Ubuntu 9.10 x86
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Ubuntu 9.10 x86
 
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I compiled revision 3054 on a freshly installed Ubuntu 9.10 x86.
There were some changes that I had to make in the source (and in one header of my system). After doing all this I was able to start Micromanager. However I haven't tested it on real hardware yet as the new Motherboard lacks RS-232. I tried to use all dependencies from the Ubuntu package system. So I installed the Ubuntu imagej [note: I ran into problems when I upgraded this imagej as root from 1.43b to 1.43g with Help->Upgrade ImageJ... . The error looked like this: martin@cyberpower:~/mm1005/micromanager1.3/mmstudio$ make test -d build || mkdir build rm -rf build/* cp ./bin/plugins_mmstudio.config build/plugins.config javac -source 1.5 -target 1.5 -sourcepath ../MMCoreJ_wrap:./src:../hcs/src:. -classpath /usr/share/imagej/../java/ij.jar:/usr/share/java/bsh.jar:/usr/share/java/swingx.jar:/bin/MMCoreJ.jar:. ./src/*.java ./src/org/micromanager/utils/AutofocusBase.java -d build ./src/org/micromanager/image5d/Image5D.java:1357: cannot find symbol symbol : class Resizer location: package ij.plugin.filter PlugInFilter crop = new ij.plugin.filter.Resizer(); ^ Note: ./src/org/micromanager/utils/GUIUtils.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 1 error make: *** [MMJ_.jar] Error 1 sudo apt-get remove imagej; sudo apt-get install imagej resolved the problem.] I also installed the Ubuntu packages for beanshell and swingx. I had to set the links into the imagej plugin directory like this: ln -s /usr/share/java/swingx.jar /usr/share/imagej/plugins first problem: some file didn't compile because of error: ‘snprintf’ was not declared in this scope [I installed the manpages and looked what header is missing. sudo apt-get install manpages-dev man snprintf -> turns out you need stdio.h] second problem: martin@cyberpower:~/mm1005/micromanager1.3/MMCore$ g++ -DPACKAGE_NAME=\"Micro-Manager\" -DPACKAGE_TARNAME=\"micro-manager\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRI NG=\"Micro-Manager\ 1.3.0\" -DPACKAGE_BUGREPORT=\"[hidden email]\" -DPACKAGE_URL=\"\" -DPACKAGE=\"micro-manager\" -DVERSION=\"1.3.0\" -DSTDC_HEADERS=1 -DHAVE_ SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DH AVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_LIBDL=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DSTDC_HEADERS=1 -DHAVE_MEMSET=1 -I. -g -O -MT MMCore.o -MD -MP -MF .deps/MMCore.Tpo -c -o MMCore.o MMCore.cpp -Wall -W -Wextra In file included from MMCore.cpp:70: CircularBuffer.h:36: warning: ignoring #pragma warning In file included from /usr/include/ace/OS_NS_dirent.h:149, from /usr/include/ace/OS.h:32, from MMCore.cpp:50: /usr/include/ace/OS_NS_dirent.inl: In function ‘int ACE_OS::scandir(const ACE_TCHAR*, dirent***, int (*)(const dirent*), int (*)(const dirent**, const dirent**))’: /usr/include/ace/OS_NS_dirent.inl:131: error: invalid conversion from ‘int (*)(const void*, const void*)’ to ‘int (*)(const dirent**, const dirent**)’ /usr/include/ace/OS_NS_dirent.inl:131: error: initializing argument 4 of ‘int scandir(const char*, dirent***, int (*)(const dirent*), int (*)(const dirent**, const dirent**))’ /usr/include/ace/OS_NS_dirent.inl: In function ‘int ACE_OS::alphasort(const void*, const void*)’: /usr/include/ace/OS_NS_dirent.inl:152: error: invalid conversion from ‘const void*’ to ‘const dirent**’ /usr/include/ace/OS_NS_dirent.inl:152: error: initializing argument 1 of ‘int alphasort(const dirent**, const dirent**)’ /usr/include/ace/OS_NS_dirent.inl:152: error: invalid conversion from ‘const void*’ to ‘const dirent**’ /usr/include/ace/OS_NS_dirent.inl:152: error: initializing argument 2 of ‘int alphasort(const dirent**, const dirent**)’ In file included from MMCore.cpp:64: ../MMDevice/ImageMetadata.h: At global scope: ../MMDevice/ImageMetadata.h:92: warning: type qualifiers ignored on function return type to fix this error I commented the line //#define ACE_SCANDIR_CMP_USES_CONST_VOIDPTR in /usr/include/ace/config.h third error: /home/martin/mm1005/micromanager1.3/DeviceAdapters/Arduino Arduino.cpp: In member function ‘virtual int CArduinoSwitch::Initialize()’: Arduino.cpp:296: error: ‘snprintf’ was not declared in this scope [add #include <stdio.h> at the top of the Arduino.cpp] 4th error: can't find sprintf add stdio.h to /home/martin/mm1005/micromanager1.3/DeviceAdapters/ASIFW1000/ASIFW1000.cpp snprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/ASIFW1000/ASIFW1000Hub.cpp sscanf /home/martin/mm1005/micromanager1.3/DeviceAdapters/ASIStage/ASIStage.cpp snprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/DemoCamera/DemoCamera.cpp printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/DemoRGBCamera/DemoRGBCamera.cpp printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/DemoStreamingCamera/DemoStreamingCamera.cpp printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/SerialManagerUNIX/SerialManager.cpp printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/SerialManagerUNIX/SerialPort.cpp printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/LeicaDMI/LeicaDMIScopeInterface.cpp sprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/LeicaDMR/LeicaDMR.cpp #ifdef WIN32 //#include <windows.h> #define snprintf _snprintf #endif snprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/Ludl/Ludl.cpp snprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/LudlLow/Ludl.cpp snprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/Prior/Prior.cpp sprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/Pecon/Pecon.cpp snprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/ZeissCAN/ZeissCAN.cpp snprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/ZeissCAN29/ZeissCAN29.cpp printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/Conix/Conix.cpp printf sprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/NikonTE2000/NikonTE2000.cpp sprintf /home/martin/mm1005/micromanager1.3/DeviceAdapters/NikonTE2000/TEHub.cpp snprintf printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/K8055/K8055.cpp printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/K8055/K8055Interface.cpp snprintf printf /home/martin/mm1005/micromanager1.3/DeviceAdapters/K8061/K8061.cpp that is a lot of work. i just add stdio.h everywhere! cd /home/martin/mm1005/micromanager1.3/DeviceAdapters for i in `find .|grep \\.cpp$` do echo "#include <stdio.h>" > /dev/shm/o cat $i >> /dev/shm/o cp /dev/shm/o $i done /home/martin/mm1005/micromanager1.3/DeviceAdapters/SpectralLMM5/SpectralLMM5.h:64: error: ‘uint16_t’ was not declared in this scope -> add #include <stdint.h> to that file so now everything is compiled when I try to start Micromanager studio from within the imagej plugin menu I get java.lang.UnsatisfiedLinkError: no MMCoreJ_wrap in java.library.path and the hardwaredetection doesn't work use sudo update-alternatives --config java to switch to java-6-sun export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/micro-manager/ martin@cyberpower:/usr/share/imagej$ java -jar ij.jar -- Martin Kielhorn Randall Division of Cell & Molecular Biophysics King's College London, New Hunt's House Guy's Campus, London SE1 1UL, U.K. tel: +44 (0) 207 848 6519, fax: +44 (0) 207 848 6435 ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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I have sent a patch about including <stdio.h> back in July on some of the files due to the changes in GCC on newer linux distributions. Looking at that patch, it only corrected SpectralLMM5,ASIFW1000, HubASIFW1000, and SerialPort. On 10/06/2009 07:44 AM, Martin Kielhorn wrote: I compiled revision 3054 on a freshly installed Ubuntu 9.10 x86. ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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2009/10/6 Karl Bellve <[hidden email]>
I guess as there are so many files that would need editing, an easy way would be to figure out the right command line argument, so that gcc will automatically parse the stdio.h header. The best solution would be to write a script that includes stdio.h if the platform is Linux and if the file refers to some printf. However I couldn't figure out how to make a replacement over several lines with 'sed'. -- Martin Kielhorn Randall Division of Cell & Molecular Biophysics King's College London, New Hunt's House Guy's Campus, London SE1 1UL, U.K. tel: +44 (0) 207 848 6519, fax: +44 (0) 207 848 6435 ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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Hi Martin,
If the plan is to edit all the files to add the relevant #include, then I usually use 'ed' wrapped in a loop using the << operator to feed in the commands, something like this bash script: --------8<-------------------------- #!/bin/bash for file in $(find . -name "*.[ch]" -exec grep -l printf "{}" \;) do ed $file <<_EOF_ 1i #include <stdio.h> . w q _EOF_ done --------8<-------------------------- That should put the #include as the first line of every file that contains any printf, including the sprintf snprintf fprintf etc. variants. It would not, of course handle PRINTF macros unless you add a -i to the grep. Caution: I've only tested this particular on a group of three small files. Explanations in case any of this is unfamiliar: The for/do/dome iterates over a list of filenames supplied by the pre-executed find+grep. The $( ... ) causes the pre-execution, leaving the filenames on the command line. ready for use. The word 'file' is just a variable, substituted at $file in the loop 1i starts an insert on line 1 The next two lines are the insert The . ends the insert. w and q write out the file and quit 'ed'. The _EOF_ is just a finish label for the <<_EOF_ inline commands mode. 'done' loops to the next value of 'file', of course. Bits I sometimes add for testing: echo "----- $file" (or similar just before the ed) p within the ed commands prints the current line -5,+5p (iirc) prints a short context. a '| more' after the done, usually with stderr redirection. When the script runs, ed prints the number of chars read and the number of chars written for each file. HTH. ATB, Gordon. -- Gordon Scott Design Engineering Custom Interconnect Ltd. http://www.cil-uk.co.uk CoolLED http://www.coolled.com Phone +44-1264-321321 CIL House, Charlton Road, Andover SP10 3JL, UK > -----Original Message----- > From: Martin Kielhorn [mailto:[hidden email]] > Sent: 6 October 2009 19:27 > To: Micro-Manager General > Subject: Re: [micro-manager-general] Ubuntu 9.10 x86 > > > > 2009/10/6 Karl Bellve <[hidden email]> > > > > I have sent a patch about including <stdio.h> back in > July on some of the files due to the changes in GCC on newer > linux distributions. > > > > I guess as there are so many files that would need editing, > an easy way would be to figure out the right command line > argument, so that gcc will automatically parse the stdio.h header. > > > The best solution would be to write a script that includes > stdio.h if the platform is Linux and if the file refers to > some printf. However I couldn't figure out how to make a > replacement over several lines with 'sed'. > > -- > Martin Kielhorn > Randall Division of Cell & Molecular Biophysics > King's College London, New Hunt's House > Guy's Campus, London SE1 1UL, U.K. > tel: +44 (0) 207 848 6519, fax: +44 (0) 207 848 6435 > > > > > This message has been scanned by MailController > <http://www.mailcontroller.altohiway.com/> . > > This message has been scanned by MailController - www.MailController.altohiway.com This message and any attachments are strictly confidential and intended solely for the addressee. Any unauthorized use or disclosure, in whole or in part, is prohibited. E-mails are subject to possible alteration. Custom Interconnect Ltd and the sender decline any liability if this message and/or any attachments have been altered, changed or falsified. If you are not the intended recipient of this message, please delete it and notify the sender immediately. Custom Interconnect Limited is a limited company registered in England and Wales. Registered number: 2026753. Registered office: CIL House 48 Charlton road Andover, Hampshire United Kingdom SP103JL. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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2009/10/7 Gordon Scott <[hidden email]> #!/bin/bash Neat! -- Martin Kielhorn ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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> Neat! Unix :-) A hand variant .. you can search for and edit individual lines with something like g/some-regex/ s/this-regex/new-string/g which can be great for thing like name changes. Never forget regex 'hungry' behaviour, though! ATB, Gordon. -- Gordon Scott Design Engineering Custom Interconnect Ltd. http://www.cil-uk.co.uk CoolLED http://www.coolled.com Phone +44-1264-321321 CIL House, Charlton Road, Andover SP10 3JL, UK This message has been scanned by MailController - www.MailController.altohiway.com This message and any attachments are strictly confidential and intended solely for the addressee. Any unauthorized use or disclosure, in whole or in part, is prohibited. E-mails are subject to possible alteration. Custom Interconnect Ltd and the sender decline any liability if this message and/or any attachments have been altered, changed or falsified. If you are not the intended recipient of this message, please delete it and notify the sender immediately. Custom Interconnect Limited is a limited company registered in England and Wales. Registered number: 2026753. Registered office: CIL House 48 Charlton road Andover, Hampshire United Kingdom SP103JL. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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In reply to this post by Martin Kielhorn
On Oct 6, 2009, at 4:44 AM, Martin Kielhorn wrote:
> I ran into problems when I upgraded > this imagej as root from 1.43b to 1.43g with Help->Upgrade > ImageJ... . The error looked like this: > > ./src/org/micromanager/image5d/Image5D.java:1357: cannot find symbol > symbol : class Resizer > location: package ij.plugin.filter > PlugInFilter crop = new ij.plugin.filter.Resizer(); The class Resizer() moved form ij.plugin.filter to ij.plugin sometime between 1.43b and 1.43g. We'll stay with the older version until there are compelling reasons to upgrade. > first problem: > > you need stdio.h > > [add > #include <stdio.h> Quite interesting that stdio.h is not needed on Mac and with older gcc versions. Is there some configuration/environment variable that includes it automatically. In any case, it seems that the correct approach is to include it explicitly. Do you happen to have a patch for this or shall I add these all directly? Best, Nico ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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2009/10/8 Nico Stuurman <[hidden email]> So a patch from my current sources is probably no good idea.
I lost patience and eventually added stdio.h to the top of all .cpp files with the given script. According to the man page of g++ 'g++ -include stdio.h ...' could do but I'm not sure. -- Martin Kielhorn Randall Division of Cell & Molecular Biophysics King's College London, New Hunt's House Guy's Campus, London SE1 1UL, U.K. tel: +44 (0) 207 848 6519, fax: +44 (0) 207 848 6435 ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
Re: Ubuntu 9.10 x86
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> -----Original Message----- > From: Martin Kielhorn [mailto:[hidden email]] > I lost patience and eventually added stdio.h to the top of > all .cpp files with the given script. Presuming it was the script I offered, modified for .cpp and .hpp, it should only have added the include to files that use sprintf, which presumably should have stdio.h. Including the file twice is untidy but should be harmless if stdio.h has the usual and sendible #ifndef __STDIO_H wrapper around its contents. > So a patch from my current sources is probably no good idea. I think that _Should_ be harmless and fairly sensible, though the obvious caveats apply. An alternative would be to do the include within some other 'always included' file, if there is one. Files with duplicate includes for tidying can probably be found fairly easily with a combination of find/grep/wc. ATB, Gordon. -- Gordon Scott Design Engineering Custom Interconnect Ltd. http://www.cil-uk.co.uk CoolLED http://www.coolled.com Phone +44-1264-321321 CIL House, Charlton Road, Andover SP10 3JL, UK This message has been scanned by MailController - www.MailController.altohiway.com This message and any attachments are strictly confidential and intended solely for the addressee. Any unauthorized use or disclosure, in whole or in part, is prohibited. E-mails are subject to possible alteration. Custom Interconnect Ltd and the sender decline any liability if this message and/or any attachments have been altered, changed or falsified. If you are not the intended recipient of this message, please delete it and notify the sender immediately. Custom Interconnect Limited is a limited company registered in England and Wales. Registered number: 2026753. Registered office: CIL House 48 Charlton road Andover, Hampshire United Kingdom SP103JL. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ micro-manager-general mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/micro-manager-general |
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