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

Wed Oct 2 16:35:55 BST 2019

On Tue, Oct 1, 2019 at 9:24 PM Mathieu Malaterre <malat at debian.org> wrote:
>
> 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.

So issue was introduced when switching from subdirs() to
add_subdirectory(). You may want to cherry-pick:

36ad8a228e602b4724ff627cda3b2ba427640ddc

Also I needed:

d24eaa39ed041d91c414069149a344d20fb9adf8

to fix a compilation error (parallel build).

You'll also need to fix d/rules:

# See #664188
sed -i -e "s/FATAL_ERROR/STATUS/g"
obj-*/CMake/ExportConfiguration/CMakeFiles/Export/lib/x86_64-linux-gnu/gdcm-2.8/GDCMTargets-*.cmake

Maybe use an '*' instead of '2.8'

I am releasing 3.0.3 in a couple of minutes so you may want to wait
for this release (it does contains two of your patches, thanks !)

-M

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