gdcmSerieHelper.h: No such file or directory

[KrisThielemans]

Issue:
Using this package on ubuntu 18.04 leads to the following error

In file included from /home/sirfuser/devel/STIR/src/IO/ITKImageInputFileFormat.cxx:41:0:
/home/sirfuser/miniconda3/include/ITK-5.0/itkGDCMSeriesFileNames.h:25:10: fatal error: gdcmSerieHelper.h: No such file or directory
 #include "gdcmSerieHelper.h"
          ^~~~~~~~~~~~~~~~~~~
compilation terminated.

My understanding is that this is because I have no system GDCM, and this package does not depend on gdcm, see #1.

sudo apt install libgdcm2-dev

did not help even (just like here) though this installs /usr/include/gdcm-2.8/gdcmSerieHelper.h, which might be an ITK issue?

Environment (conda list):

``` $ conda list # packages in environment at /home/sirfuser/miniconda3: # # Name Version Build Channel _libgcc_mutex 0.1 main asn1crypto 1.2.0 py37_0 beautifulsoup4 4.8.1 py37_0 blinker 1.4 py37_0 bzip2 1.0.8 h7b6447c_0 ca-certificates 2019.11.28 hecc5488_0 conda-forge certifi 2019.11.28 py37_0 conda-forge cffi 1.13.2 py37h2e261b9_0 chardet 3.0.4 py37_1003 conda 4.8.0 py37_0 conda-forge conda-build 3.18.11 py37_0 conda-forge conda-forge-pinning 2019.12.02 0 conda-forge conda-package-handling 1.6.0 py37h7b6447c_0 conda-smithy 3.6.3 py_0 conda-forge cryptography 2.8 py37h1ba5d50_0 deprecated 1.2.6 py_0 expat 2.2.6 he6710b0_0 fftw 3.3.8 nompi_h7f3a6c3_1110 conda-forge filelock 3.0.12 py_0 git 2.23.0 pl526hacde149_0 gitdb2 2.0.6 py_0 gitpython 3.0.5 py_0 glob2 0.7 py_0 hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge idna 2.8 py37_0 isodate 0.6.0 py_1 jinja2 2.10.3 py_0 jpeg 9c h14c3975_1001 conda-forge krb5 1.16.1 h173b8e3_7 libarchive 3.3.3 h5d8350f_5 libcurl 7.67.0 h20c2e04_0 libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_2 conda-forge libitk 5.0.1 h2b26915_1 conda-forge libitk-devel 5.0.1 he1b5a44_1 conda-forge liblief 0.9.0 h7725739_2 libpng 1.6.37 hed695b0_0 conda-forge libssh2 1.8.2 h1ba5d50_0 libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.1.0 h2733197_0 libxml2 2.9.9 hea5a465_1 lz4-c 1.8.1.2 h14c3975_0 lzo 2.10 h49e0be7_2 markupsafe 1.1.1 py37h7b6447c_0 msrest 0.6.10 py_0 conda-forge ncurses 6.1 he6710b0_1 oauthlib 3.1.0 py_0 openssl 1.1.1d h516909a_0 conda-forge patchelf 0.10 he6710b0_0 pcre 8.43 he6710b0_0 perl 5.26.2 h14c3975_0 pip 19.3.1 py37_0 pkginfo 1.5.0.1 py37_0 psutil 5.6.7 py37h7b6447c_0 py-lief 0.9.0 py37h7725739_2 pycosat 0.6.3 py37h14c3975_0 pycparser 2.19 py37_0 pycrypto 2.6.1 py37h14c3975_9 pygithub 1.43.6 py37_0 conda-forge pyjwt 1.7.1 py37_0 pyopenssl 19.1.0 py37_0 pysocks 1.7.1 py37_0 python 3.7.4 h265db76_1 python-libarchive-c 2.8 py37_13 pytz 2019.3 py_0 pyyaml 5.1.2 py37h7b6447c_0 readline 7.0 h7b6447c_5 requests 2.22.0 py37_1 requests-oauthlib 1.3.0 py_0 ripgrep 0.10.0 hc07d326_0 ruamel.yaml 0.16.5 py37h7b6447c_1 ruamel.yaml.clib 0.2.0 py37h7b6447c_0 ruamel_yaml 0.15.46 py37h14c3975_0 setuptools 42.0.2 py37_0 six 1.13.0 py37_0 smmap2 2.0.5 py37_0 soupsieve 1.9.5 py37_0 sqlite 3.30.1 h7b6447c_0 tk 8.6.8 hbc83047_0 toolz 0.10.0 py_0 tqdm 4.40.0 py_0 urllib3 1.25.7 py37_0 vsts-python-api 0.1.22 py_0 conda-forge wheel 0.33.6 py37_0 wrapt 1.11.2 py37h7b6447c_0 xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zlib 1.2.11 h7b6447c_3 zstd 1.3.7 h0b5b093_0 ```

Details about conda and system ( conda info ):

$ conda info

     active environment : base
    active env location : /home/sirfuser/miniconda3
            shell level : 1
       user config file : /home/sirfuser/.condarc
 populated config files : /home/sirfuser/.condarc
          conda version : 4.8.0
    conda-build version : 3.18.11
         python version : 3.7.4.final.0
       virtual packages : __glibc=2.27
       base environment : /home/sirfuser/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/sirfuser/miniconda3/pkgs
                          /home/sirfuser/.conda/pkgs
       envs directories : /home/sirfuser/miniconda3/envs
                          /home/sirfuser/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.0 requests/2.22.0 CPython/3.7.4 Linux/4.15.0-29-generic ubuntu/18.04.2 glibc/2.27
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False

[bergtholdt]

Hi,

I have the same issue when trying to compile against libitk-devel=5.0.1. I assume that the gdcm headers from ITK's 3rd party folder aren't installed.