]> git.lyx.org Git - lyx.git/blobdiff - src/LaTeX.cpp
Fix bug #12772
[lyx.git] / src / LaTeX.cpp
index 4096ca9f63600ea7b5c568aa963d3a4ad63bf38a..7d9810aef1a8b22e147c8d571191ec98145ae693 100644 (file)
 
 #include <config.h>
 
-#include "BufferList.h"
 #include "LaTeX.h"
+
+#include "Buffer.h"
+#include "BufferList.h"
+#include "BufferParams.h"
 #include "LyXRC.h"
 #include "LyX.h"
 #include "DepTable.h"
+#include "Encoding.h"
+#include "Language.h"
 
 #include "support/debug.h"
+#include "support/docstring.h"
 #include "support/convert.h"
 #include "support/FileName.h"
 #include "support/filetools.h"
@@ -30,9 +36,8 @@
 #include "support/Systemcall.h"
 #include "support/os.h"
 
-#include "support/regex.h"
-
 #include <fstream>
+#include <regex>
 #include <stack>
 
 
@@ -105,7 +110,7 @@ LaTeX::LaTeX(string const & latex, OutputParams const & rp,
             FileName const & f, string const & p, string const & lp, 
             bool allow_cancellation, bool const clean_start)
        : cmd(latex), file(f), path(p), lpath(lp), runparams(rp), biber(false),
-       allow_cancel(allow_cancellation)
+         allow_cancel(allow_cancellation)
 {
        num_errors = 0;
        // lualatex can still produce a DVI with --output-format=dvi. However,
@@ -130,6 +135,7 @@ LaTeX::LaTeX(string const & latex, OutputParams const & rp,
 
 void LaTeX::removeAuxiliaryFiles() const
 {
+       LYXERR(Debug::OUTFILE, "Removing auxiliary files");
        // Note that we do not always call this function when there is an error.
        // For example, if there is an error but an output file is produced we
        // still would like to output (export/view) the file.
@@ -187,6 +193,7 @@ int LaTeX::run(TeXErrors & terr)
 {
        int scanres = NO_ERRORS;
        int bscanres = NO_ERRORS;
+       int iscanres = NO_ERRORS;
        unsigned int count = 0; // number of times run
        num_errors = 0; // just to make sure.
        unsigned int const MAX_RUN = 6;
@@ -224,6 +231,25 @@ int LaTeX::run(TeXErrors & terr)
        }
 
        if (had_depfile) {
+               if (runparams.includeall) {
+                       // On an "includeall" call (whose purpose is to set up/maintain counters and references
+                       // for includeonly), we remove the master from the dependency list since
+                       // (1) it will be checked anyway on the subsequent includeonly run
+                       // (2) the master is always changed (due to the \includeonly line), and this alone would
+                       //     trigger a complete, expensive run each time
+                       head.remove_file(file);
+                       // Also remove all children which are included
+                       Buffer const * buf = theBufferList().getBufferFromTmp(file.absFileName());
+                       if (buf && buf->params().maintain_unincluded_children == BufferParams::CM_Mostly) {
+                               for (auto const & incfile : buf->params().getIncludedChildren()) {
+                                       string const incm =
+                                               DocFileName(changeExtension(makeAbsPath(incfile, path)
+                                                                           .absFileName(), ".tex")).mangledFileName();
+                                       FileName inc = makeAbsPath(incm, file.onlyPath().realPath());
+                                       head.remove_file(inc);
+                               }
+                       }
+               }
                // Update the checksums
                head.update();
                // Can't just check if anything has changed because it might
@@ -254,20 +280,20 @@ int LaTeX::run(TeXErrors & terr)
                bibtex_info_old = scanAuxFiles(aux_file, runparams.only_childbibs);
 
        ++count;
-       LYXERR(Debug::LATEX, "Run #" << count);
+       LYXERR(Debug::OUTFILE, "Run #" << count);
        message(runMessage(count));
 
        int exit_code = startscript();
-       if (exit_code == Systemcall::KILLED)
-               return Systemcall::KILLED;
+       if (exit_code == Systemcall::KILLED || exit_code == Systemcall::TIMEOUT)
+               return exit_code;
 
        scanres = scanLogFile(terr);
        if (scanres & ERROR_RERUN) {
-               LYXERR(Debug::LATEX, "Rerunning LaTeX");
+               LYXERR(Debug::OUTFILE, "Rerunning LaTeX");
                terr.clearErrors();
                exit_code = startscript();
-               if (exit_code == Systemcall::KILLED)
-                       return Systemcall::KILLED;
+               if (exit_code == Systemcall::KILLED || exit_code == Systemcall::TIMEOUT)
+                       return exit_code;
                scanres = scanLogFile(terr);
        }
 
@@ -280,72 +306,31 @@ int LaTeX::run(TeXErrors & terr)
        head.update();
 
        // 1
-       // At this point we must run external programs if needed.
-       // makeindex will be run if a .idx file changed or was generated.
-       // And if there were undefined citations or changes in references
-       // the .aux file is checked for signs of bibtex. Bibtex is then run
-       // if needed.
-
-       // memoir (at least) writes an empty *idx file in the first place.
-       // A second latex run is needed.
-       FileName const idxfile(changeExtension(file.absFileName(), ".idx"));
-       rerun = idxfile.exists() && idxfile.isFileEmpty();
-
-       // run makeindex
-       if (head.haschanged(idxfile)) {
-               // no checks for now
-               LYXERR(Debug::LATEX, "Running MakeIndex.");
-               message(_("Running Index Processor."));
-               // onlyFileName() is needed for cygwin
-               int const ret = 
-                               runMakeIndex(onlyFileName(idxfile.absFileName()), runparams);
-               if (ret == Systemcall::KILLED)
-                       return Systemcall::KILLED;
-               rerun = true;
-       }
-
-       FileName const nlofile(changeExtension(file.absFileName(), ".nlo"));
-       // If all nomencl entries are removed, nomencl writes an empty nlo file.
-       // DepTable::hasChanged() returns false in this case, since it does not
-       // distinguish empty files from non-existing files. This is why we need
-       // the extra checks here (to trigger a rerun). Cf. discussions in #8905.
-       // FIXME: Sort out the real problem in DepTable.
-       if (head.haschanged(nlofile) || (nlofile.exists() && nlofile.isFileEmpty())) {
-               int const ret = runMakeIndexNomencl(file, ".nlo", ".nls");
-               if (ret == Systemcall::KILLED)
-                       return Systemcall::KILLED;
-               rerun = true;
-       }
-
-       FileName const glofile(changeExtension(file.absFileName(), ".glo"));
-       if (head.haschanged(glofile)) {
-               int const ret = runMakeIndexNomencl(file, ".glo", ".gls");
-               if (ret)
-                       return ret;
-               rerun = true;
-       }
-
-
-       // check if we're using biber instead of bibtex
+       // At this point we must run the bibliography processor if needed.
+       // First, check if we're using biber instead of bibtex --
        // biber writes no info to the aux file, so we just check
-       // if a bcf file exists (and if it was updated)
+       // if a bcf file exists (and if it was updated).
        FileName const bcffile(changeExtension(file.absFileName(), ".bcf"));
        biber |= head.exist(bcffile);
 
-       // run bibtex
-       // if (scanres & UNDEF_CIT || scanres & RERUN || run_bibtex)
-       if (scanres & UNDEF_CIT || run_bibtex) {
+       // If (scanres & UNDEF_CIT || scanres & RERUN || run_bibtex)
+       // We do not run bibtex/biber on an "includeall" call (whose purpose is
+       // to set up/maintain counters and references for includeonly) since
+       // (1) bibliographic references will be updated on the subsequent includeonly run
+       // (2) this would trigger a complete run each time (as references in non-included
+       //     children are removed on subsequent includeonly runs)
+       if (!runparams.includeall && (scanres & UNDEF_CIT || run_bibtex)) {
                // Here we must scan the .aux file and look for
                // "\bibdata" and/or "\bibstyle". If one of those
                // tags is found -> run bibtex and set rerun = true;
                // no checks for now
-               LYXERR(Debug::LATEX, "Running BibTeX.");
-               message(_("Running BibTeX."));
+               LYXERR(Debug::OUTFILE, "Running Bibliography Processor.");
+               message(_("Running Bibliography Processor."));
                updateBibtexDependencies(head, bibtex_info);
                int exit_code;
                rerun |= runBibTeX(bibtex_info, runparams, exit_code);
-               if (exit_code == Systemcall::KILLED)
-                       return Systemcall::KILLED;
+               if (exit_code == Systemcall::KILLED || exit_code == Systemcall::TIMEOUT)
+                       return exit_code;
                FileName const blgfile(changeExtension(file.absFileName(), ".blg"));
                if (blgfile.exists())
                        bscanres = scanBlgFile(head, terr);
@@ -357,7 +342,7 @@ int LaTeX::run(TeXErrors & terr)
        }
 
        // 2
-       // we know on this point that latex has been run once (or we just
+       // We know on this point that latex has been run once (or we just
        // returned) and the question now is to decide if we need to run
        // it any more. This is done by asking if any of the files in the
        // dependency file has changed. (remember that the checksum for
@@ -372,11 +357,11 @@ int LaTeX::run(TeXErrors & terr)
                rerun = false;
                ++count;
                LYXERR(Debug::DEPEND, "Dep. file has changed or rerun requested");
-               LYXERR(Debug::LATEX, "Run #" << count);
+               LYXERR(Debug::OUTFILE, "Run #" << count);
                message(runMessage(count));
                int exit_code = startscript();
-               if (exit_code == Systemcall::KILLED)
-                       return Systemcall::KILLED;
+               if (exit_code == Systemcall::KILLED || exit_code == Systemcall::TIMEOUT)
+                       return exit_code;
                scanres = scanLogFile(terr);
 
                // update the depedencies
@@ -387,55 +372,102 @@ int LaTeX::run(TeXErrors & terr)
        }
 
        // 3
-       // rerun bibtex?
+       // Rerun bibliography processor?
        // Complex bibliography packages such as Biblatex require
        // an additional bibtex cycle sometimes.
-       if (scanres & UNDEF_CIT) {
+       // We do not run bibtex/biber on an "includeall" call (whose purpose is
+       // to set up/maintain counters and references for includeonly) since
+       // (1) bibliographic references will be updated on the subsequent includeonly run
+       // (2) this would trigger a complete run each time (as references in non-included
+       //     children are removed on subsequent includeonly runs)
+       if (!runparams.includeall && scanres & UNDEF_CIT) {
                // Here we must scan the .aux file and look for
                // "\bibdata" and/or "\bibstyle". If one of those
                // tags is found -> run bibtex and set rerun = true;
                // no checks for now
-               LYXERR(Debug::LATEX, "Running BibTeX.");
-               message(_("Running BibTeX."));
+               LYXERR(Debug::OUTFILE, "Re-Running Bibliography Processor.");
+               message(_("Re-Running Bibliography Processor."));
                updateBibtexDependencies(head, bibtex_info);
                int exit_code;
                rerun |= runBibTeX(bibtex_info, runparams, exit_code);
-               if (exit_code == Systemcall::KILLED)
-                       return Systemcall::KILLED;
+               if (exit_code == Systemcall::KILLED || exit_code == Systemcall::TIMEOUT)
+                       return exit_code;
                FileName const blgfile(changeExtension(file.absFileName(), ".blg"));
                if (blgfile.exists())
                        bscanres = scanBlgFile(head, terr);
        }
 
        // 4
-       // The inclusion of files generated by external programs such as
-       // makeindex or bibtex might have done changes to pagenumbering,
-       // etc. And because of this we must run the external programs
-       // again to make sure everything is redone correctly.
-       // Also there should be no need to run the external programs any
-       // more after this.
-
-       // run makeindex if the <file>.idx has changed or was generated.
-       if (head.haschanged(idxfile)) {
+       // After the bibliography was processed, we need more passes of LaTeX
+       // in order to resolve the citations. We need to do this before the index
+       // is being generated (since we need the correct pagination, see #2696).
+       // With bibliography environment, another LaTeX run might be needed
+       // as well to resolve citations.
+       // Also, memoir (at least) writes an empty *idx file in the first place.
+       // A further latex run is needed in that case as well.
+       FileName const idxfile(changeExtension(file.absFileName(), ".idx"));
+       if (run_bibtex || (scanres & UNDEF_CIT) || (idxfile.exists() && idxfile.isFileEmpty())) {
+               while ((head.sumchange() || rerun || (scanres & RERUN) || (scanres & UNDEF_CIT))
+                      && count < MAX_RUN) {
+                       // Yes rerun until message goes away, or until
+                       // MAX_RUNS are reached.
+                       rerun = false;
+                       ++count;
+                       LYXERR(Debug::OUTFILE, "Run #" << count);
+                       message(runMessage(count));
+                       startscript();
+                       scanres = scanLogFile(terr);
+       
+                       // keep this updated
+                       head.update();
+               }
+       }
+
+       // 5
+       // Now that we have final pagination, run the index and nomencl processors
+       if (idxfile.exists()) {
                // no checks for now
-               LYXERR(Debug::LATEX, "Running MakeIndex.");
+               LYXERR(Debug::OUTFILE, "Running Index Processor.");
                message(_("Running Index Processor."));
                // onlyFileName() is needed for cygwin
-               int const ret = runMakeIndex(onlyFileName(changeExtension(
-                               file.absFileName(), ".idx")), runparams);
-               if (ret == Systemcall::KILLED)
-                       return Systemcall::KILLED;
-               rerun = true;
+               int const ret = 
+                               runMakeIndex(onlyFileName(idxfile.absFileName()), runparams);
+               if (ret == Systemcall::KILLED || ret == Systemcall::TIMEOUT)
+                       return ret;
+               else if (ret != Systemcall::OK) {
+                       iscanres |= INDEX_ERROR;
+                       terr.insertError(0,
+                                        _("Index Processor Error"),
+                                        _("The index processor did not run successfully. "
+                                          "Please check the output of View > Messages Pane!"));
+               }
+               FileName const ilgfile(changeExtension(file.absFileName(), ".ilg"));
+               if (ilgfile.exists())
+                       iscanres = scanIlgFile(terr);
+               rerun = true;
+       }
+       FileName const nlofile(changeExtension(file.absFileName(), ".nlo"));
+       // If all nomencl entries are removed, nomencl writes an empty nlo file.
+       // DepTable::hasChanged() returns false in this case, since it does not
+       // distinguish empty files from non-existing files. This is why we need
+       // the extra checks here (to trigger a rerun). Cf. discussions in #8905.
+       // FIXME: Sort out the real problem in DepTable.
+       if (head.haschanged(nlofile) || (nlofile.exists() && nlofile.isFileEmpty())) {
+               int const ret = runMakeIndexNomencl(file, ".nlo", ".nls");
+               if (ret == Systemcall::KILLED || ret == Systemcall::TIMEOUT)
+                       return ret;
+               rerun = true;
+       }
+       FileName const glofile(changeExtension(file.absFileName(), ".glo"));
+       if (head.haschanged(glofile)) {
+               int const ret = runMakeIndexNomencl(file, ".glo", ".gls");
+               if (ret)
+                       return ret;
+               rerun = true;
        }
 
-       // MSVC complains that bool |= int is unsafe. Not sure why.
-       if (head.haschanged(nlofile))
-               rerun |= (runMakeIndexNomencl(file, ".nlo", ".nls") != 0);
-       if (head.haschanged(glofile))
-               rerun |= (runMakeIndexNomencl(file, ".glo", ".gls") != 0);
-
-       // 5
-       // we will only run latex more if the log file asks for it.
+       // 6
+       // We will re-run latex if the log file asks for it,
        // or if the sumchange() is true.
        //     -> rerun asked for:
        //             run latex and
@@ -450,7 +482,7 @@ int LaTeX::run(TeXErrors & terr)
                // MAX_RUNS are reached.
                rerun = false;
                ++count;
-               LYXERR(Debug::LATEX, "Run #" << count);
+               LYXERR(Debug::OUTFILE, "Run #" << count);
                message(runMessage(count));
                startscript();
                scanres = scanLogFile(terr);
@@ -469,11 +501,14 @@ int LaTeX::run(TeXErrors & terr)
                scanres |= NONZERO_ERROR;
        }
 
-       LYXERR(Debug::LATEX, "Done.");
+       LYXERR(Debug::OUTFILE, "Done.");
 
        if (bscanres & ERRORS)
                return bscanres; // return on error
 
+       if (iscanres & ERRORS)
+               return iscanres; // return on error
+
        return scanres;
 }
 
@@ -500,14 +535,53 @@ int LaTeX::runMakeIndex(string const & f, OutputParams const & rp,
        if (!rp.index_command.empty())
                tmp = rp.index_command;
 
-       LYXERR(Debug::LATEX,
+       Language const * doc_lang = languages.getLanguage(rp.document_language);
+       
+       if (contains(tmp, "$$x")) {
+               // This adds appropriate [te]xindy options
+               // such as language and codepage (for the
+               // main document language/encoding) as well
+               // as input markup (latex or xelatex)
+               string xdyopts = doc_lang ? doc_lang->xindy() : string();
+               if (!xdyopts.empty())
+                       xdyopts = "-L " + xdyopts;
+               if (rp.isFullUnicode() && rp.encoding->package() == Encoding::none) {
+                       if (!xdyopts.empty())
+                               xdyopts += " ";
+                       // xelatex includes lualatex
+                       xdyopts += "-I xelatex";
+               }
+               else if (rp.encoding->iconvName() == "UTF-8") {
+                       if (!xdyopts.empty())
+                               xdyopts += " ";
+                       // -I not really needed for texindy, but for xindy
+                       xdyopts += "-C utf8 -I latex";
+               }
+               else {
+                       if (!xdyopts.empty())
+                               xdyopts += " ";
+                       // not really needed for texindy, but for xindy
+                       xdyopts += "-I latex";
+               }
+               tmp = subst(tmp, "$$x", xdyopts);
+       }
+
+       if (contains(tmp, "$$b")) {
+               // advise xindy to write a log file
+               tmp = subst(tmp, "$$b", removeExtension(f));
+       }
+
+       LYXERR(Debug::OUTFILE,
                "idx file has been made, running index processor ("
                << tmp << ") on file " << f);
 
-       tmp = subst(tmp, "$$lang", rp.document_language);
+       if (doc_lang) {
+               tmp = subst(tmp, "$$lang", doc_lang->babel());
+               tmp = subst(tmp, "$$lcode", doc_lang->code());
+       }
        if (rp.use_indices) {
                tmp = lyxrc.splitindex_command + " -m " + quoteName(tmp);
-               LYXERR(Debug::LATEX,
+               LYXERR(Debug::OUTFILE,
                "Multiple indices. Using splitindex command: " << tmp);
        }
        tmp += ' ';
@@ -523,8 +597,8 @@ int LaTeX::runMakeIndex(string const & f, OutputParams const & rp,
 int LaTeX::runMakeIndexNomencl(FileName const & fname,
                string const & nlo, string const & nls)
 {
-       LYXERR(Debug::LATEX, "Running MakeIndex for nomencl.");
-       message(_("Running MakeIndex for nomencl."));
+       LYXERR(Debug::OUTFILE, "Running Nomenclature Processor.");
+       message(_("Running Nomenclature Processor."));
        string tmp = lyxrc.nomencl_command + ' ';
        // onlyFileName() is needed for cygwin
        tmp += quoteName(onlyFileName(changeExtension(fname.absFileName(), nlo)));
@@ -582,7 +656,7 @@ AuxInfo const LaTeX::scanAuxFile(FileName const & fname)
 
 void LaTeX::scanAuxFile(FileName const & fname, AuxInfo & aux_info)
 {
-       LYXERR(Debug::LATEX, "Scanning aux file: " << fname);
+       LYXERR(Debug::OUTFILE, "Scanning aux file: " << fname);
 
        ifstream ifs(fname.toFilesystemEncoding().c_str());
        string token;
@@ -602,7 +676,7 @@ void LaTeX::scanAuxFile(FileName const & fname, AuxInfo & aux_info)
                        while (!data.empty()) {
                                string citation;
                                data = split(data, citation, ',');
-                               LYXERR(Debug::LATEX, "Citation: " << citation);
+                               LYXERR(Debug::OUTFILE, "Citation: " << citation);
                                aux_info.citations.insert(citation);
                        }
                } else if (regex_match(token, sub, reg2)) {
@@ -613,7 +687,7 @@ void LaTeX::scanAuxFile(FileName const & fname, AuxInfo & aux_info)
                                string database;
                                data = split(data, database, ',');
                                database = changeExtension(database, "bib");
-                               LYXERR(Debug::LATEX, "BibTeX database: `" << database << '\'');
+                               LYXERR(Debug::OUTFILE, "BibTeX database: `" << database << '\'');
                                aux_info.databases.insert(database);
                        }
                } else if (regex_match(token, sub, reg3)) {
@@ -621,7 +695,7 @@ void LaTeX::scanAuxFile(FileName const & fname, AuxInfo & aux_info)
                        // token is now the style file
                        // pass it to the helper
                        style = changeExtension(style, "bst");
-                       LYXERR(Debug::LATEX, "BibTeX style: `" << style << '\'');
+                       LYXERR(Debug::OUTFILE, "BibTeX style: `" << style << '\'');
                        aux_info.styles.insert(style);
                } else if (regex_match(token, sub, reg4)) {
                        string const file2 = sub.str(1);
@@ -684,7 +758,7 @@ bool LaTeX::runBibTeX(vector<AuxInfo> const & bibtex_info,
                                it->aux_file.absFileName())));
                Systemcall one;
                Systemcall::Starttype const starttype = 
-               allow_cancel ? Systemcall::WaitLoop : Systemcall::Wait;
+                       allow_cancel ? Systemcall::WaitLoop : Systemcall::Wait;
                exit_code = one.startscript(starttype, tmp, path, lpath, true);
                if (exit_code) {
                        return result;
@@ -710,8 +784,8 @@ int LaTeX::scanLogFile(TeXErrors & terr)
        int retval = NO_ERRORS;
        string tmp =
                onlyFileName(changeExtension(file.absFileName(), ".log"));
-       LYXERR(Debug::LATEX, "Log file: " << tmp);
-       FileName const fn = FileName(makeAbsPath(tmp));
+       LYXERR(Debug::OUTFILE, "Log file: " << tmp);
+       FileName const fn = makeAbsPath(tmp);
        // FIXME we should use an ifdocstream here and a docstring for token
        // below. The encoding of the log file depends on the _output_ (font)
        // encoding of the TeX file (T1, TU etc.). See #10728.
@@ -719,6 +793,7 @@ int LaTeX::scanLogFile(TeXErrors & terr)
        bool fle_style = false;
        static regex const file_line_error(".+\\.\\D+:[0-9]+: (.+)");
        static regex const child_file("[^0-9]*([0-9]+[A-Za-z]*_.+\\.tex).*");
+       static regex const undef_ref(".*Reference `(\\w+)\\' on page.*");
        // Flag for 'File ended while scanning' message.
        // We need to wait for subsequent processing.
        string wait_for_error;
@@ -730,6 +805,7 @@ int LaTeX::scanLogFile(TeXErrors & terr)
        terr.clearRefs();
 
        string token;
+       string ml_token;
        while (getline(ifs, token)) {
                // MikTeX sometimes inserts \0 in the log file. They can't be
                // removed directly with the existing string utility
@@ -739,11 +815,14 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                token = subst(token, "\r", "");
                smatch sub;
 
-               LYXERR(Debug::LATEX, "Log line: " << token);
+               LYXERR(Debug::OUTFILE, "Log line: " << token);
 
                if (token.empty())
                        continue;
 
+               if (!ml_token.empty())
+                       ml_token += token;
+
                // Track child documents
                for (size_t i = 0; i < token.length(); ++i) {
                        if (token[i] == '(') {
@@ -781,52 +860,90 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                //TODO: TL 2020 engines will contain new commandline switch --cnf-line which we  
                //can use to set max_print_line variable for appropriate length and detect all
                //errors correctly.
-               if (contains(token, "There were undefined citations."))
+               if (!runparams.includeall && (contains(token, "There were undefined citations.") ||
+                   prefixIs(token, "Package biblatex Warning: The following entry could not be found")))
                        retval |= UNDEF_CIT;
 
-               if (prefixIs(token, "LaTeX Warning:") ||
-                   prefixIs(token, "! pdfTeX warning")) {
+               if (prefixIs(token, "LaTeX Warning:")
+                   || prefixIs(token, "! pdfTeX warning")
+                   || prefixIs(ml_token, "LaTeX Warning:")
+                   || prefixIs(ml_token, "! pdfTeX warning")) {
                        // Here shall we handle different
                        // types of warnings
                        retval |= LATEX_WARNING;
-                       LYXERR(Debug::LATEX, "LaTeX Warning.");
+                       LYXERR(Debug::OUTFILE, "LaTeX Warning.");
                        if (contains(token, "Rerun to get cross-references")) {
                                retval |= RERUN;
-                               LYXERR(Debug::LATEX, "We should rerun.");
+                               LYXERR(Debug::OUTFILE, "We should rerun.");
                        // package clefval needs 2 latex runs before bibtex
                        } else if (contains(token, "Value of")
                                   && contains(token, "on page")
                                   && contains(token, "undefined")) {
                                retval |= ERROR_RERUN;
-                               LYXERR(Debug::LATEX, "Force rerun.");
+                               LYXERR(Debug::OUTFILE, "Force rerun.");
                        // package etaremune
                        } else if (contains(token, "Etaremune labels have changed")) {
                                retval |= ERROR_RERUN;
-                               LYXERR(Debug::LATEX, "Force rerun.");
+                               LYXERR(Debug::OUTFILE, "Force rerun.");
                        // package enotez
                        } else if (contains(token, "Endnotes may have changed. Rerun")) {
                                retval |= RERUN;
-                               LYXERR(Debug::LATEX, "We should rerun.");
+                               LYXERR(Debug::OUTFILE, "We should rerun.");
                        //"Citation `cit' on page X undefined on input line X."
-                       } else if (contains(token, "Citation")
+                       } else if (!runparams.includeall && contains(token, "Citation")
                                   //&& contains(token, "on input line") //often split to newline
                                   && contains(token, "undefined")) {
                                retval |= UNDEF_CIT;
                                terr.insertRef(getLineNumber(token), from_ascii("Citation undefined"),
                                        from_utf8(token), child_name);
                        //"Reference `X' on page Y undefined on input line Z."
-                       } else if (contains(token, "Reference")
-                                  //&& contains(token, "on input line")) //often split to new line
+                       // This warning might be broken accross multiple lines with long labels.
+                       // Thus we check that
+                       } else if (contains(token, "Reference `") && !contains(token, "on input line")) {
+                               // Rest of warning in next line(s)
+                               // Save to ml_token
+                               ml_token = token;
+                       } else if (!ml_token.empty() && contains(ml_token, "Reference `")
+                                  && !contains(ml_token, "on input line")) {
+                               // not finished yet. Continue with next line.
+                               continue;
+                       } else if (!ml_token.empty() && contains(ml_token, "Reference `")
+                                  && contains(ml_token, "on input line")) {
+                               // We have collected the whole warning now.
+                               if (!contains(ml_token, "undefined")) {
+                                       // Not the warning we are looking for
+                                       ml_token.clear();
+                                       continue;
+                               }
+                               if (regex_match(ml_token, sub, undef_ref)) {
+                                       string const ref = sub.str(1);
+                                       Buffer const * buf = theBufferList().getBufferFromTmp(file.absFileName());
+                                       if (!buf || !buf->masterBuffer()->activeLabel(from_utf8(ref))) {
+                                               terr.insertRef(getLineNumber(ml_token), from_ascii("Reference undefined"),
+                                                       from_utf8(ml_token), child_name);
+                                               retval |= UNDEF_UNKNOWN_REF;
+                                       }
+                               }
+                               ml_token.clear();
+                               retval |= UNDEF_REF;
+                       } else if (contains(token, "Reference `")
+                                  && contains(token, "on input line")
                                   && contains(token, "undefined")) {
+                               if (regex_match(token, sub, undef_ref)) {
+                                       string const ref = sub.str(1);
+                                       Buffer const * buf = theBufferList().getBufferFromTmp(file.absFileName());
+                                       if (!buf || !buf->masterBuffer()->activeLabel(from_utf8(ref))) {
+                                               terr.insertRef(getLineNumber(token), from_ascii("Reference undefined"),
+                                                       from_utf8(token), child_name);
+                                               retval |= UNDEF_UNKNOWN_REF;
+                                       }
+                               }
                                retval |= UNDEF_REF;
-                               terr.insertRef(getLineNumber(token), from_ascii("Reference undefined"),
-                                       from_utf8(token), child_name);
-
-                       //If label is too long pdlaftex log line splitting will make the above fail
-                       //so we catch at least this generic statement occuring for both CIT & REF.
-                       } else if (contains(token, "There were undefined references.")) {
+                       // In case the above checks fail we catch at least this generic statement
+                       // occuring for both CIT & REF.
+                       } else if (!runparams.includeall && contains(token, "There were undefined references.")) {
                                if (!(retval & UNDEF_CIT)) //if not handled already
-                                        retval |= UNDEF_REF;
+                                       retval |= UNDEF_REF;
                        }
 
                } else if (prefixIs(token, "Package")) {
@@ -834,7 +951,8 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                        retval |= PACKAGE_WARNING;
                        if (contains(token, "natbib Warning:")) {
                                // Natbib warnings
-                               if (contains(token, "Citation")
+                               if (!runparams.includeall
+                                   && contains(token, "Citation")
                                    && contains(token, "on page")
                                    && contains(token, "undefined")) {
                                        retval |= UNDEF_CIT;
@@ -842,9 +960,9 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                                        terr.insertRef(getLineNumber(token), from_ascii("Citation undefined"),
                                                from_utf8(token), child_name);
                                }
-                       } else if (contains(token, "run BibTeX")) {
+                       } else if (!runparams.includeall && contains(token, "run BibTeX")) {
                                retval |= UNDEF_CIT;
-                       } else if (contains(token, "run Biber")) {
+                       } else if (!runparams.includeall && contains(token, "run Biber")) {
                                retval |= UNDEF_CIT;
                                biber = true;
                        } else if (contains(token, "Rerun LaTeX") ||
@@ -852,20 +970,20 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                                   contains(token, "Rerun to get")) {
                                // at least longtable.sty and bibtopic.sty
                                // might use this.
-                               LYXERR(Debug::LATEX, "We should rerun.");
+                               LYXERR(Debug::OUTFILE, "We should rerun.");
                                retval |= RERUN;
                        }
                } else if (prefixIs(token, "LETTRE WARNING:")) {
                        if (contains(token, "veuillez recompiler")) {
                                // lettre.cls
-                               LYXERR(Debug::LATEX, "We should rerun.");
+                               LYXERR(Debug::OUTFILE, "We should rerun.");
                                retval |= RERUN;
                        }
                } else if (token[0] == '(') {
                        if (contains(token, "Rerun LaTeX") ||
                            contains(token, "Rerun to get")) {
                                // Used by natbib
-                               LYXERR(Debug::LATEX, "We should rerun.");
+                               LYXERR(Debug::OUTFILE, "We should rerun.");
                                retval |= RERUN;
                        }
                } else if (prefixIs(token, "! ")
@@ -888,7 +1006,7 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                                if (prefixIs(token, "! File ended while scanning use of \\Hy@setref@link.")){
                                        // bug 7344. We must rerun LaTeX if hyperref has been toggled.
                                        retval |= ERROR_RERUN;
-                                       LYXERR(Debug::LATEX, "Force rerun.");
+                                       LYXERR(Debug::OUTFILE, "Force rerun.");
                                } else {
                                        // bug 6445. At this point its not clear we finish with error.
                                        wait_for_error = desc;
@@ -905,7 +1023,7 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                        if (prefixIs(token, "! Paragraph ended before \\Hy@setref@link was complete.")){
                                        // bug 7344. We must rerun LaTeX if hyperref has been toggled.
                                        retval |= ERROR_RERUN;
-                                       LYXERR(Debug::LATEX, "Force rerun.");
+                                       LYXERR(Debug::OUTFILE, "Force rerun.");
                        }
 
                        if (!wait_for_error.empty() && prefixIs(token, "! Emergency stop.")){
@@ -931,10 +1049,15 @@ int LaTeX::scanLogFile(TeXErrors & terr)
 
                        // get the next line
                        int count = 0;
+                       // We also collect intermediate lines
+                       // This is needed for errors in preamble
+                       string intermediate;
                        do {
                                if (!getline(ifs, tmp))
                                        break;
                                tmp = rtrim(tmp, "\r");
+                               if (!prefixIs(tmp, "l."))
+                                       intermediate += tmp;
                                // 15 is somewhat arbitrarily chosen, based on practice.
                                // We used 10 for 14 years and increased it to 15 when we
                                // saw one case.
@@ -956,6 +1079,15 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                                sscanf(tmp.c_str(), "l.%d", &line);
                                // get the rest of the message:
                                string errstr(tmp, tmp.find(' '));
+                               bool preamble_error = false;
+                               if (suffixIs(errstr, "\\begin{document}")) {
+                                       // this is an error in preamble
+                                       // the real error is in the
+                                       // intermediate lines
+                                       errstr = intermediate;
+                                       tmp = intermediate;
+                                       preamble_error = true;
+                               }
                                errstr += '\n';
                                getline(ifs, tmp);
                                tmp = rtrim(tmp, "\r");
@@ -968,8 +1100,11 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                                        getline(ifs, tmp);
                                        tmp = rtrim(tmp, "\r");
                                }
-                               LYXERR(Debug::LATEX, "line: " << line << '\n'
-                                       << "Desc: " << desc << '\n' << "Text: " << errstr);
+                               if (preamble_error)
+                                       // Add a note that the error is to be found in preamble
+                                       errstr += "\n" + to_utf8(_("(NOTE: The erroneous command is in the preamble)"));
+                               LYXERR(Debug::OUTFILE, "line: " << line << '\n'
+                                                               << "Desc: " << desc << '\n' << "Text: " << errstr);
                                if (line == last_line)
                                        ++line_count;
                                else {
@@ -999,7 +1134,7 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                                retval |= TEX_WARNING;
                        } else if (prefixIs(token, "Underfull ")) {
                                retval |= TEX_WARNING;
-                       } else if (contains(token, "Rerun to get citations")) {
+                       } else if (!runparams.includeall && contains(token, "Rerun to get citations")) {
                                // Natbib seems to use this.
                                retval |= UNDEF_CIT;
                        } else if (contains(token, "No pages of output")
@@ -1049,7 +1184,7 @@ int LaTeX::scanLogFile(TeXErrors & terr)
                        }
                }
        }
-       LYXERR(Debug::LATEX, "Log line: " << token);
+       LYXERR(Debug::OUTFILE, "Log line: " << token);
        return retval;
 }
 
@@ -1427,7 +1562,7 @@ void LaTeX::deplog(DepTable & head)
 int LaTeX::scanBlgFile(DepTable & dep, TeXErrors & terr)
 {
        FileName const blg_file(changeExtension(file.absFileName(), "blg"));
-       LYXERR(Debug::LATEX, "Scanning blg file: " << blg_file);
+       LYXERR(Debug::OUTFILE, "Scanning blg file: " << blg_file);
 
        ifstream ifs(blg_file.toFilesystemEncoding().c_str());
        string token;
@@ -1450,7 +1585,7 @@ int LaTeX::scanBlgFile(DepTable & dep, TeXErrors & terr)
                if (regex_match(token, sub, reg1)) {
                        string data = sub.str(3);
                        if (!data.empty()) {
-                               LYXERR(Debug::LATEX, "Found bib file: " << data);
+                               LYXERR(Debug::OUTFILE, "Found bib file: " << data);
                                handleFoundFile(data, dep);
                        }
                }
@@ -1482,10 +1617,9 @@ int LaTeX::scanBlgFile(DepTable & dep, TeXErrors & terr)
                } else if (regex_match(token, sub, biberError)) {
                        retval |= BIBTEX_ERROR;
                        string errstr = N_("Biber error: ") + sub.str(2);
-                       string msg = token;
                        terr.insertError(0,
                                         from_local8bit(errstr),
-                                        from_local8bit(msg));
+                                        from_local8bit(token));
                }
                prevtoken = token;
        }
@@ -1493,4 +1627,40 @@ int LaTeX::scanBlgFile(DepTable & dep, TeXErrors & terr)
 }
 
 
+int LaTeX::scanIlgFile(TeXErrors & terr)
+{
+       FileName const ilg_file(changeExtension(file.absFileName(), "ilg"));
+       LYXERR(Debug::OUTFILE, "Scanning ilg file: " << ilg_file);
+
+       ifstream ifs(ilg_file.toFilesystemEncoding().c_str());
+       string token;
+       int retval = NO_ERRORS;
+
+       string prevtoken;
+       while (getline(ifs, token)) {
+               token = rtrim(token, "\r");
+               if (prefixIs(token, "!! "))
+                       prevtoken = token;
+               else if (!prevtoken.empty()) {
+                       retval |= INDEX_ERROR;
+                       string errstr = N_("Makeindex error: ") + prevtoken;
+                       string msg = prevtoken + '\n';
+                       msg += token;
+                       terr.insertError(0,
+                                        from_local8bit(errstr),
+                                        from_local8bit(msg));
+                       prevtoken.clear();
+               } else if (prefixIs(token, "ERROR: ")) {
+                       retval |= BIBTEX_ERROR;
+                       string errstr = N_("Xindy error: ") + token.substr(6);
+                       terr.insertError(0,
+                                        from_local8bit(errstr),
+                                        from_local8bit(token));
+               }
+       }
+       return retval;
+}
+
+
+
 } // namespace lyx