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
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https://bugs.launchpad.net/bugs/1556997
Title:
JAVA_HOME auto-detection fails due to whitespace in update-java-
alternatives output
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