Re: Cant compile jai-imageio-bioformats ( resume work on bioformats)
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.
Regards,
-Melissa
On Fri, Jul 27, 2012 at 05:24:56PM +0200, Mathieu Malaterre wrote:
> Hi Melissa,
>
> On Fri, May 25, 2012 at 4:17 PM, Melissa Linkert
> <melissa@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:
>
> 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:
>
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/common/PackageUtil.java:85:
> package com.sun.medialib.codec.jiio does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageReader.java:114:
> package com.sun.medialib.codec.jiio does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageReader.java:115:
> package com.sun.medialib.codec.jiio does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageWriter.java:108:
> package com.sun.medialib.codec.jiio does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageWriter.java:109:
> package com.sun.medialib.codec.jiio does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageReader.java:110:
> package com.sun.medialib.codec.jpeg does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageReader.java:111:
> package com.sun.medialib.codec.jiio does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageWriter.java:105:
> package com.sun.medialib.codec.jpeg does not exist
> [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageWriter.java:106:
> package com.sun.medialib.codec.jiio does not exist
>
>
> Could you please let me (again?) how am I supposed to compile
> bioformats when I decided NOT to use 'clibwrapper_jiio.jar'.
>
> Thanks much,
> --
> Mathieu
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