9.1/src/CUDAQuickSurf.cu
++++ b/vmd-1.9.1/src/CUDAQuickSurf.cu
+@@ -22,6 +22,7 @@
+ #include <stdlib.h>
+ #include <string.h>
+ #include <cuda.h>
++#include <thrust/device_ptr.h>
+
+ #if CUDART_VERSION < 4000
+ #error The VMD QuickSurf feature requires CUDA 4.0 or later
diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch
new file mode 100644
index 000000000000..0c3e45dd39c3
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch
@@ -0,0 +1,25 @@
+ plugins/molfile_plugin/src/webpdbplugin.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/plugins/molfile_plugin/src/webpdbplugin.c b/plugins/molfile_plugin/src/webpdbplugin.c
+index 80b3bb9..78597f5 100644
+--- a/plugins/molfile_plugin/src/webpdbplugin.c
++++ b/plugins/molfile_plugin/src/webpdbplugin.c
+@@ -202,7 +202,7 @@ static void *open_file_read(const char *filename, const char *filetype,
+ sprintf(url, "http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=%s",filename);
+ sprintf(cmd, "set token [::http::geturl \"%s\"]", url);
+ if (Tcl_Eval(interp, cmd) != TCL_OK) {
+- fprintf(stderr, "Error loading PDB: %s\n",interp->result);
++ fprintf(stderr, "Error loading PDB: %s\n",Tcl_GetStringResult(interp));
+ Tcl_DeleteInterp(interp);
+ return NULL;
+ }
+@@ -211,7 +211,7 @@ static void *open_file_read(const char *filename, const char *filetype,
+
+ result = Tcl_GetVar2(interp, (char *)"state", "body", TCL_GLOBAL_ONLY);
+ if (!result) {
+- fprintf(stderr, "Error loading PDB: %s\n", interp->result);
++ fprintf(stderr, "Error loading PDB: %s\n", Tcl_GetStringResult(interp));
+ Tcl_DeleteInterp(interp);
+ return NULL;
+ }
diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
new file mode 100644
index 000000000000..3f9ea5c8c2ef
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
@@ -0,0 +1,16 @@
+ plugins/molfile_plugin/src/maeffplugin.cxx | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx
+index cfe1223..41d92bb 100644
+--- a/plugins/molfile_plugin/src/maeffplugin.cxx
++++ b/plugins/molfile_plugin/src/maeffplugin.cxx
+@@ -1979,7 +1979,7 @@ namespace {
+ }
+ }
+ catch (std::exception &e) {
+- fprintf(stderr, e.what());
++ fprintf(stderr, "%s", e.what());
+ return MOLFILE_ERROR;
+ }
+ return MOLFILE_SUCCESS;