[0;90mINFO: === SciTeX Writer v2.0.0a0 ===[0m
[0;90mINFO: Running ./scripts/shell/compile_supplementary.sh...[0m
[0;32mSUCC: Configuration Loaded for supplementary (v2.0.0a0)[0m
[0;90mINFO: Running ./scripts/shell/compile_supplementary.sh...[0m
[0;90mINFO: [02:23:51] Starting: Dependency Check[0m
[0;90mINFO: Running ./scripts/shell/modules/check_dependancy_commands.sh...[0m
[0;90mINFO: Warmup: 3ms[0m
[0;90mINFO: Parallel checks: 281ms[0m
[0;32mSUCC: Required tools:[0m
pdflatex ✓
bibtex ✓
latexdiff ✓
texcount ✓
xlsx2csv ✓
csv2latex ✓
parallel ✓
[0;32mSUCC: [02:23:52] Completed: Dependency Check (1s elapsed, 4s total)[0m
[0;90mINFO: [02:23:52] Starting: Bibliography Merge[0m
[0;32mSUCC: [02:23:52] Completed: Bibliography Merge (0s elapsed, 4s total)[0m
[0;90mINFO: [02:23:52] Starting: Citation Style[0m
[0;32mSUCC: Citation style already set to: unsrtnat[0m
[0;32mSUCC: [02:23:52] Completed: Citation Style (0s elapsed, 4s total)[0m
[0;90mINFO: [02:23:52] Starting: Parallel Processing (Figures, Tables, Word Count)[0m
[0;90mINFO: Figure Processing:[0m
[0;90mINFO: Running ./scripts/shell/modules/process_figures.sh ...[0m
[0;90mINFO: No figure source files found, creating placeholders only...[0m
[0;90mINFO: Cleaning jpg_for_compilation directory...[0m
[0;90mINFO: Skipping conversion pipeline (no source files)[0m
[0;90mINFO: Checking for missing figures...[0m
[0;90mINFO: Optimizing figures with Python script...[0m
[0;90mINFO: Table Processing:[0m
[0;90mINFO: Running ./scripts/shell/modules/process_tables.sh ...[0m
[0;90mINFO: [02:23:52] Initializing tables[0m
[0;32mSUCC: [02:23:52] Initializing tables (0s)[0m
[0;90mINFO: [02:23:52] Converting XLSX to CSV[0m
[0;32mSUCC: [02:23:52] Converting XLSX to CSV (0s)[0m
[0;90mINFO: [02:23:52] Ensuring captions exist[0m
[0;32mSUCC: [02:23:52] Ensuring captions exist (0s)[0m
[0;90mINFO: [02:23:52] Converting CSV to LaTeX[0m
[0;90mINFO: Using csv2latex for table processing[0m
[0;32mSUCC: [02:23:52] Converting CSV to LaTeX (0s)[0m
[0;90mINFO: [02:23:52] Gathering table files[0m
[0;90mINFO: Created table header template with instructions[0m
[0;32mSUCC: 1 tables compiled[0m
[0;32mSUCC: [02:23:52] Gathering table files (0s)[0m
[0;90mINFO: Word Count:[0m
[0;90mINFO: Running ./scripts/shell/modules/count_words.sh ...[0m
[0;32mSUCC: Word counts updated:[0m
[0;32mSUCC: Figures: 0[0m
[0;32mSUCC: Tables: 0[0m
[0;32mSUCC: Supplementary text: 1077 words[0m
[0;32mSUCC: [02:23:52] Completed: Parallel Processing (0s elapsed, 4s total)[0m
[0;90mINFO: [02:23:52] Starting: TeX Compilation (Structure)[0m
[0;90mINFO: Running ./scripts/shell/modules/compilation_structure_tex_to_compiled_tex.sh ...[0m
[0;32mSUCC: ./02_supplementary/supplementary.tex compiled[0m
[0;32mSUCC: [02:23:52] Completed: TeX Compilation (Structure) (0s elapsed, 4s total)[0m
[0;90mINFO: [02:23:52] Starting: PDF Generation[0m
[0;90mINFO: Running ./scripts/shell/modules/compilation_compiled_tex_to_compiled_pdf.sh ...[0m
[0;90mINFO: Converting ./02_supplementary/supplementary.tex to PDF...[0m
[0;90mINFO: Using latexmk (intelligent compilation)[0m
[0;33mWARN: Compilation completed with warnings (check citations/references)[0m
[0;32mSUCC: Total compilation: 2s[0m
[0;32mSUCC: ./02_supplementary/supplementary.pdf ready (264K)[0m
[0;32mSUCC: Symlink updated: ./02_supplementary/manuscript-latest.pdf -> supplementary.pdf (no archive yet)[0m
[0;32mSUCC: [02:23:55] Completed: PDF Generation (3s elapsed, 7s total)[0m
[0;90mINFO: [02:23:55] Starting: Diff Generation[0m
[0;90mINFO: Running ./scripts/shell/modules/process_diff.sh ...[0m
[0;90mINFO: Creating diff between archive...[0m
[0;32mSUCC: ./02_supplementary/supplementary_diff.tex created[0m
[0;90mINFO: Compiling diff document...[0m
[0;90mINFO: Using latexmk (intelligent compilation)[0m
Rc files read:
/etc/LatexMk
Latexmk: Run number 1 of rule 'pdflatex'
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
Latexmk: Missing bbl file '02_supplementary/supplementary_diff.bbl' in following:
No file supplementary_diff.bbl.
Latexmk: Summary of warnings from last run of *latex:
Latex failed to resolve 2 reference(s)
Collected error summary (may duplicate other messages):
pdflatex: Command for 'pdflatex' gave return code 1
Refer to '02_supplementary/supplementary_diff.log' for details
Latexmk: Use the -f option to force complete processing,
unless error was exceeding maximum runs, or warnings treated as errors.
[0;32mSUCC: ./02_supplementary/supplementary_diff.pdf ready (264K)[0m
[0;90mINFO: Total time: 3s[0m
[0;32mSUCC: [02:23:58] Completed: Diff Generation (3s elapsed, 10s total)[0m
[0;90mINFO: [02:23:58] Starting: Archive/Versioning[0m
[0;90mINFO: Running ./scripts/shell/modules/process_archive.sh...[0m
[0;32mSUCC: Version allocated as: v003[0m
[0;32mSUCC: [02:23:58] Completed: Archive/Versioning (0s elapsed, 10s total)[0m
[0;90mINFO: [02:23:58] Starting: Cleanup[0m
[0;90mINFO: Running ./scripts/shell/modules/cleanup.sh...[0m
[0;90mINFO: Removing versioned files from current directory...[0m
[0;32mSUCC: [02:23:58] Completed: Cleanup (0s elapsed, 10s total)[0m
[0;90mINFO: [02:23:58] Starting: Directory Tree[0m
[0;90mINFO: ./scripts/shell/modules/custom_tree.sh...[0m
[0;32mSUCC: ./02_supplementary/docs/tree.txt created[0m
[0;32mSUCC: [02:23:58] Completed: Directory Tree (0s elapsed, 10s total)[0m
[0;32mSUCC: ====================================================[0m
[0;32mSUCC: TOTAL COMPILATION TIME: 10s[0m
[0;32mSUCC: ====================================================[0m
[0;32mSUCC: See ./02_supplementary/logs/global.log[0m
/