java problem?

Help
grace
2009-04-16
2013-05-20
  • grace
    grace
    2009-04-16

    Whenever I open MeV and attempt to load files, the opening boxes are solid black.  I have the latest Java installed and have verified that it works.  I've also redownloaded MeV.  Is there some setting on my laptop that could be messing with the program?

     
  • ste
    ste
    2009-09-23

    Also in my mac after upgraded it with snow leopard I had this problem. When I try to open tav files they are visible but I am not able to open it.
    Suggestions?

     
  • ste
    ste
    2009-09-23

    Java problem in my mac are:

    Process:         JavaApplicationStub
    Path:            /Users/stefanocagnin/Downloads/TMEV_3_1_with_source/MacOSX_MeV_3_1.app/Contents/MacOS/JavaApplicationStub
    Identifier:      JavaApplicationStub
    Version:         ??? (???)
    Code Type:       X86 (Native)
    Parent Process:  launchd

    Date/Time:       2009-09-24 01:01:17.730 +0200
    OS Version:      Mac OS X 10.6.1 (10B504)
    Report Version:  6

    Interval Since Last Report:          252675 sec
    Crashes Since Last Report:           27
    Per-App Crashes Since Last Report:   26
    Anonymous UUID:                      68203DCD-C5F5-4EE7-82AF-B0FD2CB38C38

    Exception Type:  EXC_BREAKPOINT (SIGTRAP)
    Exception Codes: 0x0000000000000002, 0x0000000000000000
    Crashed Thread:  3

    Thread 0:  Dispatch queue: com.apple.main-thread
    0   libSystem.B.dylib             0x9808b7da mach_msg_trap + 10
    1   libSystem.B.dylib             0x9808bf47 mach_msg + 68
    2   com.apple.CoreFoundation      0x90c4cdbf __CFRunLoopRun + 2447
    3   com.apple.CoreFoundation      0x90c4bd34 CFRunLoopRunSpecific + 452
    4   com.apple.CoreFoundation      0x90c4bb61 CFRunLoopRunInMode + 97
    5   …ple.JavaApplicationLauncher 0x0000841e startupJava(LauncherArgsStruct*) + 342
    6   …ple.JavaApplicationLauncher 0x0000775f launchJavaApplication + 1355
    7   JavaApplicationStub           0x00001e3a 0x1000 + 3642
    8   JavaApplicationStub           0x00001c99 0x1000 + 3225
    9   JavaApplicationStub           0x00001bc8 0x1000 + 3016

    Thread 1:  Dispatch queue: com.apple.libdispatch-manager
    0   libSystem.B.dylib             0x980b203a kevent + 10
    1   libSystem.B.dylib             0x980b2768 _dispatch_mgr_invoke + 215
    2   libSystem.B.dylib             0x980b1bf9 _dispatch_queue_invoke + 183
    3   libSystem.B.dylib             0x980b198a _dispatch_worker_thread2 + 234
    4   libSystem.B.dylib             0x980b1401 _pthread_wqthread + 390
    5   libSystem.B.dylib             0x980b1246 start_wqthread + 30

    Thread 2:
    0   libSystem.B.dylib             0x980b1092 __workq_kernreturn + 10
    1   libSystem.B.dylib             0x980b1628 _pthread_wqthread + 941
    2   libSystem.B.dylib             0x980b1246 start_wqthread + 30

    Thread 3 Crashed:
    0   libhotspot.dylib              0x019c3cb4 JVM_RaiseSignal + 288532
    1   libhotspot.dylib              0x0192c907 pss + 273191
    2   libhotspot.dylib              0x019bf8bc JVM_RaiseSignal + 271132
    3   libhotspot.dylib              0x018cade7 0x1800000 + 830951
    4   libhotspot.dylib              0x018cc04c 0x1800000 + 835660
    5   libhotspot.dylib              0x0190d0c5 pss + 144101
    6   libhotspot.dylib              0x01a11a2c JVM_RaiseSignal + 607372
    7   libhotspot.dylib              0x0193583b JNI_CreateJavaVM_Impl + 171
    8   …ple.JavaApplicationLauncher 0x00009119 startJavaApplication + 3134
    9   …ple.JavaApplicationLauncher 0x000084d9 runJava(LauncherArgsStruct*) + 78
    10  …ple.JavaApplicationLauncher 0x00008483 java_main_stub(void*) + 17
    11  libSystem.B.dylib             0x980b8f39 _pthread_start + 345
    12  libSystem.B.dylib             0x980b8dbe thread_start + 34

    Thread 4:
    0   libSystem.B.dylib             0x9808b7da mach_msg_trap + 10
    1   libSystem.B.dylib             0x9808bf47 mach_msg + 68
    2   libhotspot.dylib              0x019c1a92 JVM_RaiseSignal + 279794
    3   libhotspot.dylib              0x01a0e855 JVM_RaiseSignal + 594613
    4   libhotspot.dylib              0x019c3842 JVM_RaiseSignal + 287394
    5   libSystem.B.dylib             0x9818205e _pthread_body + 27

    Thread 3 crashed with X86 Thread State (32-bit):
      eax: 0x01a6904c  ebx: 0x0192c8ee  ecx: 0x00000000  edx: 0x019c0fa5
      edi: 0xb0903f68  esi: 0x01b00080  ebp: 0xb0903f08  esp: 0xb0903f08
       ss: 0x0000001f  efl: 0x00000246  eip: 0x019c3cb4   cs: 0x00000017
       ds: 0x0000001f   es: 0x0000001f   fs: 0x0000001f   gs: 0x00000037
      cr2: 0x01a46ac0

    Binary Images:
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        0x6000 -    0x10ff7  com.apple.JavaApplicationLauncher 13.0.0 (13.0.0) <523841BE-CB41-7803-44FE-4538DEF247D6> /System/Library/PrivateFrameworks/JavaApplicationLauncher.framework/Versions/A/JavaApplicationLauncher
       0x18000 -    0x1fff7  com.apple.JavaVM 13.0.0 (13.0.0) <73B4CB4C-7C91-D148-E6DD-CFD578055BF7> /System/Library/Frameworks/JavaVM.framework/Versions/A/JavaVM
    0x1800000 -  0x1a68fe2  libhotspot.dylib ??? (???) <3ED0053D-5F2D-149B-183A-6919DB39C3C7> /System/Library/Frameworks/JavaVM.framework/Versions/1.4.2-leopard/Libraries/libhotspot.dylib
    0x8fe00000 - 0x8fe4162b  dyld 132.1 (???) <211AF0DD-42D9-79C8-BB6A-1F4BEEF4B4AB> /usr/lib/dyld
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    0x908a3000 - 0x908b7ffb  com.apple.speech.synthesis.framework 3.10.35 (3.10.35) <57DD5458-4F24-DA7D-0927-C3321A65D743> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
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    0x91e20000 - 0x91e64fe7  com.apple.Metadata 10.6.0 (507.1) <CBD1B22B-5F10-C784-03A2-35106B97DF3F> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
    0x91eaa000 - 0x91f42fe7  edu.mit.Kerberos 6.5.8 (6.5.8) <BA9BD282-FF56-3BFD-E78C-7DBE73B48480> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
    0x92ba6000 - 0x92e16ffb  com.apple.Foundation 6.6 (751) <A61B645E-1A15-5BCA-3043-C8AB85C6AD30> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
    0x92e17000 - 0x92e20ff7  com.apple.DiskArbitration 2.3 (2.3) <E9C40767-DA6A-6CCB-8B00-2D5706753000> /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
    0x930f0000 - 0x93198ff7  com.apple.QD 3.31 (???) <40FCAC85-4E4F-2290-90D4-F66D550ADFDC> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
    0x93242000 - 0x932dfff3  com.apple.LaunchServices 360.3 (360.3) <C8590D53-E46A-F58A-7CF2-03A8159D8569> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
    0x93315000 - 0x933cefe7  libsqlite3.dylib ??? (???) <16CEF8E8-8C9A-94CD-EF5D-05477844C005> /usr/lib/libsqlite3.dylib
    0x93426000 - 0x93434fe7  libz.1.dylib ??? (???) <7B7A02AB-DA99-6180-880E-D28E4F9AA8EB> /usr/lib/libz.1.dylib
    0x93554000 - 0x93558ff7  libGIF.dylib ??? (???) <51848EBF-27D4-0F85-C22A-D1AE10D328F3> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
    0x935d7000 - 0x935fbff7  libJPEG.dylib ??? (???) <265DBF67-994E-E320-4CB1-9C3DE792C3B2> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
    0x935fc000 - 0x936fdfe7  libxml2.2.dylib ??? (???) <C242A74D-280A-90C3-3F79-891624AA45D2> /usr/lib/libxml2.2.dylib
    0x93741000 - 0x937f3ffb  libFontParser.dylib ??? (???) <EB089832-660F-0B34-3AC8-CCDA937987D9> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
    0x939ab000 - 0x93a5afef  com.apple.ColorSync 4.6.0 (4.6.0) <66ABAE86-B0EC-D641-913D-08ACA965F9FA> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
    0x93a92000 - 0x93ea8ff7  libBLAS.dylib ??? (???) <C4FB303A-DB4D-F9E8-181C-129585E59603> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    0x93f68000 - 0x93fd2fe7  libstdc++.6.dylib ??? (???) <411D87F4-B7E1-44EB-F201-F8B4F9227213> /usr/lib/libstdc++.6.dylib
    0x94017000 - 0x9402bfe7  libbsm.0.dylib ??? (???) <14CB053A-7C47-96DA-E415-0906BA1B78C9> /usr/lib/libbsm.0.dylib
    0x9402c000 - 0x9402cff7  com.apple.Accelerate.vecLib 3.5 (vecLib 3.5) <3E039E14-2A15-56CC-0074-EE59F9FBB913> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
    0x94795000 - 0x94842fe7  libobjc.A.dylib ??? (???) <410DD065-A18F-F054-0457-65525F4D1039> /usr/lib/libobjc.A.dylib
    0x94ec4000 - 0x94f1eff7  com.apple.framework.IOKit 2.0 (???) <7618DDEC-2E3B-9C6E-FDC9-15169E24B4FB> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
    0x94f60000 - 0x950e2fe7  libicucore.A.dylib ??? (???) <FBB66376-CBA9-8149-A1AA-10AB8578C3B3> /usr/lib/libicucore.A.dylib
    0x95177000 - 0x9521efe7  com.apple.CFNetwork 454.4 (454.4) <7C563385-9893-3B48-8607-5BC81DA2C4CF> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
    0x95790000 - 0x957b0fe7  libresolv.9.dylib ??? (???) <A48921CB-3FA7-3071-AF9C-2D86FB493A3A> /usr/lib/libresolv.9.dylib
    0x9587a000 - 0x95adcff3  com.apple.security 6.0 (36910) <F045B57C-054F-F06F-EF7E-EABEC2700274> /System/Library/Frameworks/Security.framework/Versions/A/Security
    0x95add000 - 0x962be497  com.apple.CoreGraphics 1.535.5 (???) <0B93D29C-D957-AD00-10F3-94112D75D6D9> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
    0x962bf000 - 0x9647bfef  com.apple.ImageIO.framework 3.0.0 (3.0.0) <A37E541F-3D6A-2BE9-AB32-F60CCDE13608> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
    0x9647c000 - 0x964fcfeb  com.apple.SearchKit 1.3.0 (1.3.0) <9E18AEA5-F4B4-8BE5-EEA9-818FC4F46FD9> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
    0x96516000 - 0x96576fe7  com.apple.CoreText 3.0.0 (???) <8F4FCAE2-8E6F-F0DE-A6AA-15D0228B7F13> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/Versions/A/CoreText
    0x96577000 - 0x96577ff7  com.apple.CoreServices 44 (44) <AC35D112-5FB9-9C8C-6189-5F5945072375> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
    0x96edf000 - 0x97314ff7  libLAPACK.dylib ??? (???) <5E2D2283-57DE-9A49-1DB0-CD027FEFA6C2> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
    0x9731a000 - 0x97363fe7  libTIFF.dylib ??? (???) <6EF87001-6FB4-1405-C588-F6D8042D3534> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
    0x97364000 - 0x973d3ff7  libvMisc.dylib ??? (???) <59243A8C-2B98-3E71-8032-884D4853E79F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
    0x973d4000 - 0x97416fe7  libvDSP.dylib ??? (???) <8F8FFFB3-81E3-2969-5688-D5B0979182E6> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
    0x97466000 - 0x974b7ff7  com.apple.HIServices 1.8.0 (???) <B8EC13DB-A81A-91BF-8C82-66E840C64C91> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
    0x974fd000 - 0x975efff7  libcrypto.0.9.8.dylib ??? (???) <792B8722-3091-5E9F-E25F-67499CFE0599> /usr/lib/libcrypto.0.9.8.dylib
    0x9760f000 - 0x9761bff7  libkxld.dylib ??? (???) <152C8DBB-0149-5827-3240-E57CA85CFE5F> /usr/lib/system/libkxld.dylib
    0x97b0e000 - 0x97b42ff7  libcups.2.dylib ??? (???) <9078BA07-DEE1-6597-D15D-7BE3A20CB5A0> /usr/lib/libcups.2.dylib
    0x97bb3000 - 0x97bceff7  libPng.dylib ??? (???) <38DD4AA1-0643-85A0-F2F5-EE9269729975> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
    0x97e0c000 - 0x97e52ff7  libauto.dylib ??? (???) <FAB17F30-A28B-E33D-6E21-C7119C9C83ED> /usr/lib/libauto.dylib
    0x97ee9000 - 0x97eecfe7  libmathCommon.A.dylib ??? (???) <1622A54F-1A98-2CBE-B6A4-2122981A500E> /usr/lib/system/libmathCommon.A.dylib
    0x97eed000 - 0x97f7efe3  com.apple.print.framework.PrintCore 6.0 (312) <C588530A-0F2C-DD72-E308-3B8735125189> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
    0x97f7f000 - 0x9801bfe7  com.apple.ApplicationServices.ATS 4.0 (???) <81700C90-2614-F7E2-CC6A-B01C24A2BD75> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
    0x9808b000 - 0x9822ffeb  libSystem.B.dylib ??? (???) <E58B649F-FFDC-AB09-2028-8B706BEF7C0F> /usr/lib/libSystem.B.dylib
    0x98261000 - 0x98580fe7  com.apple.CoreServices.CarbonCore 859.1 (859.1) <2E72AF56-4BE6-294A-7372-19C360688B8B> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
    0x985b6000 - 0x985deff7  libxslt.1.dylib ??? (???) <769EF4B2-C1AD-73D5-AAAD-1564DAEA77AF> /usr/lib/libxslt.1.dylib
    0x9885b000 - 0x9888eff7  com.apple.AE 496 (496) <B638FDD4-7322-F0E4-ACEB-777D8A1399E1> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
    0x98da6000 - 0x98da6ff7  com.apple.ApplicationServices 38 (38) <8012B504-3D83-BFBB-DA65-065E061CFE03> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
    0x99409000 - 0x9942ffff  com.apple.DictionaryServices 1.1 (1.1) <07694B30-56A9-5C98-B8BC-DA0628715FA8> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
    0xffff0000 - 0xffff1fff  libSystem.B.dylib ??? (???) <E58B649F-FFDC-AB09-2028-8B706BEF7C0F> /usr/lib/libSystem.B.dylib

    Model: MacBookPro5,5, BootROM MBP55.00AC.B03, 2 processors, Intel Core 2 Duo, 2.53 GHz, 4 GB, SMC 1.47f2
    Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB
    Memory Module: global_name
    AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.91.19)
    Bluetooth: Version 2.2.1f7, 2 service, 0 devices, 1 incoming serial ports
    Network Service: AirPort, AirPort, en1
    Serial ATA Device: FUJITSU MJA2250BH FFS G1, 232.89 GB
    Serial ATA Device: HL-DT-ST DVDRW  GS23N
    USB Device: Internal Memory Card Reader, 0x05ac  (Apple Inc.), 0x8403, 0x26500000
    USB Device: Built-in iSight, 0x05ac  (Apple Inc.), 0x8507, 0x24400000
    USB Device: BRCM2046 Hub, 0x0a5c  (Broadcom Corp.), 0x4500, 0x06100000
    USB Device: Bluetooth USB Host Controller, 0x05ac  (Apple Inc.), 0x8213, 0x06110000
    USB Device: Apple Internal Keyboard / Trackpad, 0x05ac  (Apple Inc.), 0x0236, 0x04600000
    USB Device: IR Receiver, 0x05ac  (Apple Inc.), 0x8242, 0x04500000

    What do this means?

     
  • Sarita Nair
    Sarita Nair
    2009-09-24

    Hi,

    Thanks for using MeV.  I am not sure if you are aware of this but , the TAV file loader just needs to know the directory in which your files are present. The loader will list the names of any TAV  files present in the directory.

    Just so I have a better understanding of your problem, could you please clarify a couple of things for me?

    1. After upgrading to snow leopard,  you are still able to launch MeV and  also get to the TAV file loader interface?
    2. Does MeV crash when you try to load TAV files?
    3. The error output that you have sent in your post does not contain any MeV specific exceptions so can you please confirm if this is what you see in the console window that comes up when you launch MeV?

    I work on a Windows and would need to get help from my colleagues to  troubleshoot your problem, hence the questions.

    Thanks,
    Sarita

     
  • ste
    ste
    2009-09-24

    Hi Sarita,
    Yes after upgrading to snow leopard the only Java SE present on my mac was 6 32 and 64 bit with I was not able to open my tav files even if I was able to open MeV 4 (not the version 3, the java error is referred to the open process of the version number 3), search the folder in which there are my files and enter in. Even if i see my files they are like transparent and it is impossible to select them to upload.
    I have another old mac where is installed Leopard with the Java SE versions 1.4.2 (32 bit), 1.5  and 6 (32 and 64 bit) where all work well so I installed these java versions also in the mac with snow leopard, but risult is for the mev 3 the error I posted in the forum and for the latest mev versions my inability to upload files to analyze.
    I hope you can solve this problem.
    Thank you

     
  • Sarita Nair
    Sarita Nair
    2009-09-24

    Hi,

    I am not sure i quite understand what you mean by
    *"Even if i see my files they are like transparent and it is impossible to select them to upload"*
    You do not need to select individual files,  just the directory which contains them.  The  files also need to have a *.tav extension.

    I unfortunately cannot paste a screenshot here, but the MeV manual has a section on how to load tav files. I would suggest taking a look at the section.

    I would also highly recommend using the latest MeV version. Each release comes with lots of new features. It is also easier for us to track down any bugs and provide support.

    Hope that helps,
    Sarita

     
  • Sarita Nair
    Sarita Nair
    2009-09-24

    Hi,

    Another thing to try if you are quite sure you are loading the files the right way would be to switch back to Java 1.5 on the machine running snow leopard and see if it works. Our Mac distribution gets complied on Java 1.5.

    Let us know how it goes,
    Thanks,
    Sarita

     
  • ste
    ste
    2009-09-25

    Hi, I have yet switched to all Java version I installed on my Mac, but MeV 3 doesn't start and the other MeV versions do not allow me to upload tav files.

    Bye

     
  • ste
    ste
    2009-09-25

    I performed some tests trying to upload sample files proposed with the MeV4_4. Summering I used Mev Mac version with Leopard and installed Java 1.4.2, 5 and 6 without problems. Usually I use tav files. When I upgraded OSX to Snow Leopard started my problems. Upgrading Mac OSX disappear Java 1.4.2 and 5 keeping the only version number 6. I installed previously mentioned java versions to have my Mac with Snow Leopard and java version number 1.4.2, 5 and 6. Unfortunately I am not able to run MeV 3_1 causing a java crash posted in the forum. For me it is fundamental use this MeV version because is the only version that can perform PCA analysis and save the work. Other version(I do not tested 4_4) perform the analysis but do not allow to save the work (.anl file).
    Moreover if I try to use upper MeV versions to perform different analysis from PCA I can not upload my tav experimental files even if I can run MeV. I can open MeV_4_2, 4_3_02, 4_4_1, search the folder localization to upload files to analyze, but I can't upload my tav files. I tried to upload TM4 sample files, but I had same problems with .mev files (appear transparent, see image I sent by e-mail) while I had no problems to upload affymetrix, tab delimited multiple sample, CGH tab delimited files. I concluded that the problem is in the recognition of TIGR files (see image I sent by e-mail). Can you solve this problem?
    Sincerely
    Ste

     
  • Sarita Nair
    Sarita Nair
    2009-09-28

    Hi,

    We are sorry for the inconvenience. The latest version of MeV that was released in May 2009 was not tested on Snow Leopard and no one in our lab has a  machine running Snow Leopard either.

    So we can only provide you with suggestions on what could be wrong. Like I mentioned before we no longer support  MeV 3.1. In order for us to help you  and fix any bug that might be causing the trouble you will have to switch to  the latest version of MeV.

    MeV 4.4 has a lot of fixes in place that took care of the state saving problem. Can you please try these steps with MeV 4.4 and let us know how it goes:

    1. Open a terminal in Mac and run the tmev.sh file from the terminal.
    2. Try loading your tav files.
    3.  Copy paste any errors that you see in the terminal in to a text file and send it over to us.

    Best,
    Sarita

     
  • Sarita Nair
    Sarita Nair
    2009-09-28

    Please send the file containing the output from the terminal window to mev@jimmy.harvard.edu

     
  • ste
    ste
    2009-09-28

    Hi
    thanks for your replay, but where can I find the tmev.sh file? I do not find it in the unzipped folder of the software.

     
  • Sarita Nair
    Sarita Nair
    2009-09-28

    Hi,

    The simplest way of using the tmev.sh file would be to download the Linux distribution of MeV. On unzipping, you should be able to see the tmev.sh file in the root directory.

    Open the terminal window and navigate to the location where you downloaded MeV.  Use the cd command to go to  MeV directory and run tmev.sh from there.

    Best,
    Sarita

     
  • ste
    ste
    2009-09-28

    dhcp-209:MeV_4_4_1 stefanocagnin$ sh tmev.sh
    Error: no known VMs. (check for corrupt jvm.cfg file)
    dhcp-209:MeV_4_4_1 stefanocagnin$
    this was the error and MeV doesn't start

     
  • Sarita Nair
    Sarita Nair
    2009-09-28

    Hi,

    This is a Java error than a MeV problem. It is unfortunately  not possible for us to troubleshoot this for you. We would advise getting in touch with your systems administrator or IT department to help fix this problem.

    Thanks,

     
  • ste
    ste
    2009-09-28

    Hi, I am sorry if I insist with this problem but I solved java problems on my mac, but I can't upload mev or tav files while I can upload the other files (tab delimited, affy etc).
    Now running tmev.sh by the mac terminal I have these messages and the program run. How can I upload mev and tav files?
    Last login: Mon Sep 28 22:34:31 on ttys000
    host432:~ stefanocagnin$ cd Desktop/
    host432:Desktop stefanocagnin$ cd MeV_4_4_1/
    host432:MeV_4_4_1 stefanocagnin$ sh tmev.sh
    MultiExperimentViewer - version 4.4.1 - Mac OS X
    Java Runtime Environment version: 1.6.0_15
    Java Runtime Environment vendor: Apple Inc.
    Java Virtual Machine name: Java HotSpot(TM) 64-Bit Server VM
    Java Virtual Machine version: 14.1-b02-90
    Java Virtual Machine vendor: Apple Inc.
    Java 3D Runtime Environment: Java 3D Core Runtime Environment
    Java 3D Runtime Environment vendor: Apple Computer, Inc.
    Java 3D Runtime Environment version:1.3.1
    Operating System name: Mac OS X
    Operating System version: 10.6.1
    Operating System architecture: x86_64
    MeV Build: 1836
    MeV Revision Date: 2009/06/30 11:18:56
    MeV Branch: https://mev-tm4.svn.sourceforge.net/svnroot/mev-tm4/branches/MeV_4_4

     
  • ste
    ste
    2009-10-01

    I did not receive replay to my question. As you can see java work:
    Last login: Thu Oct  1 02:28:43 on ttys000
    host432:~ stefanocagnin$ cd Desktop/
    host432:Desktop stefanocagnin$ cd MeV_4_4_1/
    host432:MeV_4_4_1 stefanocagnin$ sh tmev.sh
    MultiExperimentViewer - version 4.4.1 - Mac OS X
    Java Runtime Environment version: 1.6.0_15
    Java Runtime Environment vendor: Apple Inc.
    Java Virtual Machine name: Java HotSpot(TM) Client VM
    Java Virtual Machine version: 14.1-b02-90
    Java Virtual Machine vendor: Apple Inc.
    Java 3D Runtime Environment: Java 3D Core Runtime Environment
    Java 3D Runtime Environment vendor: Apple Computer, Inc.
    Java 3D Runtime Environment version:1.3.1
    Operating System name: Mac OS X
    Operating System version: 10.6
    Operating System architecture: i386
    MeV Build: 1836
    MeV Revision Date: 2009/06/30 11:18:56
    MeV Branch: https://mev-tm4.svn.sourceforge.net/svnroot/mev-tm4/branches/MeV_4_4
    host432:MeV_4_4_1 stefanocagnin$

    MeV start but nowaday I can not upload mev or tav files :(
    I wrote to apple for this problem but they do not reply…
    What do you suggest?

     
  • Eleanor Howe
    Eleanor Howe
    2009-10-01

    Hi there,

    Ok, since we can't replicate the bug you have and we probably won't be able to soon, how about we try getting your data into a different format? Those tav files you use are pretty obsolete anyways. Can we convert them into a TDMS file and have you load with the TDMS loader? If you are willing to send me the files I'd be happy to convert them to the new format. If not, I can help you figure out how to convert them.

    Where are you getting .tav files, anyways? That file format was deprecated years and years ago.

    Eleanor

     
  • ste
    ste
    2009-10-04

    Hi,
    thank you for your suggestions and helpfulness. I solved the problem reading the un-compiled software; in fact it expect not a file to upload mev or tav file but a folder containing files to upload.
    I suggest you do not substitute tav and mev files with txt because the first two files permit a filtering method considering single channel intensity.
    Thank you

     
  • Eleanor Howe
    Eleanor Howe
    2009-10-05

    Hi there,

    I'm glad to hear that you are able to load your data now. We don't plan to disable support for .tav or .mev files, but I recommend that you use .mev files if you can, since they are a better format overall and are easier for us to support. Thank you for using MEV!

    Eleanor

     
  • rajsris
    rajsris
    2009-11-09

    Hello,

    I am using MeV4.4.1, the latest version, running on Windows XP. Each time I try to start MeV, I get this error:

    Exception in thread "main" java.lang.NoClassDefFoundError: org/tigr/microarray/mev/TMEV

    What do I do to resolve this? I downloaded MeV multiple times, and it is stored in C:\MeV4_4_1

    Thanks.

     
  • raktim
    raktim
    2009-11-09

    Hello,

    Could you open a cmd prompt and then type java -version and let us know what you see?

    Thanks,
    Raktim

     
  • Jose
    Jose
    2010-11-22

    Hi all,

    I'm running 64bit Ubuntu linux machine and I've problems with java. I've installed java 32bit version but I don't know how to tell Tmev to use it.
    Could anyone help me?

    Thanks in advance.