Public bug reported: Running imagej fails with the following message:
Open other images in this ImageJ panel as follows: imagej -p 3 <image1> [<image2> ... <imageN>] No JVM found to run ImageJ Please apt-get install a JVM to run ImageJ or set JAVA_HOME if it's not a JVM from a Debian Package. even though multiple JVM's are installed here. The problem is that the /usr/bin/imagej script detects JAVA_HOME using JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | grep openjdk | sort | tail -1 | cut -d' ' -f 3) which is empty as the output of update-java-alternatives -l is (note multiple spaces between columns): java-1.6.0-openjdk-amd64 1061 /usr/lib/jvm/java-1.6.0-openjdk-amd64 java-1.7.0-openjdk-amd64 1071 /usr/lib/jvm/java-1.7.0-openjdk-amd64 java-1.8.0-openjdk-amd64 1081 /usr/lib/jvm/java-1.8.0-openjdk-amd64 and cut -d' ' -f3 selects space. The solution is to squeeze multiple spaces before running cut, so the line should read: JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | grep openjdk | sort | tail -1 | tr -s ' ' | cut -d' ' -f 3) which then gives the correct output (/usr/lib/jvm/java-1.8.0-openjdk- amd64 in my case) and makes imagej run as expected. ProblemType: Bug DistroRelease: Ubuntu 16.04 Package: imagej 1.50d+dfsg-1 ProcVersionSignature: Ubuntu 3.19.0-49.55-lowlatency 3.19.8-ckt12 Uname: Linux 3.19.0-49-lowlatency x86_64 NonfreeKernelModules: btrfs ufs qnx4 hfsplus hfs minix ntfs msdos jfs xfs libcrc32c pci_stub binfmt_misc cfg80211 joydev hid_logitech_hidpp snd_hda_codec_hdmi snd_hda_intel snd_hda_controller eeepc_wmi asus_wmi sparse_keymap snd_hda_codec x86_pkg_temp_thermal intel_powerclamp video snd_hwdep snd_pcm snd_seq_midi kvm_intel snd_seq_midi_event kvm snd_rawmidi crct10dif_pclmul snd_seq crc32_pclmul snd_seq_device snd_timer snd aesni_intel sb_edac aes_x86_64 lrw soundcore gf128mul glue_helper edac_core ablk_helper serio_raw mei_me cryptd mei lpc_ich tpm_infineon 8250_fintek shpchp mac_hid nct6775 hwmon_vid coretemp parport_pc ppdev nfsd lp auth_rpcgss nfs_acl lockd grace sunrpc parport autofs4 raid10 raid456 async_raid6_recov async_memcpy async_pq async_xor async_tx xor raid6_pq raid0 multipath linear hid_logitech_dj usbhid hid raid1 amdkfd amd_iommu_v2 mxm_wmi radeon igb ttm drm_kms_helper dca psmouse ptp drm ahci pps_core libahci i2c_algo_bit wmi ApportVersion: 2.20-0ubuntu3 Architecture: amd64 CurrentDesktop: XFCE Date: Mon Mar 14 15:56:23 2016 PackageArchitecture: all SourcePackage: imagej UpgradeStatus: Upgraded to xenial on 2012-03-12 (1463 days ago) ** Affects: imagej (Ubuntu) Importance: Undecided Status: New ** Tags: amd64 apport-bug xenial -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1556997 Title: JAVA_HOME auto-detection fails due to whitespace in update-java- alternatives output To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/imagej/+bug/1556997/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs