Error message when updating imageJ and opening large "-dimensional image with imageJ

updater
fiji
bio-formats
Tags: #<Tag:0x00007fb8828a1ff0> #<Tag:0x00007fb8828a1d70> #<Tag:0x00007fb8828a1be0>

#1

Hi,
I am getting error messages such as below when trying to update Fiji. Can any one help to resolve this. Also I have difficulty opening 3G 2-dimensional image on my system. I have increase the memory assign to imageJ up-to 15G but without any success,

Installer failed:java.lang.RuntimeException

[ERROR] Problem digesting C:\Users\SHEREE~1\Desktop\Fiji.app\jars\bio-formats\formats-bsd-5.6.1-20170815.141833-1.jar
[ERROR] Problem digesting C:\Users\SHEREE~1\Desktop\Fiji.app\jars\imagescience.jar
[ERROR] Problem digesting C:\Users\SHEREE~1\Desktop\Fiji.app\plugins\ij_shape_smoothing-1.2.jar
[ERROR] Problem digesting C:\Users\SHEREE~1\Desktop\Fiji.app\jars\bio-formats\formats-bsd-5.6.1-20170815.141833-1.jar
[ERROR] Problem digesting C:\Users\SHEREE~1\Desktop\Fiji.app\jars\imagescience.jar
java.net.SocketException: Connection reset
	at java.net.SocketInputStream.read(SocketInputStream.java:209)
	at java.net.SocketInputStream.read(SocketInputStream.java:141)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.net.www.MeteredStream.read(MeteredStream.java:134)
	at java.io.FilterInputStream.read(FilterInputStream.java:133)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3336)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3329)
	at net.imagej.updater.util.Downloader.download(Downloader.java:128)
	at net.imagej.updater.util.Downloader.start(Downloader.java:98)
	at net.imagej.updater.Installer.start(Installer.java:154)
	at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	at net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)
java.lang.RuntimeException: Incorrect file size for C:\Users\SHEREE~1\Desktop\Fiji.app\update\jars\bio-formats\formats-gpl-5.6.1-20170815.141842-1.jar: 1150 (expected 1306387)
	at net.imagej.updater.Installer.verify(Installer.java:293)
	at net.imagej.updater.Installer$VerifyFiles.itemDone(Installer.java:270)
	at net.imagej.updater.util.AbstractProgressable.itemDone(AbstractProgressable.java:87)
	at net.imagej.updater.util.Downloader.download(Downloader.java:138)
	at net.imagej.updater.util.Downloader.start(Downloader.java:98)
	at net.imagej.updater.Installer.start(Installer.java:154)
	at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	at net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)

#2

Dear @Sab6,

could you please check if you are following the Bio-Formats update site?

The most recent, stable Bio-Formats version is shipped via the Java-8 update site. The Bio-Formats update site ships (probably unstable) development versions. Hence, you should be able to deactivate that one if you have the Java-8 update site activated.

Best,
Stefan


#3

Thank you @stelfrich I have the box next to java 8 checked and bioformat unchecked but I still get the same error message. How do I get the stable bioformat?


#4

@Sab6

Were you able to update Fiji in the end?

Too - what are the image file formats you need to open? Bio-Formats has had a few recent updates… might be worth testing on your datasets - so you could activate the Bio-Formats updater, so check the Bio-Formats box. At least give it a try and report back…

eta


#5

I was wondering where @Sab6 got formats-bsd-5.6.1-20170815.141833-1.jar from, which is an unreleased version of Bio-Formats. Did you try to install Bio-Formats manually?

Could you check with a fresh download of Fiji if your original issue persists?


#6

Many thanks @etarena and @stelfrich. I don’t think I intsalled bioformat manually. The error message still persist with the newest version of Fiji. I cannot update Fiji with bioformat activated but without bioformat activated I can update Fiji.
Here are the error message

WARNING: core mtj jar files are not available as resources to this classloader (sun.misc.Launcher$AppClassLoader@764c12b6)
java.net.SocketException: Connection reset
	java.net.SocketInputStream.read(SocketInputStream.java:209)
	java.net.SocketInputStream.read(SocketInputStream.java:141)
	java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	sun.net.www.MeteredStream.read(MeteredStream.java:134)
	java.io.FilterInputStream.read(FilterInputStream.java:133)
	sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3336)
	sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3329)
	net.imagej.updater.util.Downloader.download(Downloader.java:128)
	net.imagej.updater.util.Downloader.start(Downloader.java:98)
	net.imagej.updater.Installer.start(Installer.java:154)
	net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)

	at java.net.SocketInputStream.read(SocketInputStream.java:209)
	at java.net.SocketInputStream.read(SocketInputStream.java:141)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.net.www.MeteredStream.read(MeteredStream.java:134)
	at java.io.FilterInputStream.read(FilterInputStream.java:133)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3336)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3329)
	at net.imagej.updater.util.Downloader.download(Downloader.java:128)
	at net.imagej.updater.util.Downloader.start(Downloader.java:98)
	at net.imagej.updater.Installer.start(Installer.java:154)
	at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	at net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)
java.net.SocketException: Connection reset
	java.net.SocketInputStream.read(SocketInputStream.java:209)
	java.net.SocketInputStream.read(SocketInputStream.java:141)
	java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	sun.net.www.MeteredStream.read(MeteredStream.java:134)
	java.io.FilterInputStream.read(FilterInputStream.java:133)
	sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3336)
	sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3329)
	net.imagej.updater.util.Downloader.download(Downloader.java:128)
	net.imagej.updater.util.Downloader.start(Downloader.java:98)
	net.imagej.updater.Installer.start(Installer.java:154)
	net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)

	at java.net.SocketInputStream.read(SocketInputStream.java:209)
	at java.net.SocketInputStream.read(SocketInputStream.java:141)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.net.www.MeteredStream.read(MeteredStream.java:134)
	at java.io.FilterInputStream.read(FilterInputStream.java:133)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3336)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3329)
	at net.imagej.updater.util.Downloader.download(Downloader.java:128)
	at net.imagej.updater.util.Downloader.start(Downloader.java:98)
	at net.imagej.updater.Installer.start(Installer.java:154)
	at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	at net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)
java.net.SocketException: Connection reset
	java.net.SocketInputStream.read(SocketInputStream.java:209)
	java.net.SocketInputStream.read(SocketInputStream.java:141)
	java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	sun.net.www.MeteredStream.read(MeteredStream.java:134)
	java.io.FilterInputStream.read(FilterInputStream.java:133)
	sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3336)
	sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3329)
	net.imagej.updater.util.Downloader.download(Downloader.java:128)
	net.imagej.updater.util.Downloader.start(Downloader.java:98)
	net.imagej.updater.Installer.start(Installer.java:154)
	net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)

	at java.net.SocketInputStream.read(SocketInputStream.java:209)
	at java.net.SocketInputStream.read(SocketInputStream.java:141)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.net.www.MeteredStream.read(MeteredStream.java:134)
	at java.io.FilterInputStream.read(FilterInputStream.java:133)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3336)
	at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3329)
	at net.imagej.updater.util.Downloader.download(Downloader.java:128)
	at net.imagej.updater.util.Downloader.start(Downloader.java:98)
	at net.imagej.updater.Installer.start(Installer.java:154)
	at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
	at net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)


#7

Did you download a fresh version from https://fiji.sc/#download? I have just checked https://downloads.imagej.net/fiji/latest/fiji-win64.zip and it does not contain the files that you have issues with. Could you please check if the problem persists when you extract the downloaded archive to C:\?

Also, are you behind a firewall / proxy in your institute? It seems that the updater has an issue with connecting to the servers to download some files.


#8

I am having similar problems updating FIJI. A fresh download of the latest version works fine, as does the life-line version from May 30 2017. But if I try to update any version, I get error messages like this:

Installer failed: java.io.IOException: Server returned HTTP response code: 503 for URL: http://sites.imagej.net/Java-8/jars/bio-formats/formats-api-5.6.0.jar-20170815150316

(or http://sites.imagej.net/Java-8/jars/javaassist-3.22.0-CR1.jar-20170530201750)

For me, a fresh download of the latest version solves my update issue, but it would be great if I didn’t have to get a fresh download to get updates. Thanks for your help!

(fyi: I have experienced this issue on two different computers. I have Java 8 Update 121, and I have granted access past any firewall.)


#9

Dear @HSeidel,

I know that @ctrueden was/is working on item 1 on his priority list which is making the web server that serves the update sites more robust. You might have experienced some issues in that context.

Is it still an issue for you? I can’t reproduce the issue on my machine…

Best,
Stefan


#10

I also cannot reproduce. Does this still happen?

Does it happen in your web browser with the URLs you gave? Does it still happen if you change http: to https: in the browser?

If HTTPS works, but HTTP doesn’t, then it is highly likely to be an issue with your ISP’s network configuration. It is possible for ISPs to arbitrarily control and/or corrupt the behavior of HTTP traffic (e.g., to cache stale versions and states, which we have unfortunately seen happen at major universities for example), but not HTTPS.


#11

@stelfrich and @ctrueden thank you for your help. The issue is now solved. I have been able to update Fiji. Back to the second question, no one has responded to this[quote=“Sab6, post:1, topic:6592”]
Also I have difficulty opening 3G 2-dimensional image on my system. I have increase the memory assign to imageJ up-to 15G but without any success,
[/quote]


#12

While the underlying data structures of ImageJ can handle extremely large image planes well, ImageJ’s user interface currently cannot display images with planes larger than 2 gigapixels. See this Troubleshooting entry for some advice on working around this limit.