On Wed, Aug 1, 2012 at 8:36 PM, Melissa Linkert <meli...@glencoesoftware.com> wrote: > Hi Mathieu, > >> >> What I still do not really understand is that after a git clone of >> >> bioformat I can see I am getting the non-free >> >> ./jar/clibwrapper_jiio.jar; but I cannot find the shared lib anywhere. >> >> Should use download/install it separately ? >> > >> > The shared library is not required by Bio-Formats, and in fact having it >> > does not even improve functionality. So it is expected that the user >> > will download and install it themselves, if they feel that they need it. >> >> I think I misunderstood your comment. Here is what I am doing: > > No worries, I think I misunderstood what you were asking as well. > >> wget https://github.com/openmicroscopy/bioformats/tarball/v4.4.1 >> tar xvfz v4.4.1 >> cd openmicroscopy-bioformats-68cf74c >> find . -name \*.jar -delete >> export ANT_OPTS=-Dbuild.sysclasspath=first >> export >> CLASSPATH=/usr/share/java/velocity.jar:/usr/share/java/forms.jar:/usr/share/java/commons-logging.jar:/usr/share/java/ij.jar:/usr/share/java/slf4j-api.jar:/usr/share/java/bnd.jar:/usr/share/java/net.luminis.build.plugin.jar:/usr/share/java/testng.jar:/usr/share/java/ncCore-4.3.jar:/usr/share/java/ant-contrib.jar >> ant -f build.xml jar-jai >> >> which leads to error like: > *snip* >> Could you please let me (again?) how am I supposed to compile >> bioformats when I decided NOT to use 'clibwrapper_jiio.jar'. > > You do need clibwrapper_jiio.jar in order to compile the JAI JAR. What > you do not need is the corresponding libclib_jiio.so library, which is what > I assumed you were referring to originally. > > If clibwrapper_jiio.jar is a problem, we might be able to eliminate the > dependency on it by removing the classes the require it (basically, > eliminating anything that would require libclib_jiio.so to function > correctly). > Bio-Formats already does not rely on or benefit from libclib_jiio.so being > installed, so this shouldn't cause any loss of functionality. > > If eliminating the need for clibwrapper_jiio.jar would help, let me know and > I will investigate further in the next few days.
That would be just awesome. From a debian point of view I cannot touch this clibwrapper_jiio.jar at any point in time (build time / run-time) since no source is available. If you make the compilation conditional, just let me know the name of the switch. Thanks *much* again for your help ! -- Mathieu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CA+7wUsy3etBcJ+o2wn9R6VH244whm6y8=-qggqe9d9dgvj-...@mail.gmail.com
