166 Commits

Author SHA1 Message Date
Scott R Charlton
efc0591a59 updated for common/PhreeqcKeywords reorg
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10309 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-09-25 06:18:12 +00:00
Scott R Charlton
eae91e7682 delete .RData before and after running CMD; added --resave-data to build command
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9102 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-12-11 06:59:30 +00:00
Scott R Charlton
9b1282df50 removed R/phreeqc/doc directory; Changed Title/DESCRIPTION based on
email from Kurt.Hornik@wu.ac.at 12/03/2014

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9087 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-12-04 06:14:53 +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
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
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
39b9991b5c removed pedantic
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8687 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-29 23:55:55 +00:00
Scott R Charlton
f97b048e82 changes req'd for CRAN
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8686 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-29 23:30:39 +00:00
Scott R Charlton
c291d0a462 removed unneeded --resave-data from build target
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8673 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-24 03:04:25 +00:00
Scott R Charlton
29b9061378 fixed non-ASCII issues; added \dontrun to examples 15 and 21
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8672 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-24 03:02:14 +00:00
Scott R Charlton
f33dc3654f after removing CO2 example
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8671 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-24 01:34:39 +00:00
Scott R Charlton
2e78b88623 after removing CO2 example
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8670 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-24 01:32:16 +00:00
Scott R Charlton
5c05b1019a before removing CO2 example
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8669 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-24 01:31:23 +00:00
Scott R Charlton
b68ae05507 working on databases and examples
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8667 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-22 00:16:59 +00:00
Scott R Charlton
4f08f1c2bb added documentation for the databases
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8665 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-19 05:26:02 +00:00
Scott R Charlton
e5c2b5b865 working on making CRAN compliant
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8664 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-19 04:11:03 +00:00
Scott R Charlton
6dc48d6a56 working on making CRAN compliant
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8663 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-19 03:56:39 +00:00
Scott R Charlton
08872129ce working on making CRAN compliant
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8662 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-19 03:52:33 +00:00
Scott R Charlton
77c5fcde7b version sent to David
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8655 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-12 00:47:25 +00:00
Scott R Charlton
dd9428c86b updated phrSetLogFileName
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8652 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-11 01:24:38 +00:00
Scott R Charlton
73486ab2a1 updated phrSetLogFileOn
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8647 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-10 07:04:11 +00:00