153 Commits

Author SHA1 Message Date
Max Lübke
7cc00e335a Bump Phreecq to version 3.8.2 2024-10-23 13:43:30 +02:00
Charlton, Scott R
d77b07649c
Updated tm6-A43.pdf links 2023-12-06 16:36:07 -07:00
Charlton, Scott R
35521760a5
Missed adding R.cpp 2023-12-06 12:13:58 -07:00
Charlton, Scott R
220db26eb7
Fixes v3.7.5 for CRAN 2023-12-06 11:58:57 -07:00
Charlton, Scott R
09619534e7
[iphreeqc] Issue 8 -- change sprintf to snprintf for CRAN (#9) 2023-01-14 22:14:20 -07:00
Charlton, Scott R
49d5fb6b00 Updated source target
reordered r-build steps
2023-01-13 11:46:06 -07:00
Charlton, Scott R
2119993bda Working on R building 2023-01-13 10:41:19 -07:00
Charlton, Scott R
07351449c0 working on R build automation 2022-03-26 11:50:02 -07:00
Charlton, Scott R
42cd779af8 working on R dist 2022-03-26 09:58:00 -07:00
Scott R Charlton
25eafc137d for debugging on jenkins linux 2021-11-02 12:51:03 -06:00
Charlton, Scott R
0110abd368 Reverted to old version for now 2021-11-01 18:51:59 -06:00
Charlton, Scott R
547c6ed33d cleaning up r-build 2021-09-27 18:01:34 -07:00
Charlton, Scott R
d990665808 try running check a different way 2021-09-23 17:21:44 -07:00
Charlton, Scott R
cc826688f2 cran update 2021-09-21 20:01:43 +00:00
Charlton, Scott R
ceb559b87f [iphreeqc] fix for CRAN (forwarding urls and DOI format) 2021-09-06 15:18:39 -06:00
Charlton, Scott R
6d12dec390 [iphreeqc] Closes coupled/iphreeqc#9 2021-04-20 20:22:38 -06:00
Charlton, Scott R
3091de68dd added src/phreeqcpp/common/PHRQ_exports.h 2020-09-15 20:29:41 -06:00
Scott R Charlton
5728339070 removed no longer existing frezchem URL 2020-05-11 12:10:50 -06:00
Scott R Charlton
ff660e7451 Fixed make for frezchem.dat 2020-01-30 12:20:42 -07:00
Scott R Charlton
1f074edce7 [iphreeqc] Added core10.dat, frezchem.dat, and Tipping_Hurley.dat to R distribution 2020-01-30 12:09:20 -07:00
Scott R Charlton
108fe635ec updated urls; fixed jenkins-R-dist.sh 2020-01-30 10:44:35 -07:00
Scott Charlton
f3c1fcabb5 IPhreeqc: moved all output files to tempdir(); Fixed some of the documentation 2019-11-29 15:45:19 -08:00
Scott Charlton
c60ec7be3e removed .Rbuildignore 2019-11-25 18:27:05 -08:00
Scott Charlton
78ac5357ab working on CRAN submission 2019-11-25 17:50:08 -08:00
Scott Charlton
567af3ee45 working on CRAN submission 2019-11-25 17:39:00 -08:00
Scott R Charlton
2e210e2a86 [IPhreeqc] Changed license 2018-08-13 18:56:56 -06:00
Scott R Charlton
718f801af7 [iphreeqc] fixed makefile examples 2018-08-09 13:48:27 -06:00
Scott Charlton
3e57c50456 [iphreeqc] Changes for CRAN 3.4.7 2018-08-09 12:42:50 -06:00
Scott R Charlton
2f5071790c added remaining .Call routines
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@12664 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2017-04-08 05:30:39 +00:00
Scott R Charlton
2807ca2045 working on CRAN dist
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@12663 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2017-04-08 05:16:29 +00:00
Scott R Charlton
1d7e2cb9e9 adding ColdChem.dat to R dist
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@12482 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2017-03-03 02:44:40 +00:00
Scott R Charlton
f6c2243d59 removed dw.cpp
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@11296 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2016-06-17 01:02:38 +00:00
Scott R Charlton
e3021d24e3 removed dw.cpp
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@11295 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2016-06-17 00:48:07 +00:00
Scott R Charlton
94cac8272b updated for Dictionary/Serializer
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10619 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-12-29 05:23:30 +00:00
Scott R Charlton
68ca880ccb updated to run valgrind in jenkins
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10604 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-12-24 00:30:33 +00:00
Scott R Charlton
12402a92ab updated Description for cran submittal
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10323 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-09-30 21:35:41 +00:00
Scott R Charlton
6cb0d3fd08 updated for cran submittal
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10322 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-09-30 21:04:49 +00:00
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