The user manual does not build when creating the Debian package...
J'ai l'impression qu'au moment de la fabrication du manuel, il ne se trouve pas là où on pense. De ce fait, il ne trouve pas les images. J'ai mis les extensions aux noms de fichiers image dans le .tex. Les fichiers graphiques PDF sont bien générés, mais à la compilation du LaTeX il ne les trouve pas...
Pourtant si je construis le paquet en faisant make pdf, alors là le manuel est correct. Il est généré dans ./share/doc/masschroq-doc/masschroq_manual.pdf, ce qui est un peu inattendu, franchement.
Ensuite, je me suis rendu compte qu'en faisant deux fois le paquet (dpkg-buildpackage -nc), le manuel était bien fabriqué...
Il est trois heures du mat, je vais me coucher...
[ 16%] Converting SVG files...
cd /home/rusconi/devel/masschroq/development/doc/manual/images && /bin/bash /home/rusconi/devel/masschroq/development/CMakeStuff/modules/convert_svg.bash /home/rusconi/devel/masschroq/development/doc/manual/images/figure_detection.svg /home/rusconi/devel/masschroq/development/doc/manual/images/masschroq.svg /home/rusconi/devel/masschroq/development/doc/manual/images/pappso.svg
Converting svg file /home/rusconi/devel/masschroq/development/doc/manual/images/figure_detection.svg to pdf file /home/rusconi/devel/masschroq/development/doc/manual/images/figure_detection.pdf
Converting svg file /home/rusconi/devel/masschroq/development/doc/manual/images/masschroq.svg to pdf file /home/rusconi/devel/masschroq/development/doc/manual/images/masschroq.pdf
Converting svg file /home/rusconi/devel/masschroq/development/doc/manual/images/pappso.svg to pdf file /home/rusconi/devel/masschroq/development/doc/manual/images/pappso.pdf
make[5]: Leaving directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
[ 16%] Built target svg2pdf
make -f doc/manual/CMakeFiles/pdf.dir/build.make doc/manual/CMakeFiles/pdf.dir/depend
make[5]: Entering directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
cd /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/rusconi/devel/masschroq/development /home/rusconi/devel/masschroq/development/doc/manual /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual/CMakeFiles/pdf.dir/DependInfo.cmake --color=
Dependee "/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual/CMakeFiles/pdf.dir/DependInfo.cmake" is newer than depender "/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual/CMakeFiles/pdf.dir/depend.internal".
Dependee "/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual/CMakeFiles/pdf.dir/depend.internal".
Scanning dependencies of target pdf
make[5]: Leaving directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
make -f doc/manual/CMakeFiles/pdf.dir/build.make doc/manual/CMakeFiles/pdf.dir/build
make[5]: Entering directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
[ 50%] Generating ../../share/doc/masschroq-doc/masschroq_complete_input_example.xml
[ 50%] Generating ../../share/doc/masschroq-doc/masschroq_manual.tex
[ 50%] Generating ../../share/doc/masschroq-doc/masschroq_manual.bib
cd /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual && /usr/bin/cmake -E copy /home/rusconi/devel/masschroq/development/doc/manual/masschroq_manual.bib /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/share/doc/masschroq-doc/masschroq_manual.bib
cd /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual && /usr/bin/cmake -E copy /home/rusconi/devel/masschroq/development/doc/manual/masschroq_manual.tex /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/share/doc/masschroq-doc/masschroq_manual.tex
cd /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual && /usr/bin/cmake -E copy /home/rusconi/devel/masschroq/development/doc/manual/masschroq_complete_input_example.xml /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/share/doc/masschroq-doc/masschroq_complete_input_example.xml
[ 66%] Generating ../../share/doc/masschroq-doc/images/transforms.pdf
cd /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual && /usr/bin/cmake -E copy /home/rusconi/devel/masschroq/development/doc/manual/images/transforms.pdf /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/share/doc/masschroq-doc/images/transforms.pdf
[ 83%] Generating ../../share/doc/masschroq-doc/peptide_example_tsv_file.txt
cd /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual && /usr/bin/cmake -E copy /home/rusconi/devel/masschroq/development/doc/manual/peptide_example_tsv_file.txt /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/share/doc/masschroq-doc/peptide_example_tsv_file.txt
[100%] Generating ../../share/doc/masschroq-doc/masschroq_manual.pdf
cd /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/doc/manual && /usr/bin/cmake -E chdir /home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu/share/doc/masschroq-doc /usr/bin/pdflatex -interaction=nonstopmode masschroq_manual.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./masschroq_manual.tex
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-09-24>
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk12.clo))
[snip]
LaTeX Warning: File `images/masschroq.pdf' not found on input line 159.
! Package pdftex.def Error: File `images/masschroq.pdf' not found: using draft
setting.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help.
...
l.159 \includegraphics{images/masschroq.pdf}
(/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/var/lib/texmf/font
s/map/pdftex/updmap/pdftex.map}]
LaTeX Warning: File `images/pappso.pdf' not found on input line 168.
! Package pdftex.def Error: File `images/pappso.pdf' not found: using draft set
ting.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help.
...
l.168 \includegraphics{images/pappso.pdf}
\\
Excluding 'htmlonly' comment. [2] [1] [2]
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/jknapltx/ursfs.fd)
LaTeX Warning: Reference `intro' on page iii undefined on input line 241.
LaTeX Warning: Reference `running-sec' on page iii undefined on input line 244.
LaTeX Warning: Reference `works-sec' on page iii undefined on input line 247.
LaTeX Warning: Reference `xml-sec' on page iii undefined on input line 251.
LaTeX Warning: Reference `pep-sec' on page iii undefined on input line 255.
LaTeX Warning: Reference `cheat-sheet' on page iii undefined on input line 258.
[3] [4]
Chapter 1.
LaTeX Warning: Citation `masschroq' on page 1 undefined on input line 275.
Overfull \hbox (12.88263pt too wide) in paragraph at lines 301--303
[]\T1/cmtt/m/n/12 libmasschroq\T1/cmr/m/n/12 , a li-brary for in-te-gra-tion in
other soft-ware or pro-teomic pipelines;
pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has
been already used, duplicate ignored
<to be read again>
\relax
l.303 \item \ttt
{MassChroQ Studio}, a graphical interface allowing the user
[1]
Underfull \hbox (badness 10000) in paragraph at lines 316--319
[]\T1/cmr/m/n/12 On the Mass-ChroQ de-vel-op-ment page hosted by Source-Sup at
LaTeX Warning: Reference `git' on page 2 undefined on input line 321.
Overfull \hbox (209.83026pt too wide) in paragraph at lines 320--324
[]\T1/cmr/m/n/12 The source code is anony-mously avail-able through the Source-
Sup forge [][]https://sourcesup.renater.fr/projects/masschroq/[][]
pdfTeX warning (ext4): destination with the same identifier (name{page.2}) has
been already used, duplicate ignored
<to be read again>
\relax
l.353 \item D
etermination of items of interest to be quantified. These items
[2]
LaTeX Warning: Reference `groups' on page 3 undefined on input line 362.
LaTeX Warning: Reference `pep-sec' on page 3 undefined on input line 387.
[3]
LaTeX Warning: Reference `git' on page 4 undefined on input line 416.
[4]
Chapter 2.
[5] [6]
LaTeX Warning: Reference `xml-app' on page 7 undefined on input line 525.
LaTeX Warning: Reference `pep-subsec' on page 7 undefined on input line 543.
LaTeX Warning: Reference `pep-sec' on page 7 undefined on input line 544.
LaTeX Warning: Reference `xml-sec' on page 7 undefined on input line 546.
[7]
Overfull \hbox (1.49382pt too wide) in paragraph at lines 588--593
\T1/cmr/m/it/12 gen-er-ated [][]\T1/cmtt/m/n/12 parsed-peptides_input_file.xml
[]\T1/cmr/m/it/12 per-form-ing the anal-y-sis in-struc-tions
[8] [9] [10]
Chapter 3.
LaTeX Warning: Reference `xml-sec' on page 11 undefined on input line 644.
LaTeX Warning: Reference `pep-subsec' on page 11 undefined on input line 675.
LaTeX Warning: Reference `pep-sec' on page 11 undefined on input line 676.
[11]
LaTeX Warning: Reference `iso-labels' on page 12 undefined on input line 695.
Overfull \hbox (8.95709pt too wide) in paragraph at lines 698--698
[]\T1/cmr/bx/n/17.28 Parsing of LC-MS/MS files in mzXML or mzML
[12] [13]
LaTeX Warning: Reference `smart_quanti' on page 14 undefined on input line 802.
[14] [15]
Overfull \hbox (8.17963pt too wide) in paragraph at lines 873--875
[]\T1/cmr/m/n/12 the \T1/cmr/m/it/12 Moulon peak-detection \T1/cmr/m/n/12 metho
d : a sim-ple thresh-old peak de-tec-tion method;
LaTeX Warning: Citation `serra' on page 16 undefined on input line 919.
LaTeX Warning: Citation `handbook' on page 16 undefined on input line 922.
LaTeX Warning: Citation `edge' on page 16 undefined on input line 922.
[16]
LaTeX Warning: Citation `leymarie' on page 17 undefined on input line 929.
LaTeX Warning: Citation `kluwer' on page 17 undefined on input line 930.
[17 <./images/transforms.pdf>]
LaTeX Warning: File `images/figure_detection.pdf' not found on input line 951.
! Package pdftex.def Error: File `images/figure_detection.pdf' not found: using
draft setting.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help.
...
l.951 ...\textheight]{images/figure_detection.pdf}
Overfull \hbox (13.55396pt too wide) in paragraph at lines 951--952
[][]
[18] [19] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
LaTeX Warning: Citation `meyer' on page 20 undefined on input line 1039.
[20]
Underfull \vbox (badness 1275) has occurred while \output is active [21]
LaTeX Warning: Citation `obiwarp' on page 22 undefined on input line 1094.
Underfull \hbox (badness 10000) in paragraph at lines 1093--1095
[]\T1/cmr/m/n/12 For more in-for-ma-tion on the OBI-Warp align-ment li-brary se
e
[22]
LaTeX Warning: Reference `peak_matching' on page 23 undefined on input line 117
2.
[23] [24]
LaTeX Warning: Reference `alignment_files' on page 25 undefined on input line 1
232.
LaTeX Warning: Reference `data_files' on page 25 undefined on input line 1240.
[25] [26] [27] [28]
Chapter 4.
LaTeX Warning: Reference `xml-app' on page 29 undefined on input line 1431.
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(./masschroq_complete_input_example.xml
consecutive:
) [29] (./masschroq_complete_input_example.xml
consecutive:
) [30] (./masschroq_complete_input_example.xml
consecutive:
) [31] (./masschroq_complete_input_example.xml
consecutive:
) [32] [33] (./masschroq_complete_input_example.xml
consecutive:
) [34] (./masschroq_complete_input_example.xml
consecutive:
)
LaTeX Warning: Reference `cheat-sheet' on page 35 undefined on input line 1603.
[35] (./masschroq_complete_input_example.xml
consecutive:
)
Overfull \hbox (3.41837pt too wide) in paragraph at lines 1642--1644
[]\T1/cmr/m/n/12 The size of the mass tol-er-ance win-dow of ex-trac-tion in \T
1/cmtt/m/n/12 ppm_range \T1/cmr/m/n/12 or \T1/cmtt/m/n/12 mz_range
[36] (./masschroq_complete_input_example.xml
consecutive:
) [37] (./masschroq_complete_input_example.xml
consecutive:
)
LaTeX Warning: Reference `peak_matching' on page 38 undefined on input line 170
2.
LaTeX Warning: Reference `post_matching' on page 38 undefined on input line 171
1.
[38] [39] (./masschroq_complete_input_example.xml
consecutive:
)
LaTeX Warning: Reference `iso-labels' on page 40 undefined on input line 1723.
(./masschroq_complete_input_example.xml
consecutive:
) (./masschroq_complete_input_example.xml
consecutive:
) [40] (./masschroq_complete_input_example.xml
consecutive:
)
LaTeX Warning: Reference `xml-app' on page 41 undefined on input line 1781.
[41] [42] (./masschroq_complete_input_example.xml
consecutive:
) [43] [44] [45] [46]
Chapter 5.
(./masschroq_complete_input_example.xml
consecutive:
) [47]
LaTeX Warning: Reference `pep-app' on page 48 undefined on input line 1942.
(./peptide_example_tsv_file.txt) (./peptide_example_tsv_file.txt) [48] [49]
[50]
Chapter 6.
Overfull \hbox (4.34296pt too wide) in paragraph at lines 2033--2035
[]\T1/cmr/bx/n/12 write_time_values_output_dir (di-rec-tory path)\T1/cmr/m/n/12
: the di-rec-tory where
[51] [52] [53]
Overfull \hbox (3.13634pt too wide) in paragraph at lines 2164--2170
[]\T1/cmr/bx/n/12 detection_threshold_on_min (in-ten-sity value)\T1/cmr/m/n/12
: thresh-old on the open
LaTeX Warning: Reference `peak_matching' on page 54 undefined on input line 217
7.
LaTeX Warning: Reference `post_matching' on page 54 undefined on input line 218
0.
[54] [55] [56] [57] [58]
Appendix A.
(./masschroq_complete_input_example.xml [59]
Underfull \vbox (badness 10000) has occurred while \output is active [60]
Underfull \vbox (badness 10000) has occurred while \output is active [61])
[62]
Appendix B.
(./peptide_example_tsv_file.txt [63]) [64]
No file masschroq_manual.bbl.
(./masschroq_manual.aux)
Package rerunfilecheck Warning: File `masschroq_manual.out' has changed.
(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)
[snip]
Output written on masschroq_manual.pdf (70 pages, 637079 bytes).
Transcript written on masschroq_manual.log.
make[5]: *** [doc/manual/CMakeFiles/pdf.dir/build.make:87: share/doc/masschroq-doc/masschroq_manual.pdf] Error 1
make[5]: *** Deleting file 'share/doc/masschroq-doc/masschroq_manual.pdf'
make[5]: Leaving directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
make[4]: *** [CMakeFiles/Makefile2:557: doc/manual/CMakeFiles/pdf.dir/all] Error 2
make[4]: Leaving directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:564: doc/manual/CMakeFiles/pdf.dir/rule] Error 2
make[3]: Leaving directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:390: pdf] Error 2
make[2]: Leaving directory '/home/rusconi/devel/masschroq/development/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" pdf VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:29: override_dh_auto_build] Error 2
make[1]: Leaving directory '/home/rusconi/devel/masschroq/development'
make: *** [debian/rules:15: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2