[Debian-med-packaging] Bug#924834: librostlab-blast: FTBFS: mv: cannot stat 'refman.pdf': No such file or directory
Lucas Nussbaum
lucas at debian.org
Sun Mar 17 18:22:31 GMT 2019
Source: librostlab-blast
Version: 1.0.1-9
Severity: serious
Tags: buster sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20190315 qa-ftbfs
Justification: FTBFS in buster on amd64
Hi,
During a rebuild of all packages in buster (in a buster chroot, not a
sid chroot), your package failed to build on amd64.
Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/lib'
> rm -rf ../doxygen-doc
> SRCDIR='.' PROJECT='librostlab-blast' DOCDIR='../doxygen-doc' VERSION='1.0.1' PERL_PATH='/usr/bin/perl' HAVE_DOT='YES' DOT_PATH='/usr/bin' GENERATE_MAN='NO' GENERATE_RTF='NO' GENERATE_XML='NO' GENERATE_HTMLHELP='NO' GENERATE_CHI='NO' GENERATE_HTML='YES' GENERATE_LATEX='YES' /usr/bin/doxygen ./Doxyfile
> warning: Tag `SYMBOL_CACHE_SIZE' at line 290 of file `./Doxyfile' has become obsolete.
> To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> warning: Tag `SHOW_DIRECTORIES' at line 490 of file `./Doxyfile' has become obsolete.
> To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> warning: Tag `HTML_ALIGN_MEMBERS' at line 847 of file `./Doxyfile' has become obsolete.
> To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> warning: Tag `USE_INLINE_TREES' at line 1032 of file `./Doxyfile' has become obsolete.
> To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> warning: Tag `XML_SCHEMA' at line 1257 of file `./Doxyfile' has become obsolete.
> To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> warning: Tag `XML_DTD' at line 1263 of file `./Doxyfile' has become obsolete.
> To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> warning: doxygen no longer ships with the FreeSans font.
> You may want to clear or change DOT_FONTNAME.
> Otherwise you run the risk that the wrong font is being used for dot generated graphs.
> error: Tag file `/usr/share/doc/librostlab-doc/librostlab.tag' does not exist or is not a file. Skipping it...
> /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-location.h:34: warning: the name `location.hh' supplied as the second argument in the \file statement is not an input file
> /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-parser.h:35: warning: the name `y.tab.h' supplied as the second argument in the \file statement is not an input file
> Notice: Output directory `../doxygen-doc' does not exist. I have created it for you.
> Searching for include files...
> Searching for example files...
> Searching for files in directory /<<PKGBUILDDIR>>/examples
> Searching for images...
> Searching for dot files...
> Searching for msc files...
> Searching for dia files...
> Searching for files to exclude
> Searching INPUT for files to process...
> Searching for files in directory /<<PKGBUILDDIR>>/lib/rostlab
> Reading and parsing tag files
> Parsing files
> Preprocessing /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-driver.h...
> Parsing file /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-driver.h...
> Preprocessing /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-location.h...
> Parsing file /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-location.h...
> Preprocessing /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-parser.h...
> Parsing file /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-parser.h...
> Preprocessing /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-position.h...
> Parsing file /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-position.h...
> Preprocessing /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-stack.h...
> Parsing file /<<PKGBUILDDIR>>/lib/rostlab/blast-parser-stack.h...
> Preprocessing /<<PKGBUILDDIR>>/lib/rostlab/blast-result.h...
> Parsing file /<<PKGBUILDDIR>>/lib/rostlab/blast-result.h...
> Building group list...
> Building directory list...
> Building namespace list...
> Building file list...
> Building class list...
> Associating documentation with classes...
> Computing nesting relations for classes...
> Building example list...
> Searching for enumerations...
> Searching for documented typedefs...
> Searching for members imported via using declarations...
> Searching for included using directives...
> Searching for documented variables...
> Building interface member list...
> Building member list...
> Searching for friends...
> Searching for documented defines...
> Computing class inheritance relations...
> Computing class usage relations...
> Flushing cached template relations that have become invalid...
> Computing class relations...
> Add enum values to enums...
> Searching for member function documentation...
> Creating members for template instances...
> Building page list...
> Search for main page...
> Computing page relations...
> Determining the scope of groups...
> Sorting lists...
> Freeing entry tree
> Determining which enums are documented
> Computing member relations...
> Building full member lists recursively...
> Adding members to member groups.
> Computing member references...
> Inheriting documentation...
> Generating disk names...
> Adding source references...
> Adding xrefitems...
> Sorting member lists...
> Computing dependencies between directories...
> Generating citations page...
> Counting data structures...
> Resolving user defined references...
> Finding anchors and sections in the documentation...
> Transferring function references...
> Combining using relations...
> Adding members to index pages...
> Generating style sheet...
> Generating search indices...
> Generating example documentation...
> Generating file sources...
> Generating code for file rostlab/blast-parser-driver.h...
> Generating code for file rostlab/blast-parser-location.h...
> Generating code for file rostlab/blast-parser-parser.h...
> Generating code for file rostlab/blast-parser-position.h...
> Generating code for file rostlab/blast-parser-stack.h...
> Generating code for file rostlab/blast-result.h...
> Generating file documentation...
> Generating docs for file rostlab/blast-parser-driver.h...
> Generating docs for file rostlab/blast-parser-location.h...
> Generating docs for file rostlab/blast-parser-parser.h...
> Generating docs for file rostlab/blast-parser-position.h...
> Generating docs for file rostlab/blast-parser-stack.h...
> Generating docs for file rostlab/blast-result.h...
> Generating page documentation...
> Generating group documentation...
> Generating class documentation...
> Generating namespace index...
> Generating docs for namespace rostlab
> Generating docs for namespace rostlab::blast
> Generating docs for compound rostlab::blast::hit...
> Generating docs for compound rostlab::blast::hsp...
> Generating docs for compound rostlab::blast::location...
> Generating docs for compound rostlab::blast::oneline...
> Generating docs for compound rostlab::blast::parser...
> Generating docs for nested compound rostlab::blast::parser::basic_symbol...
> Generating docs for nested compound rostlab::blast::parser::by_type...
> Generating docs for nested compound rostlab::blast::parser::semantic_type...
> Generating docs for nested compound rostlab::blast::parser::stack::slice...
> Generating docs for nested compound rostlab::blast::parser::symbol_type...
> Generating docs for nested compound rostlab::blast::parser::syntax_error...
> Generating docs for nested compound rostlab::blast::parser::token...
> Generating docs for compound rostlab::blast::parser_driver...
> Generating docs for compound rostlab::blast::parser_error...
> Generating docs for compound rostlab::blast::position...
> Generating docs for compound rostlab::blast::result...
> Generating docs for compound rostlab::blast::round...
> Generating graph info page...
> Generating directory documentation...
> Generating index page...
> Generating page index...
> Generating module index...
> Generating namespace index...
> Generating namespace member index...
> Generating annotated compound index...
> Generating alphabetical compound index...
> Generating hierarchical class index...
> Generating graphical class hierarchy...
> Generating member index...
> Generating file index...
> Generating file member index...
> Generating example index...
> finalizing index lists...
> writing tag file...
> Running dot...
> Generating dot graphs using 5 parallel threads...
> Running dot for graph 1/54
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> Patching output file 23/23
> lookup cache used 541/65536 hits=4560 misses=586
> finished...
> cd ../doxygen-doc/latex; \
> rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
> /usr/bin/pdflatex refman.tex; \
> /usr/bin/makeindex refman.idx; \
> /usr/bin/pdflatex refman.tex; \
> countdown=5; \
> while /bin/egrep 'Rerun (LaTeX|to get cross-references right)' \
> refman.log > /dev/null 2>&1 \
> && test $countdown -gt 0; do \
> /usr/bin/pdflatex refman.tex; \
> countdown=`expr $countdown - 1`; \
> done; \
> mv refman.pdf ../librostlab-blast.pdf
> This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
> restricted \write18 enabled.
> entering extended mode
> (./refman.tex
> LaTeX2e <2018-12-01>
> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
> Document Class: book 2018/09/03 v1.4i Standard LaTeX document class
> (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
> (/usr/share/texlive/texmf-dist/tex/latex/base/fixltx2e.sty
>
> Package fixltx2e Warning: fixltx2e is not required with releases after 2015
> (fixltx2e) All fixes are now in the LaTeX kernel.
> (fixltx2e) See the latexrelease package for details.
>
> ) (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty) (./doxygen.sty
> (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
> (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)
> (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tabu/tabu.sty
> (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/tools/tabularx.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/multirow/multirow.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjustbox.sty
> (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
> (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
> (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
> (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))
> (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjcalc.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/trimclip.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
> (/usr/share/texlive/texmf-dist/tex/latex/collectbox/collectbox.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/tc-pdftex.def))
> (/usr/share/texlive/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
> (/usr/share/texlive/texmf-dist/tex/latex/wasysym/wasysym.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
> (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
> (/usr/share/texlive/texmf-dist/tex/latex/psnfss/helvet.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/psnfss/courier.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/sectsty/sectsty.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
> (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tocloft/tocloft.sty)
> Writing index file refman.idx
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
> (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/backref.sty
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def)
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
> (/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
> (/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty))
> No file refman.aux.
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
> (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
> (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
> [Loading MPS to PDF converter (version 2006.09.02).]
> ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
> *geometry* driver: auto-detecting
> *geometry* detected driver: pdftex
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd)
> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
> nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2]
> Chapter 1.
> (./namespaces.tex
>
> LaTeX Warning: Reference `namespacerostlab' on page 1 undefined on input line 3
> .
>
>
> LaTeX Warning: Reference `namespacerostlab_1_1blast' on page 1 undefined on inp
> ut line 4.
>
> ) [1] [2]
> Chapter 2.
> (./hierarchy.tex
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1basic__symbol' on
> page 3 undefined on input line 3.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1by__type' on page
> 3 undefined on input line 4.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1basic__symbol' on
> page 3 undefined on input line 6.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1symbol__type' on
> page 3 undefined on input line 8.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1hit' on page 3 undefined on
> input line 11.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1hsp' on page 3 undefined on
> input line 12.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1location' on page 3 undefine
> d on input line 13.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1oneline' on page 3 undefine
> d on input line 14.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser' on page 3 undefined
> on input line 15.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser__driver' on page 3 un
> defined on input line 16.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1position' on page 3 undefine
> d on input line 17.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1result' on page 3 undefined
> on input line 18.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1round' on page 3 undefined
> on input line 19.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser__error' on page 3 und
> efined on input line 21.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1syntax__error' on
> page 3 undefined on input line 24.
>
>
> LaTeX Warning: Reference `unionrostlab_1_1blast_1_1parser_1_1semantic__type' on
> page 3 undefined on input line 26.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser_1_1stack_1_1slice' on
> page 3 undefined on input line 27.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1token' on page 3
> undefined on input line 28.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1basic__symbol' on
> page 3 undefined on input line 30.
>
> ) [3] [4]
> Chapter 3.
> (./annotated.tex
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1basic__symbol' on
> page 5 undefined on input line 3.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1by__type' on page
> 5 undefined on input line 4.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1hit' on page 5 undefined on
> input line 5.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1hsp' on page 5 undefined on
> input line 6.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1location' on page 5 undefine
> d on input line 7.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1oneline' on page 5 undefine
> d on input line 8.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser' on page 5 undefined
> on input line 9.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser__driver' on page 5 un
> defined on input line 10.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser__error' on page 5 und
> efined on input line 11.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1position' on page 5 undefine
> d on input line 12.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1result' on page 5 undefined
> on input line 13.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1round' on page 5 undefined
> on input line 14.
>
>
> LaTeX Warning: Reference `unionrostlab_1_1blast_1_1parser_1_1semantic__type' on
> page 5 undefined on input line 15.
>
>
> LaTeX Warning: Reference `classrostlab_1_1blast_1_1parser_1_1stack_1_1slice' on
> page 5 undefined on input line 16.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1symbol__type' on
> page 5 undefined on input line 17.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1syntax__error' on
> page 5 undefined on input line 18.
>
>
> LaTeX Warning: Reference `structrostlab_1_1blast_1_1parser_1_1token' on page 5
> undefined on input line 19.
>
> ) [5] [6]
> Chapter 4.
> (./files.tex
>
> LaTeX Warning: Reference `blast-parser-driver_8h' on page 7 undefined on input
> line 3.
>
>
> LaTeX Warning: Reference `blast-parser-location_8h' on page 7 undefined on inpu
> t line 4.
>
>
> LaTeX Warning: Reference `blast-parser-parser_8h' on page 7 undefined on input
> line 5.
>
>
> LaTeX Warning: Reference `blast-parser-position_8h' on page 7 undefined on inpu
> t line 6.
>
>
> LaTeX Warning: Reference `blast-parser-stack_8h' on page 7 undefined on input l
> ine 7.
>
>
> LaTeX Warning: Reference `blast-result_8h' on page 7 undefined on input line 8.
>
>
> ) [7] [8]
> Chapter 5.
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> Chapter 5.
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> Transcript written on refman.log.
> mv: cannot stat 'refman.pdf': No such file or directory
> make[2]: *** [Makefile:902: ../doxygen-doc/librostlab-blast.pdf] Error 1
The full build log is available from:
http://aws-logs.debian.net/2019/03/15/librostlab-blast_1.0.1-9_testing.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
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