Blosc support on macOS?

[perlman]

Hi,

I am unable to get the 0.3rc3 release to work with Blosc on my Mac.

I have c-blosc installed via homebrew (brew install c-blosc).

I had edited the final line in bioformats2raw-0.3.0-rc3/bin/bioformats2raw to add various forms of -Djna.library.path= without success, e.g. exec "$JAVACMD" -Djna.library.path=/usr/local/Cellar/c-blosc/1.21.0/lib/libblosc.dylib "$@".

Am I missing something obvious on how this should be run?

I always get the error java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll.

Thanks,
Eric

[tdmorello]

I am having the same problem with 0.3.0-rc4.

c-blosc: version 1.21.0
macos (big sur) 11.3.1

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.esotericsoftware.reflectasm.AccessClassLoader (file:/Users/tim/Desktop/bioformats2raw-0.3.0-rc4/lib/kryo-2.24.0.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.reflectasm.AccessClassLoader
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2021-05-12 18:58:53,104 [pool-1-thread-4] ERROR c.g.bioformats2raw.Converter - Failure processing tile; resolution=0 plane=0 xx=1024 yy=0 width=1024 height=1024
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
	at org.blosc.JBlosc.compressCtx(JBlosc.java:213) ~[jblosc-1.0.1.jar:na]
	at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327) ~[jzarr-0.3.3-gs-SNAPSHOT.jar:na]
	at com.bc.zarr.chunk.ChunkReaderWriterImpl_Short.write(ChunkReaderWriterImpl_Short.java:83) ~[jzarr-0.3.3-gs-SNAPSHOT.jar:na]
	at com.bc.zarr.ZarrArray.write(ZarrArray.java:278) ~[jzarr-0.3.3-gs-SNAPSHOT.jar:na]
	at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:771) ~[bioformats2raw-0.3.0-rc4.jar:0.3.0-rc4]
	at com.glencoesoftware.bioformats2raw.Converter.processTile(Converter.java:975) ~[bioformats2raw-0.3.0-rc4.jar:0.3.0-rc4]
	at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1109) ~[bioformats2raw-0.3.0-rc4.jar:0.3.0-rc4]
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130) ~[na:na]
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630) ~[na:na]
	at java.base/java.lang.Thread.run(Thread.java:832) ~[na:na]

[tdmorello]

Does anyone have advice for fixing this?

[tdmorello]

I ended up installing this with Anaconda.

https://anaconda.org/ome/bioformats2raw

conda install -c ome bioformats2raw

[muhanadz]

I managed to solve this issue, with the help of @erindiel and @chris-allan:
On MacOS, after brew install c-blosc, run export JAVA_OPTS='-Djna.library.path=/usr/local/Cellar/c-blosc/1.21.0/lib'.

For windows:set JAVA_OPTS="-Djna.library.path=C:\path\to\blosc\folder" which can be downloaded here. Just make sure to rename the file to .dll

@perlman used the path to libblosc.dylib and not the folder containing libblosc.dylib. One thing to note here is to make sure to add the path to the folder containing libblosc and not path to libblosc itself. I also added export JAVA_OPTS='-Djna.library.path=/usr/local/Cellar/c-blosc/1.21.0/lib' to my .zshrc

[chris-allan]

@muhanadz: Can you take a stab at opening a PR against master updating the README?