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Build fails without any apparent error #934

Closed admercs closed 5 years ago

admercs commented 5 years ago

Description

Build fails on a LaTeX article without any apparent error, per the log file shown below. The file builds without issues online.

Log console

``` ReadyLatexmk: applying rule 'bibtex intercomparison_paper'... For rule 'bibtex intercomparison_paper', running '&run_bibtex( )' ... This is BibTeX, Version 0.99d (TeX Live 2018) The top-level auxiliary file: intercomparison_paper.aux The style file: abbrvnat.bst Database file #1: ref.bib Warning--string name "pub-iso" is undefined --line 537 of file ref.bib Warning--string name "pub-iso:adr" is undefined --line 538 of file ref.bib Warning--empty publisher in ISO:1998:IIP (There were 3 warnings) Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex LaTeX2e <2018-04-01> patch level 2 Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (/usr/local/texlive/2018/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/local/texlive/2018/texmf-dist/tex/latex/base/size12.clo)) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def)) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty)) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/local/texlive/2018/texmf-dist/tex/latex/booktabs/booktabs.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/units/nicefrac.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ifthen.sty)) (/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/microtype.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/microtype-pdftex.def) (/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/microtype.cfg)) (/usr/local/texlive/2018/texmf-dist/tex/latex/natbib/natbib.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/lineno/lineno.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/preprint/authblk.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/local/texlive/2018/texmf-dist/tex/latex/geometry/geometry.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/rotating.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/adjustbox/adjustbox.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkvutils.tex))) (/usr/local/texlive/2018/texmf-dist/tex/latex/adjustbox/adjcalc.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/adjustbox/trimclip.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/collectbox/collectbox.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/adjustbox/tc-pdftex.def)) (/usr/local/texlive/2018/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/varwidth/varwidth.sty)) (/usr/local/texlive/2018/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/tools/dcolumn.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/tools/array.sty)) (/usr/local/texlive/2018/texmf-dist/tex/latex/float/float.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/subfig/subfig.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/caption/caption.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/caption/caption3.sty))) (/usr/local/texlive/2018/texmf-dist/tex/latex/was/gensymb.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/appendix/appendix.sty) (./intercomparison_paper.aux LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. LaTeX Warning: Label `' multiply defined. ) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./intercomparison_paper.out) (./intercomparison_paper.out) (/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/mt-cmr.cfg) (/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex Package gensymb Warning: Not defining \perthousand. Package gensymb Warning: Not defining \micro. (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/mt-msa.cfg) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/local/texlive/2018/texmf-dist/tex/latex/microtype/mt-msb.cfg) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] (./intercomparison_paper.toc) [2] (./intercomparison_paper.lof) [3] (./intercomparison_paper.lot) [4] (/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1cmss.fd)Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'bibtex intercomparison_paper': File changes, etc: Non-existent destination files: 'intercomparison_paper.bbl' ------------ Run number 1 of rule 'bibtex intercomparison_paper' ------------ ------------ Running 'bibtex "intercomparison_paper"' ------------ Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'intercomparison_paper.aux' 'intercomparison_paper.bbl' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -synctex=1 -interaction=nonstopmode -file-line-error -recorder "/Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex"' ------------ Package natbib Warning: Citation `Bugmann1996' on page 5 undefined on input line 114. Package natbib Warning: Citation `Keane2004c' on page 5 undefined on input line 114. Package natbib Warning: Citation `Mladenoff2004a' on page 5 undefined on input line 114. Package natbib Warning: Citation `He2008a' on page 5 undefined on input line 114. Package natbib Warning: Citation `Xi2009' on page 5 undefined on input line 114. Package natbib Warning: Citation `Shifley2017' on page 5 undefined on input line 114. Package natbib Warning: Citation `Fisher2014' on page 5 undefined on input line 114. Package natbib Warning: Citation `Fisher2017' on page 5 undefined on input line 114. Package natbib Warning: Citation `Sulman2018' on page 5 undefined on input line 114. Package natbib Warning: Citation `Parton1983' on page 5 undefined on input line 114. Package natbib Warning: Citation `Parton1987' on page 5 undefined on input line 114. Package natbib Warning: Citation `Warszawski2014' on page 5 undefined on input line 116. Package natbib Warning: Citation `Lischke2016' on page 5 undefined on input line 116. Package natbib Warning: Citation `Hanson2004' on page 5 undefined on input line 116. Package natbib Warning: Citation `Bugmann1996' on page 5 undefined on input line 118. Package natbib Warning: Citation `Kimmins1999' on page 5 undefined on input line 118. Package natbib Warning: Citation `Mbabazi2011' on page 5 undefined on input line 118. Package natbib Warning: Citation `Fisher2010' on page 5 undefined on input line 118. Package natbib Warning: Citation `Ahlstroem2015' on page 5 undefined on input line 118. Package natbib Warning: Citation `Sitch2003' on page 5 undefined on input line 120. Package natbib Warning: Citation `Moorcroft2001' on page 5 undefined on input line 120. Package natbib Warning: Citation `Medvigy2009' on page 5 undefined on input line 120. Package natbib Warning: Citation `Weng2015' on page 5 undefined on input line 120. Package natbib Warning: Citation `Strigul2008' on page 5 undefined on input line 120. Package natbib Warning: Citation `Davis2013' on page 5 undefined on input line 120. Package natbib Warning: Citation `Seidl2012' on page 5 undefined on input line 120. Package natbib Warning: Citation `Strigul2008' on page 5 undefined on input line 120. Package natbib Warning: Citation `Seidl2012' on page 5 undefined on input line 120. [5] Package natbib Warning: Citation `Giasson2013' on page 6 undefined on input line 122. Package natbib Warning: Citation `Urbanski2007' on page 6 undefined on input line 122. Package natbib Warning: Citation `Urbanski2007' on page 6 undefined on input line 122. Package natbib Warning: Citation `Strigul2008' on page 6 undefined on input line 122. Package natbib Warning: Citation `Purves2008' on page 6 undefined on input line 122. Package natbib Warning: Citation `Scheller2007b' on page 6 undefined on input line 122. Package natbib Warning: Citation `Scheller2011a' on page 6 undefined on input line 122. Package natbib Warning: Citation `Wiesner2018' on page 6 undefined on input line 124. Package natbib Warning: Citation `Whelan2013' on page 6 undefined on input line 124. Package natbib Warning: Citation `Starr2015' on page 6 undefined on input line 124. Package natbib Warning: Citation `Wiesner2018' on page 6 undefined on input line 124. [6] Package natbib Warning: Citation `Urbanski2007' on page 7 undefined on input line 136. Package natbib Warning: Citation `Barford2001' on page 7 undefined on input line 136. Package natbib Warning: Citation `Urbanski2007' on page 7 undefined on input line 136. Package natbib Warning: Citation `Barford2001' on page 7 undefined on input line 138. Package natbib Warning: Citation `Urbanski2007' on page 7 undefined on input line 138. Package natbib Warning: Citation `Urbanski2007' on page 7 undefined on input line 138. [7] Overfull \hbox (17.93102pt too wide) in paragraph at lines 140--141 []\T1/cmr/m/n/12 (-20) Recent his-tor-i-cal mean daily fluxes of tem-per-a-ture ($[] \OML/cmm/m/it/12 C$\T1/cmr/m/n/12 (-20) ), ecosys-tem res-pi-ra-tion ($\OML/cmm/m/it/12 ^^Vmol CO[] m[]$\T1/cmr/m/n/12 (-20) ), [8 <./observations/hf_fluxes.pdf>] Package natbib Warning: Citation `Hendricks2005' on page 9 undefined on input line 160. Package natbib Warning: Citation `Drew1998' on page 9 undefined on input line 160. Package natbib Warning: Citation `Hendricks2005' on page 9 undefined on input line 160. Package natbib Warning: Citation `Drew1998' on page 9 undefined on input line 160. Package natbib Warning: Citation `Goebel1997' on page 9 undefined on input line 160. Package natbib Warning: Citation `Mitchell1999' on page 9 undefined on input line 162. Package natbib Warning: Citation `Hendricks2005' on page 9 undefined on input line 162. Package natbib Warning: Citation `Hendricks2005' on page 9 undefined on input line 162. [9 <./observations/hf_nee_night_day.pdf>] [10 <./observations/jerc_fluxes.pdf>] [11 <./observations/jerc_nee_night_day.pdf>] Package natbib Warning: Citation `Mladenoff1993' on page 12 undefined on input line 229. Package natbib Warning: Citation `Mladenoff1999' on page 12 undefined on input line 229. Package natbib Warning: Citation `He1999d' on page 12 undefined on input line 229. Package natbib Warning: Citation `Scheller2007b' on page 12 undefined on input line 229. Package natbib Warning: Citation `Wang2014' on page 12 undefined on input line 229. Package natbib Warning: Citation `Pennanen2002' on page 12 undefined on input line 229. Package natbib Warning: Citation `Pennanen2004' on page 12 undefined on input line 229. Package natbib Warning: Citation `Roberts1999' on page 12 undefined on input line 229. Package natbib Warning: Citation `VonNeumann1966' on page 12 undefined on input line 229. Package natbib Warning: Citation `Lindenmayer1968a' on page 12 undefined on input line 229. Package natbib Warning: Citation `Lindenmayer1968b' on page 12 undefined on input line 229. Package natbib Warning: Citation `Deussen1998' on page 12 undefined on input line 229. Package natbib Warning: Citation `Noble1980' on page 12 undefined on input line 229. Package natbib Warning: Citation `Drossel1992' on page 12 undefined on input line 229. Package natbib Warning: Citation `ISO:1998:IIP' on page 12 undefined on input line 229. Package natbib Warning: Citation `Scheller2007b' on page 12 undefined on input line 229. [12] Package natbib Warning: Citation `Keane2004c' on page 13 undefined on input line 231. Package natbib Warning: Citation `Mladenoff2004a' on page 13 undefined on input line 231. Package natbib Warning: Citation `He2008a' on page 13 undefined on input line 231. Package natbib Warning: Citation `Xi2009' on page 13 undefined on input line 231. Package natbib Warning: Citation `Shifley2017' on page 13 undefined on input line 231. Package natbib Warning: Citation `Scheller2011a' on page 13 undefined on input line 233. Package natbib Warning: Citation `Parton1983' on page 13 undefined on input line 233. Package natbib Warning: Citation `Parton1987' on page 13 undefined on input line 233. Package natbib Warning: Citation `Scheller2011a' on page 13 undefined on input line 233. Package natbib Warning: Citation `Duveneck2017' on page 13 undefined on input line 233. Package natbib Warning: Citation `Strigul2008' on page 13 undefined on input line 237. Package natbib Warning: Citation `doi:10.1139/x93-249' on page 13 undefined on input line 237. Package natbib Warning: Citation `ECY:ECY19947561794' on page 13 undefined on input line 237. Package natbib Warning: Citation `Strigul2008' on page 13 undefined on input line 237. Package natbib Warning: Citation `Strigul2008' on page 13 undefined on input line 237. Package natbib Warning: Citation `Purves2008' on page 13 undefined on input line 237. Package natbib Warning: Citation `Strigul2008' on page 13 undefined on input line 237. Package natbib Warning: Citation `Hurtt1998' on page 13 undefined on input line 237. Package natbib Warning: Citation `Moorcroft2001' on page 13 undefined on input line 237. Package natbib Warning: Citation `Fisher2017' on page 13 undefined on input line 237. Package natbib Warning: Citation `Strigul2008' on page 13 undefined on input line 237. Package natbib Warning: Citation `Strigul2008' on page 13 undefined on input line 244. Package natbib Warning: Citation `Strigul2008' on page 13 undefined on input line 244. [13] Package natbib Warning: Citation `Canham1999' on page 14 undefined on input line 246. Package natbib Warning: Citation `Case2017' on page 14 undefined on input line 246. Package natbib Warning: Citation `Chojnacky2014' on page 14 undefined on input line 246. Package natbib Warning: Citation `Raich2002' on page 14 undefined on input line 246. Package natbib Warning: Citation `Domke2017' on page 14 undefined on input line 246. Package natbib Warning: Citation `R2018' on page 14 undefined on input line 250. Package natbib Warning: Citation `Krause2005' on page 14 undefined on input line 250. [14] Package natbib Warning: Citation `Nash1970' on page 15 undefined on input line 271. [15] [16 <./models/radar_chart.pdf>] [17] [18] [19 <./models/Sortie-PPA_hf_ems_nee.pdf> <./models/Landis2_hf_ems_nee.pdf> <./models/Sortie-PPA_hf_ems_c_ag.pdf> <./models/Landis2_hf_ems_c_ag.pdf>] [20 <./models/Sortie-PPA_hf_ems_biomass_sp.pdf, page is rotated 270 degrees> <./models/Landis2_hf_ems_biomass_sp.pdf, page is rotated 270 degrees> <./models/Sortie-PPA_hf_ems_abundance_sp.pdf, page is rotated 270 degrees> <./models/Landis2_hf_ems_abundance_sp.pdf, page is rotated 270 degrees>] [21] Package natbib Warning: Citation `Parton1987' on page 22 undefined on input line 443. Package natbib Warning: Citation `bachelet2001mc1' on page 22 undefined on input line 443. [22 <./models/Sortie-PPA_jerc_rd_biomass_sp.pdf, page is rotated 270 degrees> <./models/Landis2_jerc_rd_biomass_sp.pdf, page is rotated 270 degrees> <./models/Sortie-PPA_jerc_rd_abundance_sp.pdf, page is rotated 270 degrees> <./models/Landis2_jerc_rd_abundance_sp.pdf, page is rotated 270 degrees>] [23] Package natbib Warning: Citation `Urbanski2007' on page 24 undefined on input line 506. Package natbib Warning: Citation `Hanson2004' on page 24 undefined on input line 506. [24] (./intercomparison_paper.bbl [25] [26] [27] Underfull \hbox (badness 1596) in paragraph at lines 243--251 \T1/cmr/m/n/12 (+20) ???? URL []$\T1/cmtt/m/n/12 http : / / webstore . ansi . org / ansidocstore / product . asp ? sku = ISO % Underfull \hbox (badness 10000) in paragraph at lines 243--251 \T1/cmtt/m/n/12 2FIEC + 14882 % 2D1998 ; http : / / webstore . ansi . org / ansidocstore / product . asp ? Underfull \hbox (badness 10000) in paragraph at lines 243--251 \T1/cmtt/m/n/12 sku = ISO % 2FIEC + 14882 % 3A1998 ; http : / / www . iso . ch / cate / d25845 . html ; https : Underfull \hbox (badness 2073) in paragraph at lines 243--251 \T1/cmtt/m/n/12 / / webstore . ansi . org/$[]\T1/cmr/m/n/12 (+20) . Avail-able in elec-tronic form for on-line pur-chase at Underfull \hbox (badness 1424) in paragraph at lines 267--274 []\T1/cmr/m/n/12 (+20) H. Kim-mins, J. A. Blanco, B. Seely, C. Wel-ham, and K. Scoullar. \T1/cmr/m/it/12 (+20) Fore- Underfull \hbox (badness 1997) in paragraph at lines 267--274 \T1/cmr/m/it/12 (+20) cast-ing For-est Fu-tures: A Hy-brid Mod-elling Ap-proach to the As-sess-ment of Underfull \hbox (badness 4181) in paragraph at lines 267--274 \T1/cmr/m/it/12 (+20) Sus-tain-abil-ity of For-est Ecosys-tems and Their Val-ues\T1/cmr/m/n/12 (+20) . Tay-lor & Fran-cis Underfull \hbox (badness 1577) in paragraph at lines 267--274 \T1/cmr/m/n/12 (+20) Group, apr 2010. ISBN 9781844079223. URL []$\T1/cmtt/m/n/12 https : / / www . crcpress . com / Overfull \hbox (8.32346pt too wide) in paragraph at lines 267--274 \T1/cmtt/m/n/12 Forecasting-[]Forest-[]Futures-[]A-[]Hybrid-[]Modelling-[]Approach-[]to-[]the-[]Assessment / [28] [29] [30] [31]) [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ...ax}$ & $T_{shape}$ & $T_{shape}$ & $f_C_ {fine}$ & $BTOLAI$ & $kLAI... /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ... & $PPRPTS_2$ & $PPRPTS_3$ & $r_{decay}_ w$ & $m_{wood}$ & $m_{shap... /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ... $m_{shape}$ & $drop_month$ & $f_{root}_ c$ & $f_{root}_f$ \\ /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ...$drop_month$ & $f_{root}_c$ & $f_{root}_ f$ \\ [42] [43] [44] [45] [46] [47] Package natbib Warning: Citation `R2018' on page 48 undefined on input line 1162. Package natbib Warning: There were undefined citations. [48] (./intercomparison_paper.aux Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. ) LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information)pdfTeX warning (dest): name{section*.46} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{table.caption.18} has been referenced but does not exist, replaced by a fixed one {/usr/local/texlive/2018/texmf-dist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on intercomparison_paper.pdf (48 pages, 1020828 bytes). SyncTeX written on intercomparison_paper.synctex.gz. Transcript written on intercomparison_paper.log. Latexmk: Found input bbl file 'intercomparison_paper.bbl' Latexmk: References changed. Latexmk: Log file says output to 'intercomparison_paper.pdf' Latexmk: List of undefined refs and citations: Citation `Ahlstroem2015' on page 5 undefined on input line 118 Citation `Barford2001' on page 7 undefined on input line 136 Citation `Barford2001' on page 7 undefined on input line 138 Citation `Bugmann1996' on page 5 undefined on input line 114 Citation `Bugmann1996' on page 5 undefined on input line 118 Citation `Canham1999' on page 14 undefined on input line 246 Citation `Case2017' on page 14 undefined on input line 246 Citation `Chojnacky2014' on page 14 undefined on input line 246 Citation `Davis2013' on page 5 undefined on input line 120 Citation `Deussen1998' on page 12 undefined on input line 229 Citation `Domke2017' on page 14 undefined on input line 246 Citation `Drew1998' on page 9 undefined on input line 160 Citation `Drossel1992' on page 12 undefined on input line 229 Citation `Duveneck2017' on page 13 undefined on input line 233 Citation `ECY:ECY19947561794' on page 13 undefined on input line 237 Citation `Fisher2010' on page 5 undefined on input line 118 Citation `Fisher2014' on page 5 undefined on input line 114 Citation `Fisher2017' on page 13 undefined on input line 237 Citation `Fisher2017' on page 5 undefined on input line 114 Citation `Giasson2013' on page 6 undefined on input line 122 Citation `Goebel1997' on page 9 undefined on input line 160 Citation `Hanson2004' on page 24 undefined on input line 506 Citation `Hanson2004' on page 5 undefined on input line 116 Citation `He1999d' on page 12 undefined on input line 229 Citation `He2008a' on page 13 undefined on input line 231 Citation `He2008a' on page 5 undefined on input line 114 Citation `Hendricks2005' on page 9 undefined on input line 160 Citation `Hendricks2005' on page 9 undefined on input line 162 Citation `Hurtt1998' on page 13 undefined on input line 237 Citation `ISO:1998:IIP' on page 12 undefined on input line 229 Citation `Keane2004c' on page 13 undefined on input line 231 Citation `Keane2004c' on page 5 undefined on input line 114 Citation `Kimmins1999' on page 5 undefined on input line 118 Citation `Krause2005' on page 14 undefined on input line 250 Citation `Lindenmayer1968a' on page 12 undefined on input line 229 Citation `Lindenmayer1968b' on page 12 undefined on input line 229 Citation `Lischke2016' on page 5 undefined on input line 116 Citation `Mbabazi2011' on page 5 undefined on input line 118 Citation `Medvigy2009' on page 5 undefined on input line 120 Citation `Mitchell1999' on page 9 undefined on input line 162 Citation `Mladenoff1993' on page 12 undefined on input line 229 Citation `Mladenoff1999' on page 12 undefined on input line 229 Citation `Mladenoff2004a' on page 13 undefined on input line 231 Citation `Mladenoff2004a' on page 5 undefined on input line 114 Citation `Moorcroft2001' on page 13 undefined on input line 237 Citation `Moorcroft2001' on page 5 undefined on input line 120 Citation `Nash1970' on page 15 undefined on input line 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/local/texlive/2018/texmf-dist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on intercomparison_paper.pdf (41 pages, 962036 bytes). SyncTeX written on intercomparison_paper.synctex.gz. Transcript written on intercomparison_paper.log. Latexmk: Non-existent bbl file 'intercomparison_paper.bbl' No file intercomparison_paper.bbl. Latexmk: References changed. Latexmk: References changed. 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271 Citation `Noble1980' on page 12 undefined on input line 229 Citation `Parton1983' on page 13 undefined on input line 233 Citation `Parton1983' on page 5 undefined on input line 114 Citation `Parton1987' on page 13 undefined on input line 233 Citation `Parton1987' on page 22 undefined on input line 443 Citation `Parton1987' on page 5 undefined on input line 114 Citation `Pennanen2002' on page 12 undefined on input line 229 Citation `Pennanen2004' on page 12 undefined on input line 229 Citation `Purves2008' on page 13 undefined on input line 237 Citation `Purves2008' on page 6 undefined on input line 122 Citation `R2018' on page 14 undefined on input line 250 Citation `R2018' on page 41 undefined on input line 1162 Citation `Raich2002' on page 14 undefined on input line 246 Citation `Roberts1999' on page 12 undefined on input line 229 Citation `Scheller2007b' on page 12 undefined on input line 229 Citation `Scheller2007b' on page 6 undefined on input line 122 Citation `Scheller2011a' on page 13 undefined on input line 233 Citation `Scheller2011a' on page 6 undefined on input line 122 Citation `Seidl2012' on page 5 undefined on input line 120 Citation `Shifley2017' on page 13 undefined on input line 231 Citation `Shifley2017' on page 5 undefined on input line 114 Citation `Sitch2003' on page 5 undefined on input line 120 Citation `Starr2015' on page 6 undefined on input line 124 Citation `Strigul2008' on page 13 undefined on input line 237 Citation `Strigul2008' on page 13 undefined on input line 244 Citation `Strigul2008' on page 5 undefined on input line 120 Citation `Strigul2008' on page 6 undefined on input line 122 Citation `Sulman2018' on page 5 undefined on input line 114 Citation `Urbanski2007' on page 24 undefined on input line 506 Citation `Urbanski2007' on page 6 undefined on input line 122 Citation `Urbanski2007' on page 7 undefined on input line 136 Citation `Urbanski2007' on page 7 undefined on input line 138 Citation `VonNeumann1966' on page 12 undefined on input line 229 Citation `Wang2014' on page 12 undefined on input line 229 Citation `Warszawski2014' on page 5 undefined on input line 116 Citation `Weng2015' on page 5 undefined on input line 120 Citation `Whelan2013' on page 6 undefined on input line 124 Citation `Wiesner2018' on page 6 undefined on input line 124 Citation `Xi2009' on page 13 undefined on input line 231 Citation `Xi2009' on page 5 undefined on input line 114 Citation `bachelet2001mc1' on page 22 undefined on input line 443 Citation `doi:10.1139/x93-249' on page 13 undefined on input line 237 Reference `eq:mae' on page 15 undefined on input line 264 Reference `eq:ppa' on page 13 undefined on input line 237 Reference `eq:r2' on page 14 undefined on input line 250 Reference `eq:rmse' on page 14 undefined on input line 257 Reference `fig:hf_fluxes.pdf' on page 8 undefined on input line 140 Reference `fig:hf_nee_agc' on page 18 undefined on input line 361 Reference `fig:hf_nee_night_day.pdf' on page 10 undefined on input line 172 Reference `fig:hf_nee_night_day.pdf' on page 8 undefined on input line 148 Reference `fig:hf_species' on page 19 undefined on input line 375 Reference `fig:jerc_fluxes.pdf' on page 9 undefined on input line 164 Reference `fig:jerc_species' on page 21 undefined on input line 425 Reference `fig:radar_chart.pdf' on page 16 undefined on input line 297 Reference `supplementary' on page 7 undefined on input line 128 Reference `tab:hf_ems' on page 17 undefined on input line 327 Reference `tab:jerc_rd' on page 20 undefined on input line 391 Reference `tab:metrics' on page 11 undefined on input line 198 Reference `tab:metrics' on page 15 undefined on input line 273 Reference `tab:overall_means' on page 16 undefined on input line 323 Reference `tab:timings' on page 23 undefined on input line 466 === TeX engine is 'pdfTeX' Latexmk: Found bibliography file(s) [ref.bib] Latexmk: Summary of warnings: Latex failed to resolve 21 reference(s) Latex failed to resolve 105 citation(s) Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'intercomparison_paper.log' for details Latexmk: Use the -f option to force complete processing, unless error was exceeding maximum runs of latex/pdflatex. Latexmk: Errors, so I did not complete making targets ```

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Overfull \hbox (17.93102pt too wide) in paragraph at lines 140--141 []\T1/cmr/m/n/12 (-20) Recent his-tor-i-cal mean daily fluxes of tem-per-a-ture ($[] \OML/cmm/m/it/12 C$\T1/cmr/m/n/12 (-20) ), ecosys-tem res-pi-ra-tion ($\OML/cmm/m/it/12 ^^Vmol CO[] m[]$\T1/cmr/m/n/12 (-20) ), [] File: observations/hf_fluxes.pdf Graphic file (type pdf) Package pdftex.def Info: observations/hf_fluxes.pdf used on input line 143. (pdftex.def) Requested size: 422.77664pt x 422.80096pt. LaTeX Warning: Reference `fig:hf_nee_night_day.pdf' on page 8 undefined on input line 148. File: observations/hf_nee_night_day.pdf Graphic file (type pdf) Package pdftex.def Info: observations/hf_nee_night_day.pdf used on input line 151. (pdftex.def) Requested size: 375.80544pt x 281.84966pt. [8 <./observations/hf_fluxes.pdf>] Package natbib Warning: Citation `Hendricks2005' on page 9 undefined on input line 160. Package natbib Warning: Citation `Drew1998' on page 9 undefined on input line 160. 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[13] Package natbib Warning: Citation `Canham1999' on page 14 undefined on input line 246. Package natbib Warning: Citation `Case2017' on page 14 undefined on input line 246. Package natbib Warning: Citation `Chojnacky2014' on page 14 undefined on input line 246. Package natbib Warning: Citation `Raich2002' on page 14 undefined on input line 246. Package natbib Warning: Citation `Domke2017' on page 14 undefined on input line 246. Package natbib Warning: Citation `R2018' on page 14 undefined on input line 250. Package natbib Warning: Citation `Krause2005' on page 14 undefined on input line 250. LaTeX Warning: Reference `eq:r2' on page 14 undefined on input line 250. LaTeX Warning: Reference `eq:rmse' on page 14 undefined on input line 257. [14] LaTeX Warning: Reference `eq:mae' on page 15 undefined on input line 264. Package natbib Warning: Citation `Nash1970' on page 15 undefined on input line 271. LaTeX Warning: Reference `tab:metrics' on page 15 undefined on input line 273. LaTeX Warning: Reference `tab:metrics' on page 15 undefined on input line 273. [15] LaTeX Warning: Reference `fig:radar_chart.pdf' on page 16 undefined on input line 297. File: models/radar_chart.pdf Graphic file (type pdf) Package pdftex.def Info: models/radar_chart.pdf used on input line 300. (pdftex.def) Requested size: 422.77664pt x 211.38834pt. LaTeX Warning: Reference `tab:overall_means' on page 16 undefined on input line 323. [16 <./models/radar_chart.pdf>] LaTeX Warning: Reference `tab:hf_ems' on page 17 undefined on input line 327. [17] LaTeX Warning: Reference `fig:hf_nee_agc' on page 18 undefined on input line 361. File: models/Sortie-PPA_hf_ems_nee.pdf Graphic file (type pdf) Package pdftex.def Info: models/Sortie-PPA_hf_ems_nee.pdf used on input line 364. (pdftex.def) Requested size: 225.4804pt x 225.47928pt. File: models/Landis2_hf_ems_nee.pdf Graphic file (type pdf) Package pdftex.def Info: models/Landis2_hf_ems_nee.pdf used on input line 365. 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[20 <./models/Sortie-PPA_hf_ems_biomass_sp.pdf, page is rotated 270 degrees> <./models/Landis2_hf_ems_biomass_sp.pdf, page is rotated 270 degrees> <./models/Sortie-PPA_hf_ems_abundance_sp.pdf, page is rotated 270 degrees> <./models/Landis2_hf_ems_abundance_sp.pdf, page is rotated 270 degrees>] LaTeX Warning: Reference `fig:jerc_species' on page 21 undefined on input line 425. File: models/Sortie-PPA_jerc_rd_biomass_sp.pdf Graphic file (type pdf) Package pdftex.def Info: models/Sortie-PPA_jerc_rd_biomass_sp.pdf used on input line 428. (pdftex.def) Requested size: 225.4804pt x 174.23228pt. File: models/Landis2_jerc_rd_biomass_sp.pdf Graphic file (type pdf) Package pdftex.def Info: models/Landis2_jerc_rd_biomass_sp.pdf used on input line 429. (pdftex.def) Requested size: 225.4804pt x 174.23228pt. File: models/Sortie-PPA_jerc_rd_abundance_sp.pdf Graphic file (type pdf) Package pdftex.def Info: models/Sortie-PPA_jerc_rd_abundance_sp.pdf used on input line 430. (pdftex.def) Requested size: 225.4804pt x 174.23228pt. File: models/Landis2_jerc_rd_abundance_sp.pdf Graphic file (type pdf) Package pdftex.def Info: models/Landis2_jerc_rd_abundance_sp.pdf used on input line 431. (pdftex.def) Requested size: 225.4804pt x 174.23228pt. [21] Package natbib Warning: Citation `Parton1987' on page 22 undefined on input line 443. Package natbib Warning: Citation `bachelet2001mc1' on page 22 undefined on input line 443. [22 <./models/Sortie-PPA_jerc_rd_biomass_sp.pdf, page is rotated 270 degrees> <./models/Landis2_jerc_rd_biomass_sp.pdf, page is rotated 270 degrees> <./models/Sortie-PPA_jerc_rd_abundance_sp.pdf, page is rotated 270 degrees> <./models/Landis2_jerc_rd_abundance_sp.pdf, page is rotated 270 degrees>] LaTeX Warning: Reference `tab:timings' on page 23 undefined on input line 466. [23] Package natbib Warning: Citation `Urbanski2007' on page 24 undefined on input line 506. Package natbib Warning: Citation `Hanson2004' on page 24 undefined on input line 506. [24] No file intercomparison_paper.bbl. [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ...ax}$ & $T_{shape}$ & $T_{shape}$ & $f_C_ {fine}$ & $BTOLAI$ & $kLAI... I treat `x_1_2' essentially like `x_1{}_2'. /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ... & $PPRPTS_2$ & $PPRPTS_3$ & $r_{decay}_ w$ & $m_{wood}$ & $m_{shap... I treat `x_1_2' essentially like `x_1{}_2'. /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ... $m_{shape}$ & $drop_month$ & $f_{root}_ c$ & $f_{root}_f$ \\ I treat `x_1_2' essentially like `x_1{}_2'. /Users/null/dev/forestmodelr/manuscript/intercomparison_paper.tex:1096: Double subscript. l.1096 ...$drop_month$ & $f_{root}_c$ & $f_{root}_ f$ \\ I treat `x_1_2' essentially like `x_1{}_2'. [35 ] [36] [37] [38] [39] [40] Package natbib Warning: Citation `R2018' on page 41 undefined on input line 1162. Package natbib Warning: There were undefined citations. Package atveryend Info: Empty hook `BeforeClearDocument' on input line 1164. [41 ] Package atveryend Info: Empty hook `AfterLastShipout' on input line 1164. (./intercomparison_paper.aux) Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 1164. Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 1164. Package rerunfilecheck Warning: File `intercomparison_paper.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. Package rerunfilecheck Info: Checksums for `intercomparison_paper.out': (rerunfilecheck) Before: (rerunfilecheck) After: C24826F54B4CBD873137FC34693910D9;1780. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 1164. ) Here is how much of TeX's memory you used: 10971 strings out of 492649 173781 string characters out of 6129622 330217 words of memory out of 5000000 14359 multiletter control sequences out of 15000+600000 30311 words of font info for 147 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 61i,16n,96p,2190b,516s stack positions out of 5000i,500n,10000p,200000b,80000s {/usr/local/texlive/2018/texmf-dist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on intercomparison_paper.pdf (41 pages, 962036 bytes). PDF statistics: 639 PDF objects out of 1000 (max. 8388607) 503 compressed objects within 6 object streams 147 named destinations out of 1000 (max. 500000) 26710 words of extra memory for PDF output out of 29859 (max. 10000000) ```

James-Yu commented 5 years ago

Your log message does not indicate anything wrong. It seems that the compiler is doing things wrong, instead of the extension.

admercs commented 5 years ago

How do I address this? It's MacTeX run within VS Code. I'm not sure if it's using my external program or an internal one installed by LaTeX Workshop...

James-Yu commented 5 years ago

External one. You need to refer to MacTeX for details.

admercs commented 5 years ago

Interesting. The standard pipeline works fine in Bash:

pdflatex main.tex
bibtex main.aux
pdflatex main.tex
pdflatex main.tex

It appears that latexmk uses latex and is returning an error on the figures (LaTeX Error: Cannot determine size of graphic), as latex does not support PDF figures but pdflatex does. The problem and a workaround are mentioned here:

https://tex.stackexchange.com/questions/17734/cannot-determine-size-of-graphic

A few other warnings were also preventing pdflatex from completing properly, even though it should not have stopped for warnings... WTF. I've cleaned up the files and switched my recipe back to the standard pdflatex -> bibtex -> 2 x pdflatex and that works. However, the simplest solution to this issue was to simply edit ~/.latexmkrc to include:

$latex = 'pdflatex -synctex=1 -interaction=nonstopmode -file-line-error -halt-on-error';
$pdflatex = 'pdflatex -synctex=1 -interaction=nonstopmode -file-line-error -halt-on-error';
@generated_exts = (@generated_exts, 'synctex.gz');

Now I can use latexmk when it calls latex without changing anything in VS Code.

gusbemacbe commented 5 years ago

I use Linux and contain two .bib files and I created ~/.latexmkrc and also the same file .latexmkrc in the folder where I write a .tex file, I wrote like:

$ENV{'TZ'}='America/New_York';
$latex = 'xelatex -synctex=1 -interaction=nonstopmode -file-line-error -halt-on-error -shell-escape';
$xelatex = 'xelatex -synctex=1 -interaction=nonstopmode -file-line-error -halt-on-error -shell-escape';
@generated_exts = (@generated_exts, 'synctex.gz');

And in the file settings.json:

    "latex-workshop.latex.recipes": 
    [
        {
            "name": "latexmk",
            "tools": 
            [
                "latexmk"
            ]
        },
        {
        "name": "xelatex -> bibtex -> xelatex*2",
        "tools": 
        [
            "xelatex",
            "bibtex",
            "xelatex",
            "xelatex"
        ]
        }
    ],
    "latex-workshop.latex.tools": 
    [
        {
            "name": "latexmk",
            "command": "latexmk",
            "args": 
            [
                "-xelatex",
                "-synctex=1",
                "-interaction=nonstopmode",
                "-file-line-error",
                "-shell-escape",
                "%DOC%"
            ]
        },
    ],

And it does not work when the extensions finds the bibliography file and failed to compile:

Log:

Output written on artigo.xdv (22 pages, 507496 bytes).
SyncTeX written on artigo.synctex.gz.
Transcript written on artigo.log.
Latexmk: Index file 'artigo.idx' was written
Latexmk: Missing input file: 'pythontex-files-artigo/artigo.pytxmcr' from line
  'No file pythontex-files-artigo/artigo.pytxmcr.'
Latexmk: Found input bbl file 'artigo.bbl'
Latexmk: Missing input file: 'artigo.brf' from line
  'No file artigo.brf.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'artigo.xdv'
Latexmk: List of undefined refs and citations:
  Citation `antonioleitao' on page 15 undefined on input line 897
  Citation `computacao' on page 2 undefined on input line 216
  Citation `futurasprofissoes' on page 19 undefined on input line 1030
  Citation `futuroai' on page 19 undefined on input line 1020
  Citation `henk' on page 18 undefined on input line 1004
  Citation `luisdamas' on page 15 undefined on input line 891
  Citation `novasprofissoes' on page 20 undefined on input line 1071
  Citation `raulrojas' on page 10 undefined on input line 555
  Citation `romildomalaquias' on page 15 undefined on input line 885
  Citation `schoenfinkel' on page 17 undefined on input line 998
=== TeX engine is 'XeTeX'
Latexmk: Found bibliography file(s) [/usr/local/share/texmf/bibtex/bib/abntex2/abntex2-options.bib referencias.bib]
Latexmk: Summary of warnings from last run of (pdf)latex:
  Latex failed to resolve 11 citation(s)
Collected error summary (may duplicate other messages):
  xelatex: Command for 'xelatex' gave return code 1
      Refer to 'artigo.log' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
Latexmk: Errors, so I did not complete making targets