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First argument now can be a time vector, Rcppcvode_str now is cvode. Renamed sundials_test.cpp to cvode.cpp
Package works with 3.4.2 version
cvode.cpp now returns a data frame and absolute tolerance can be a scalar also
Sundials v3.1.0 introduced changes such as sunmatrix and sunlinsol header files. This version changes the cvode to be compliant with those changes.
Based on PKG_CPPFILES - moving check_flag.h from /inst to /inst/include and removing the file checkflag.h from src
This package compiles on OS X, the same Makevars is copied to Makevars.win - to check if this compiles on Windows
With this fix, the package compiles for Windows and macOS/Linux.
Cvode_test to integrate functions defined using rcpp only
Testing build on appveyor
Adding badge from appveyor -> settings -> badges
adding .travis.yml
Removed the old cvode, and converted cvode_test to cvode. Removed all extra code and completed the vignette.
Version which was submitted to CRAN
Added contributors from SUNDIALS to Description and changed the license to GPL (>=2). Removed the MIT license file.
Changed the description based on feedback from SUNDIALS and CRAN members
Author@R changed to Authors@R
added /inst/examples/ and referred to it in cvode documentation
NV_Ith_S macro is not working on Windows. Replaced it with accessing via N_VGetArrayPointer
There is no need to have ydot as an input in the RHS function. Removed it.
Removed all the extraneous comments, solution is matching with example output and a message is displayed on attaching the package
This version contains files generated in cmake using int32_t option.
Hilari C Tiedeman - spelling was corrected.
Removed $(info ...) from the Makevars/.win to fix Solaris compilation issue
The model equations can now be written in R and Rcpp. Removed the xptr - changes in vignette and example file.
updated configure.ac to remove CR and CRLF
removing CR and CRLF
CR and CRLF line endings in configure.ac
To prevent auto-conversion of line endings to CRLF
To prevent auto-conversion of line endings to CRLF
trying to remove CRLF or CR from files
Cmake install
Download sundials source files during installation
Fix CRAN badge
GNU Make in SystemRequirements changed to cmake
CRAN submission version 0.1.6.1
See the changes suggested at #9
…11, bashism, Makevars
This commit resolves the issues that caused sundialr to be archived from CRAN
on 2025-05-12 ("issues were not corrected despite reminders"). All changes are
aimed at satisfying "Writing R Extensions" §1.6.4 and the associated R CMD
check --as-cran requirements.
--- R CMD check improvements ---
Before: 1 ERROR, 3 WARNINGs, 7 NOTEs
After: 1 ERROR*, 2 WARNINGs*, 4 NOTEs*
* ERROR and PDF WARNING are a local LaTeX environment issue (missing
inconsolata.sty), not a package defect.
* Remaining WARNINGs/NOTEs are either version-number metadata or system-
specific flags injected by the Ubuntu R build; they will not appear on
CRAN check servers.
--- SUNDIALS source patches (applied at build time in tools/cmake_call.sh) ---
CRAN policy forbids compiled code from calling abort() or writing directly to
stdout/stderr. Five SUNDIALS 7.1.1 source files are patched via sed after the
tarball is extracted, before cmake compiles them:
src/sundials/sundials_errors.c
- SUNAbortErrHandlerFn: removed abort() call. Fatal errors are now handled
by the R error handler registered via SUNContext_PushErrHandler() (see
inst/include/sundials_err_handler.h). The abort() path is unreachable at
runtime because our handler is pushed on top of the handler stack.
- SUNGlobalFallbackErrHandler: removed two fprintf(stderr, ...) calls that
wrote directly to stderr when the SUNContext itself was NULL/corrupt.
src/sundials/sundials_logger.c
- SUNLogger_Create: changed default logger->error_fp from stderr to NULL
and logger->warning_fp from stdout to NULL. With SUNDIALS_LOGGING_LEVEL=0
these handles are never used, but assigning them referenced the symbols.
- sunCloseLogFile: removed fp != stdout and fp != stderr comparisons;
replaced with a plain NULL check (safe since fps are now initialised to
NULL above).
- Removed fprintf(stderr, "[FATAL LOGGER ERROR] ...") call that fired when
log message allocation failed.
src/sundials/sundials_futils.c
- SUNDIALSFileOpen: removed the "stdout" and "stderr" filename-to-FILE*
mappings. Callers that previously passed "stdout" or "stderr" as a
filename will now receive NULL (no output), which is harmless because
sundialr never calls this function directly.
- SUNDIALSFileClose: removed the fp != stdout / fp != stderr guards before
fclose(); replaced with a plain fp != NULL check.
src/sundials/sundials_nvector.c
- N_VPrint: removed two printf("NULL...\n") debug messages. GCC -O2
optimises printf("literal\n") → puts("literal"), which CRAN flags as a
puts() reference in libsundials_core.a.
src/nvector/serial/nvector_serial.c
- N_VPrint_Serial: removed the direct N_VPrintFile_Serial(x, stdout) call,
which placed an explicit stdout reference in libsundials_nvecserial.a (and
in libsundials_cvodes.a and libsundials_idas.a, which archive the serial
nvector object). Users who need to print a vector can call
N_VPrintFile_Serial() with an explicit FILE* handle.
cmake flag added to tools/cmake_call.sh:
-D SUNDIALS_LOGGING_LEVEL=0 (disables compile-time logging; guards all
SUNLogger_QueueMsg bodies with #if SUNDIALS_LOGGING_LEVEL > 0)
--- R error handler (new file) ---
inst/include/sundials_err_handler.h
Defines sundials_r_err_handler(), a SUNErrHandlerFn that routes SUNDIALS
fatal errors to Rf_error() instead of abort(). Included in all four solver
translation units (cvode.cpp, cvodes.cpp, ida.cpp, cvsolve.cpp) and
registered immediately after SUNContext_Create() via
SUNContext_PushErrHandler().
--- Other CRAN NOTEs fixed ---
src/Makevars.in, src/Makevars
Removed CXX_STD = CXX11. Modern R defaults to C++17; CRAN now flags an
explicit C++11 request as unnecessary.
configure.ac (line 24)
Changed == to = in the shell test expression. Double-equals is a bashism;
POSIX sh requires single =.
cleanup
Fixed rm -f Makevars → rm -f src/Makevars. The old path never removed the
configure-generated src/Makevars, so R CMD build included both Makevars and
Makevars.in in the tarball, triggering a NOTE about ambiguous Makevars.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…dials_logger.c The sed pattern for patching the fprintf(stderr,...) in sundials_logger.c was wrong: it matched "[FATAL LOGGER ERROR]" at the start of the format string, but the actual code has "[ERROR][rank %d]..." as the format string with "FATAL LOGGER ERROR" as an argument on the continuation line. The patch silently failed, leaving the stderr symbol in libsundials_core.a. Replace the broken sed with a Python regex that correctly handles the multi-line fprintf call. Also fix the committed copy of sundials_logger.c directly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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