764 Commits

Author SHA1 Message Date
Scott R Charlton
bb774d3e77 seems that having padfstring receiving unsigned int fixes gfortran x64 problem
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9027 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-10-31 04:54:01 +00:00
David L Parkhurst
e7eacdd09c Made native
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9024 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-10-30 22:00:37 +00:00
Scott R Charlton
9a6cb18dbf changed all fortran string length parameters to be size_t
simplified fortran wrappers for windows


git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9015 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-10-29 01:59:37 +00:00
Scott R Charlton
9b73f65b6d Updated project
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9011 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-10-27 21:33:00 +00:00
Scott R Charlton
58da41b950 Added AM_PROG_AR and removed defines PHREEQC_CPP and PHREEQC_CLASS
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9007 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-10-23 23:51:00 +00:00
Scott R Charlton
0272550872 added test for correct exception handling
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8948 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-09-11 03:23:50 +00:00
Scott R Charlton
5bd2cae399 made catch(...) always rethrow;
changed catches to const references


git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8905 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-08-05 02:42:09 +00:00
Scott R Charlton
60c7fdfe68 Use phrGetErrorStrings.valgrind-leak.R.in in place of phreeqc.R.in when executing
'make check' -> 'R CMD check --as-cran' which produces (cran/)phreeqc.Rcheck/phreeqc-Ex.R
and is checked in as leak-Ex.R (only includes the phrGetErrorStrings example).

run using:
R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < leak-Ex.R

and running the full set of examples:
R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < (cran/)phreeqc.Rcheck/phreeqc-Ex.R


git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8844 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-15 03:49:34 +00:00
Scott R Charlton
167b08bfbb fixes valgrind memory leaks that occured when error/RF_error was called within a block containing implicit dtors; seems that R uses setjmp/longjmp to handle errors which produces undefined behavior under g++ see http://stackoverflow.com/questions/1376085/c-safe-to-use-longjmp-and-setjmp
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8843 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-15 03:36:38 +00:00
Scott R Charlton
d3537fae99 added valgrind target for memory leak detection
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8842 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-15 03:30:06 +00:00
Scott R Charlton
a5ad315911 added windows memory checker (must define WIN32_MEMORY_DEBUG in unit.vcproj and undef USE_PHRQ_ALLOC in IPhreeqc.vsprops)
no leaks

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8831 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-10 05:46:33 +00:00
Scott R Charlton
05f70fb8e7 new line at end of file
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8830 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-10 05:32:27 +00:00
Scott R Charlton
f520b61a58 TestIPhreeqcLib contains no leaks with WIN32_MEMORY_DEBUG defined
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8829 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-10 05:21:26 +00:00
Scott R Charlton
6be1451051 memory leak fix
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8828 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-10 04:57:31 +00:00
Scott R Charlton
b3cff55ac9 set but not used
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8826 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-09 23:52:45 +00:00
Scott R Charlton
4292284364 all tests passing (added "cell/soln/mix 1").
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8822 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-09 04:16:21 +00:00
Scott R Charlton
035c73c707 valgrind changes/set-but-unused vars
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8817 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-08 19:52:45 +00:00
Scott R Charlton
0e9ac7038c Added (+ file LICENSE) to DESCRIPTION.IN
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8809 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-06-27 05:04:21 +00:00
Scott R Charlton
0c02788a77 from Kurt Hornik <Kurt.Hornik@wu.ac.at>
Thanks.

Closer inspection reveals two more issues.

* Many files have

  * Copyright (c) 2002, The Regents of the University of California        *
  * Produced at the Lawrence Livermore National Laboratory                 *

That is not mentioned in the DESCRIPTION file, and hence fails to comply
with the Policy's

  The ownership of copyright and intellectual property rights of all
  components of the package must be clear and unambiguous (including
  from the authors specification in the DESCRIPTION file). Where code is
  copied (or derived) from the work of others (including from R itself),
  care must be taken that any copyright/license statements are preserved
  and authorship is not misrepresented.

  Where copyrights are held by an entity other than the authors, the
  Authors@R field can be used, or a Copyright field (if necessary
  referring to an inst/COPYRIGHTS file).

* The original license was

* Redistribution and use in source and binary forms, with or without     *
  * modification, are permitted provided that the following conditions     *
  * are met:                                                               *
  *                                                                        *
  * 1. Redistributions of source code must retain the above copyright      *
  * notice, this list of conditions and the disclaimer below.              *
  *                                                                        *
  * 2. Redistributions in binary form must reproduce the above copyright   *
  * notice, this list of conditions and the disclaimer (as noted below)    *
  * in the documentation and/or other materials provided with the          *
  * distribution.                                                          *
  *                                                                        *
  * 3. Neither the name of the UC/LLNL nor the names of its contributors   *
  * may be used to endorse or promote products derived from this software  *
  * without specific prior written permission.                             *
  *                                                                        *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS    *
  * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT      *
  * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS      *
  * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE         *
  * REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE U.S. DEPARTMENT OF ENERGY *
  * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,        *
  * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT       *
  * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,  *
  * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY  *
  * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT    *
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE  *
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.   *

and we would guess that clauses 2 and 3 are not covered by basic GPL-3,
and hence needs this to be restricted.

So to be on the safe side, you should use

   GPL-3 + file LICENSE

with file LICENSE explaining that certain parts are covered by the above
license, and then give the license.

Best

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8808 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-06-27 05:01:49 +00:00
David L Parkhurst
3ce26dc3eb source to src
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8798 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-06-24 19:28:20 +00:00
David L Parkhurst
ce505c3933 MakeItSo Makefiles
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8796 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-06-24 18:42:07 +00:00
Scott R Charlton
fef8a69b0d From Uwe Ligges<ligges@statistik.tu-dortmund.de> 6/6/2014
ligges@statistik.tu-dortmund.de

After internal discussion:

Assuming that SUNDIALS is really BSD-3-clause (please confirm):


1. BSD-3-clause is known to be compatible with GPL-3.

2. You LICENSE template is perhaps not appropriate, as it
only relates to the foreign code.

3. What we need is one license for the package which could be GPL-3 given your LICENSE.note and our interpretation is correct, but we do not give legal advice here.

So we think the only reasonable solution is to have the package under
  GPL-3 only.  I.e.,

     License: GPL-3

  and then remove files LICENSE and LICENSE.note.
But be careful to kep all copyright statement and really list all the authors of the material included in your package.

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8780 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-06-10 00:04:50 +00:00
Scott R Charlton
aa8d3d7782 Added gpl-2 and gpl-3 to licenses; added LICENSE.note
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8779 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-06-04 22:18:20 +00:00
Scott R Charlton
ca34964754 added missing paren and realigned
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8740 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-09 22:39:48 +00:00
Scott R Charlton
fe751539a1 added module paper
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8739 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-09 22:30:54 +00:00
David L Parkhurst
7904c319aa Changed description, authorship
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8738 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-09 16:10:54 +00:00
Scott R Charlton
0283e1a2ef changed } to )
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8737 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-09 01:00:31 +00:00
Scott R Charlton
c49727a006 moved CITATION to inst directory
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8736 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-09 00:42:17 +00:00
David L Parkhurst
090b4c3e9b Deleted LICENSE.note
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8735 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 23:01:34 +00:00
David L Parkhurst
c4b4aa251c added CITATION file
changed author order in .in files

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8734 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 22:48:13 +00:00
Scott R Charlton
93f89b68e0 removed period from copyright holder
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8732 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 05:13:14 +00:00
Scott R Charlton
f5d0cccea1 removed period
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8731 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 04:52:49 +00:00
Scott R Charlton
c500b38195 updated authors list
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8730 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 04:51:56 +00:00
Scott R Charlton
7768d0f599 added NO_UTF8_ENCODING to Makevars
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8728 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 02:25:58 +00:00
Scott R Charlton
139e932a31 added the three lines for the BSD-3-Clause license
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8726 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 00:33:24 +00:00
Scott R Charlton
0de02c0a41 renamed LICENSE to LICENSE.note
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8725 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-08 00:21:35 +00:00
Scott R Charlton
593024086b updated references phreeqc.R.in
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8718 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 04:41:03 +00:00
Scott R Charlton
6f5e868a2c updated license in phreeqc.R.in
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8717 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 04:27:20 +00:00
Scott R Charlton
f625b45d93 working on build automation
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8716 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 04:00:21 +00:00
Scott R Charlton
0ab51be91f added automation sed strings
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8715 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 02:53:09 +00:00
Scott R Charlton
63ce9832cd moved phreeqc.R for makefile processing
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8714 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 02:50:21 +00:00
Scott R Charlton
6bdcee2899 fixed makefile
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8713 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 02:45:04 +00:00
Scott R Charlton
238e32dced working on automation of R version
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8712 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 02:42:11 +00:00
Scott R Charlton
a3724e79a3 moved DESCRIPTION
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8711 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 02:32:05 +00:00
Scott R Charlton
eb2c924d44 added + LICENSE to BSD_3_clause
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8710 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-06 23:23:22 +00:00
Scott R Charlton
8fa61377dc added BSD license to DESCRIPTION
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8709 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-06 23:15:04 +00:00
Scott R Charlton
96ef4c5b40 rearranged R headers for CRAN
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8707 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-06 22:35:34 +00:00
Scott R Charlton
3bd482a5b9 added LICENSE
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8706 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-06 21:53:48 +00:00
Scott R Charlton
a1bb0c39e9 fixed post-build events;
removed fwrap(6,7,8).cpp from Release|x64 and Debug|x64

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8698 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-01 05:07:57 +00:00
Scott R Charlton
1ebd3748b5 updated for R defines
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8697 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-01 04:26:23 +00:00