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 > <[email protected]> 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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/20120801183645.GF20841@medusa
