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author | 2015-08-08 13:49:04 -0700 | |
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committer | 2015-08-08 17:38:18 -0700 | |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/vmd/files | |
download | gentoo-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.patch | 28 | ||||
-rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch | 25 | ||||
-rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch | 16 |
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; |