[Debian-med-packaging] Problems with gdcm-3.0.X

[Mathieu Malaterre]

On Tue, Oct 1, 2019 at 5:12 PM Mathieu Malaterre <malat at debian.org> wrote:
>
> On Tue, Oct 1, 2019 at 5:08 PM Gert Wollny <gw.fossdev at gmail.com> wrote:
> >
> > Hello Mathieu,
> >
> > I'm having problems with building the package for gdcm-3.0.X, something
> > goes wrong with the Doxygen conversion, see log:
> >
> >   https://salsa.debian.org/med-team/gdcm/-/jobs/344630
> >
> > Do you have any idea how I could fix this?
>
> Log seems either truncated, or this yet another regression in the
> latex package. Something I can only debug locally changing manually
> the value for LATEX_BATCHMODE to NO.
>
> Will keep you posted

The failure is in the VTK/doxygen step:

$ /usr/bin/bash -x
/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/doc_makeall.sh
+ export DOXYGEN_PROG=/usr/bin/doxygen
+ DOXYGEN_PROG=/usr/bin/doxygen
+ export GZIP_PROG=/usr/bin/gzip
+ GZIP_PROG=/usr/bin/gzip
+ export GNUPLOT_PROG=GNUPLOT_EXECUTABLE-NOTFOUND
+ GNUPLOT_PROG=GNUPLOT_EXECUTABLE-NOTFOUND
+ export HHC_PROG=
+ HHC_PROG=
+ export MV_PROG=/usr/bin/mv
+ MV_PROG=/usr/bin/mv
+ export CP_PROG=/usr/bin/cp
+ CP_PROG=/usr/bin/cp
+ export PERL_PROG=/usr/bin/perl
+ PERL_PROG=/usr/bin/perl
+ export RM_PROG=/usr/bin/rm
+ RM_PROG=/usr/bin/rm
+ export TAR_PROG=/usr/bin/tar
+ TAR_PROG=/usr/bin/tar
+ export WGET_PROG=/usr/bin/wget
+ WGET_PROG=/usr/bin/wget
+ export PROJECT_NAME=vtkgdcm
+ PROJECT_NAME=vtkgdcm
+ export PATH_TO_VTK_DOX_SCRIPTS=/usr/share/vtk-7.1/doxygen
+ PATH_TO_VTK_DOX_SCRIPTS=/usr/share/vtk-7.1/doxygen
+ export PATH_TO_VTKGDCM_FINAL_PATH=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/html
+ PATH_TO_VTKGDCM_FINAL_PATH=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/html
+ export SOURCE_DIR=
+ SOURCE_DIR=
+ export REL_PATH_TO_TOP=.
+ REL_PATH_TO_TOP=.
+ export DOXTEMP=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk
+ DOXTEMP=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk
+ export INTERMEDIATE_DOX_DIR=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/dox
+ INTERMEDIATE_DOX_DIR=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/dox
+ export CVSWEB_CHECKOUT=http://public.kitware.com/cgi-bin/cvsweb.cgi/~checkout~/vtkgdcm/
+ CVSWEB_CHECKOUT=http://public.kitware.com/cgi-bin/cvsweb.cgi/~checkout~/vtkgdcm/
+ export 'CVSWEB_CHECKOUT_SUFFIX=?cvsroot=vtkgdcm'
+ CVSWEB_CHECKOUT_SUFFIX='?cvsroot=vtkgdcm'
+ export DOXYFILE=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/doxyfile
+ DOXYFILE=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/doxyfile
+ export OUTPUT_DIRECTORY=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/doc
+ OUTPUT_DIRECTORY=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/doc
+ export ALLOW_ERASE_OUTPUT_DIRECTORY=ON
+ ALLOW_ERASE_OUTPUT_DIRECTORY=ON
+ export COMPILE_HTML_HELP=OFF
+ COMPILE_HTML_HELP=OFF
+ export RESULTING_HTML_HELP_FILE=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/vtkgdcm.chm
+ RESULTING_HTML_HELP_FILE=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/vtkgdcm.chm
+ export CREATE_HTML_TARZ_ARCHIVE=ON
+ CREATE_HTML_TARZ_ARCHIVE=ON
+ export RESULTING_HTML_TARZ_ARCHIVE_FILE=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/vtkgdcm-html.tar.gz
+ RESULTING_HTML_TARZ_ARCHIVE_FILE=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/vtkgdcm-html.tar.gz
+ export DOWNLOAD_VTK_TAGFILE=OFF
+ DOWNLOAD_VTK_TAGFILE=OFF
+ export VTK_TAGFILE=vtkNightlyDoc.tag
+ VTK_TAGFILE=vtkNightlyDoc.tag
+ export VTK_TAGFILE_REMOTE_DIR=http://www.vtk.org/files/nightly
+ VTK_TAGFILE_REMOTE_DIR=http://www.vtk.org/files/nightly
+ export VTK_TAGFILE_DEST_DIR=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk
+ VTK_TAGFILE_DEST_DIR=/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk
+ cd /tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk
+ echo 'Convert the VTK headers to the Doxygen format.'
Convert the VTK headers to the Doxygen format.
+ test x/usr/bin/perl '!=' xNOTFOUND
+ /usr/bin/perl /usr/share/vtk-7.1/doxygen/doc_header2doxygen.pl --to
/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/dox --relativeto
'' '' /Utilities/Xdmf2/vtk /Utilities/VTKPythonWrapping/Executable
/Utilities/VTKClientServer /Qt/Chart /Qt/Components /Qt/Core
/Qt/Python /Qt/Widgets /Qt/Testing /Applications/Client
/Applications/OverView /Applications/OverView/Core /Common/KWCommon
/Servers/Common /Servers/Filters /Servers/ServerManager
doc_header2doxygen.pl 0.9, by Sebastien Barre et al.
Collecting...
Converting...
 => 0 files converted in 0 s.
Finished in 0 s.
+ test x '!=' x
+ echo 'Convert the VTK headers to the Doxygen format - done'
Convert the VTK headers to the Doxygen format - done
+ echo 'Build the full-text index.'
Build the full-text index.
+ test x/usr/bin/perl '!=' xNOTFOUND
+ cp /usr/share/vtk-7.1/doxygen/doc_index.stop doc_index.stop
+ /usr/bin/perl /usr/share/vtk-7.1/doxygen/doc_index.pl --project
vtkgdcm --stop doc_index.stop --store doc_vtkgdcm_index.dox --to
/tmp/gdcm/obj-x86_64-linux-gnu/Utilities/doxygen/vtk/dox ''
/Utilities/Xdmf2/vtk /Utilities/VTKPythonWrapping/Executable
/Utilities/VTKClientServer /Qt/Chart /Qt/Components /Qt/Core
/Qt/Python /Qt/Widgets /Qt/Testing /Applications/Client
/Applications/OverView /Applications/OverView/Core /Common/KWCommon
/Servers/Common /Servers/Filters /Servers/ServerManager
doc_index.pl 0.22, by Sebastien Barre
Reading stop-words from doc_index.stop...
 => 722 stop-word(s) read.
Collecting files...
Indexing...
 => 0 word(s) grabbed in 0 file(s) in 0 s.
Removing...
 => 0 word(s) removed.
Grouping...
 => 0 word(s) grouped.
Normalizing...
 => normalized to lowercase.
Building page doc...
 => 0 words(s) documented in 0 s.
Illegal division by zero at /usr/share/vtk-7.1/doxygen/doc_index.pl
line 600, <STOPFILE> chunk 729.
+ echoexit 'Problem building full-text index'
+ echo 'Problem building full-text index'
Problem building full-text index
+ exit 1

I do not know how to fix this ATM. I'll try to figure out what this
script is supposed to do with vtk6 and compare behavior.


> > many thanks,
> > Gert
> >
> >
> >