NEWS

nonmem2rx 0.1.11

Add integer overflow guards in the C-level string buffer (src/sbuf.c). sAppendN, sAppend, and addLine previously computed the new allocation size as sbb->o + 2 + n + SBUF_MXBUF (or analogous expression). When the user-controlled n was large enough this expression overflowed int to a negative value, which R_Realloc then converted to a huge unsigned size and crashed. The guard converts this into a clean R error.
Document known (int)strlen(gBuf) cast in all 10 NONMEM-record parser entry-points (src/abbrec.c, src/abbrev.c, src/data.c, src/input.c, src/lst.c, src/model.c, src/omega.c, src/sub.c, src/tab.c, src/theta.c). Inputs at or above INT_MAX bytes cause silent length truncation passed to dparse(). A long-term fix will switch each call site to udparse() once dparser-R ships that symbol to CRAN.
Fix implicit ptrdiff_t to int truncation in rc_dup_str (src/records.c). When the parser passes a string segment longer than INT_MAX bytes (or a NUL-terminated string of that length), the pointer difference / strlen result was silently cast to int, truncating the length to a wrong (often negative) value. The new guard rejects such inputs with an informative R error.

Bug fix for covariance matrices that span multiple FORTRAN output pages
Bug fix for multiple errors are imported using nonmem2rx()
Change NONMEM import for mixture models to prepend NM to MIXNUM and related import items so they will not interact with rxode2/nlmixr2's handling of mixture models.

Be more forgiving in the validation and remove IDs without observations when solving the IPRED problem.
Binary linkage to dparser changed to structure only, meaning nonmem2rx may not have to be updated if dparser is updated.

When reading NONMEM results from xml will try nm: prefixed tags and non-nm: prefixed tags.
Omega and Sigma prior estimates are currently ignored (theta priors were already ignored)
Improve reading in theta values from the xml
Read all NONMEM files using latin1 encoding to allow single byte parser to work
When lines in the NONMEM input dataset start with # they are now ignored.
When all IDs are zero, NONMEM assumes restarting time gives different IDs; this is now reflected in NONMEM translation of IDs.
With linCmt() parsing, expand the scope of conflicting parameters that will be renamed with an import.
Added better parsing for ELSE where there is another IF on the next line.
Prefixed conflicting VP with rxm. when linCmt() models to be more accommodating when importing linear compartment models.

Added explicit requirement for rxode2 2.0.13
Added support of DADT(#) statements on the right side of the equation, i.e. DADT(3) = DADT(1) + DADT(2) (#164)
Added support of ADVAN#, TRANS# (#161)
Added more NONMEM-specific solving options
Fixed security related format issues as requested by CRAN #167
Now omega, thetaMat, dfObs and dfSub are incorporated into model function (by default). You can change this with the nonmem2rx keep argument
Using the rxode2 2.0.13 makes sure that the solves for models where the endpoint is not determined in the typical nlmixr2 style will validate more often (due to a bug in solving in rxode2).

Added support for ADVAN5 and ADVAN7 models
Add parsing of accept/ignore characters for example IGNORE=(C='C') (See Issue #140)
Add more robust reading of NONMEM information (and add source) in nminfo() (See issue #142)
Since NONMEM does not protect divide by zeros by default, the default for solveZero is changed to solveZero = TRUE for nonmem2rx objects.
Fixed bug for renaming eta and theta when they are renamed so that the ui$iniDf does not match the theta# or eta# (Issue #153)
Turned off testing of the as.nonmem2rx example since it took too much time (according to CRAN)