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From: <br...@sa...> - 2011-09-05 15:20:48
|
Mon Sep 5 11:20:15 EDT 2011 *** Complete logs stored at http://sauron.cs.umd.edu/110905 ============================= 128.8.126.2 - MAC OS ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST ============================= SUCCESS: ============================= UBUNTU 10.10 ============================= SUCCESS: ============================= WIN XP UPDATE FIRST ============================= SUCCESS: ============================= FEDORA 15 ============================= SUCCESS: ============================= WIN 7 UPDATE LAST ============================= SUCCESS: ============================= CENT OS 5.5 ============================= SUCCESS: ============================= WIN XP UPDATE LAST ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= UBUNTU 10.10 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= FEDORA 15 WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE LAST WITH HAWKEYE ============================= SUCCESS: ============================= CENT OS 5.5 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE LAST WITH HAWKEYE ============================= SUCCESS: |
From: <br...@sa...> - 2011-09-01 12:55:22
|
Thu Sep 1 08:54:51 EDT 2011 *** Complete logs stored at http://sauron.cs.umd.edu/110901 ============================= 128.8.126.2 - MAC OS ============================= SUCCESS: ============================= 128.8.126.10 - MAC OS WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST ============================= SUCCESS: ============================= UBUNTU 10.10 ============================= SUCCESS: ============================= WIN XP UPDATE FIRST ============================= SUCCESS: ============================= FEDORA 15 ============================= SUCCESS: ============================= WIN 7 UPDATE LAST ============================= SUCCESS: ============================= CENT OS 5.5 ============================= SUCCESS: ============================= WIN XP UPDATE LAST ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= UBUNTU 10.10 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= FEDORA 15 WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE LAST WITH HAWKEYE ============================= SUCCESS: ============================= CENT OS 5.5 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE LAST WITH HAWKEYE ============================= SUCCESS: |
From: <br...@sa...> - 2011-08-30 16:24:03
|
Tue Aug 30 12:23:34 EDT 2011 *** Complete logs stored on http://sauron.cs.umd.edu/110830 ============================= MAC OS ============================= SUCCESS: ============================= MAC OS WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST ============================= SUCCESS: ============================= UBUNTU 10.10 ============================= SUCCESS: ============================= WIN XP UPDATE FIRST ============================= SUCCESS: ============================= FEDORA 15 ============================= SUCCESS: ============================= WIN 7 UPDATE LAST ============================= SUCCESS: ============================= CENT OS 5.5 ============================= SUCCESS: ============================= WIN XP UPDATE LAST ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= UBUNTU 10.10 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= FEDORA 15 WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE LAST WITH HAWKEYE ============================= SUCCESS: ============================= CENT OS 5.5 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE LAST WITH HAWKEYE ============================= SUCCESS: |
From: <br...@sa...> - 2011-08-26 15:38:32
|
Fri Aug 26 11:38:00 EDT 2011 *** Complete logs stored at http://sauron.cs.umd.edu/110826 ============================= 128.8.126.2 - MAC OS ============================= SUCCESS: ============================= 128.8.126.10 - MAC OS WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST ============================= SUCCESS: ============================= UBUNTU 10.10 ============================= SUCCESS: ============================= WIN XP UPDATE FIRST ============================= SUCCESS: ============================= FEDORA 15 ============================= SUCCESS: ============================= WIN 7 UPDATE LAST ============================= SUCCESS: ============================= CENT OS 5.5 ============================= SUCCESS: ============================= WIN XP UPDATE LAST ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= UBUNTU 10.10 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= FEDORA 15 WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE LAST WITH HAWKEYE ============================= SUCCESS: ============================= CENT OS 5.5 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE LAST WITH HAWKEYE ============================= SUCCESS: |
From: <br...@sa...> - 2011-08-24 22:44:15
|
Wed Aug 24 17:42:44 EDT 2011 *** Complete logs stored at http://sauron.cs.umd.edu/110824 ============================= 128.8.126.2 - MAC OS ============================= SUCCESS: ============================= 128.8.126.10 - MAC OS WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST ============================= SUCCESS: ============================= UBUNTU 10.10 ============================= SUCCESS: ============================= WIN XP UPDATE FIRST ============================= SUCCESS: ============================= FEDORA 15 ============================= SUCCESS: ============================= WIN 7 UPDATE LAST ============================= SUCCESS: ============================= CENT OS 5.5 ============================= SUCCESS: ============================= WIN XP UPDATE LAST ============================= SUCCESS: ============================= WIN 7 UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= UBUNTU 10.10 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE FIRST WITH HAWKEYE ============================= SUCCESS: ============================= FEDORA 15 WITH HAWKEYE ============================= SUCCESS: ============================= WIN 7 UPDATE LAST WITH HAWKEYE ============================= SUCCESS: ============================= CENT OS 5.5 WITH HAWKEYE ============================= SUCCESS: ============================= WIN XP UPDATE LAST WITH HAWKEYE ============================= SUCCESS: |
From: Florent A. <flo...@gm...> - 2011-08-05 05:59:13
|
Yes, looks very good! Thanks, Florent On 05/08/11 13:13, Michael Schatz wrote: > Hi Florent, > > I fixed the warnings (it was complaining about using char * foo = > "string" instead of const char * foo = "string") and touched up the > qt4 automake support. > > I posted the AMOS 3.1.0 on the website. If there are any show > stoppers, of course we should fix them, otherwise we can fold any new > changes into a 3.1.1 (or 3.2) release. > > Thanks! > > Mike > > > > On Thu, Aug 4, 2011 at 8:08 PM, Florent Angly <flo...@gm... > <mailto:flo...@gm...>> wrote: > > Hi Mike, > > Excellent! The build process works fine for me now, with a very > simple './configure' command. > > In addition to the deprecated header warnings from before, the > only noteworthy glitch is the presence of a new warning related to > Hawkeye I think: > > In file included from main.cc:8:0: > icons/AAI.xpm:549:803: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from main.cc:9:0: > icons/Hawkeye.xpm:562:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from LaunchPadBase.cc:32:0: > icons/Hawkeye.xpm:562:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from MainWindow.cc:25:0: > icons/fontdecrease.xpm:23:21: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from MainWindow.cc:26:0: > icons/fontincrease.xpm:23:21: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:27:0: > icons/rangebar_horiz.xpm:37:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:28:0: > icons/rangebar_vert.xpm:37:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:29:0: > icons/rangegroove_horiz.xpm:29:1: warning: deprecated conversion > from string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:30:0: > icons/rangegroove_vert.xpm:29:1: warning: deprecated conversion > from string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:31:0: > icons/rangearrow_left.xpm:47:1: warning: deprecated conversion > from string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:32:0: > icons/rangearrow_right.xpm:47:1: warning: deprecated conversion > from string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:33:0: > icons/rangearrow_up.xpm:47:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:34:0: > icons/rangearrow_down.xpm:47:1: warning: deprecated conversion > from string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:35:0: > icons/rangegrip_left.xpm:35:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:36:0: > icons/rangegrip_right.xpm:35:1: warning: deprecated conversion > from string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:37:0: > icons/rangegrip_up.xpm:25:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:38:0: > icons/rangegrip_down.xpm:25:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > Thanks, > > Florent > > > > On 05/08/11 06:55, Michael Schatz wrote: > I just posted AMOS 3.1.0-rc2 that reworks the configure script to > detect Qt4. It should work out-of-the-box on most any system if > you have Qt installed in a standard way. If you have Qt installed > to a non-standard location, use --with-qmake-qt4=<PATH> and set > the path to the command 'qmake'. The configure script will then > call qmake to figure out what the correct build flags should be. > > http://sourceforge.net/projects/amos/files/amos/3.1.0/ > > I also "fixed" the broken warning saying that Perl was missing. > This warning is actually emitted from a broken check for Python > (not Perl), and didn't do anything useful so I completely removed it. > > Finally, I posted a tarball with the tutorial dataset described in > the AMOS protocols paper to the sample_data directory (renamed > from test_data): > http://sourceforge.net/projects/amos/files/sample_data/ > > Mike > > > > > On Thu, Aug 4, 2011 at 10:34 AM, <br...@cs... > <mailto:br...@cs...><mailto:br...@cs... > <mailto:br...@cs...>>> wrote: > > > > we've been scratching our head about the Qt4 stuff as well > - we are > > putting together an automated test harness and the results have > > been unpredictable as far as Qt was concerned (e.g., works on > > centos but not ubuntu). Now that I see your logs I think I know > > what's going on. The AMOS config files are looking for > > ${Qt4_dir}/lib, however it appears that the corresponding > > libraries are in /usr/lib/qt4 on some systems. > > > > Dan and Bryan, can you guys check if that's the problem? > > Qt4 directory has different structures on different operating systems. > Below are detailed structures on ubuntu, fedora and centos. > > 1) on Ubuntu 10.10: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/include/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > bin doc include mkspecs plugins q3porting.xml translations > > $ ls /usr/lib/qt4 > plugins > > -> there isn't a qt4/lib directory > > 2) on Fedora15: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > translations > > $ ls /usr/lib/qt4 > bin import mkspecs phrasebooks plugins q3porting.xml > > -> there is a qt4/lib directory > > 3) on Cent os: > $ whereis qt4 > qt4: /usr/lib/qt4 > > $ ls /usr/lib/qt4 > bin include lib mkspecs phrasebooks plugins q3porting.xml translation > > $ ls /usr/lib/qt4/lib > many .prl and .so files > > -> there is a qt4/lib directory containing many files. > > Bryan > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > <mailto:AMO...@li...><mailto:AMO...@li... > <mailto:AMO...@li...>> > https://lists.sourceforge.net/lists/listinfo/amos-devel > > > > -- > > Assistant Professor of Quantitative Biology > Cold Spring Harbor Laboratory > > One Bungtown Road > Koch Building #1119 > Cold Spring Harbor, NY 11724 > phone: 703-966-1987 <tel:703-966-1987> > email: ms...@cs... > <mailto:ms...@cs...><mailto:ms...@cs... > <mailto:ms...@cs...>> > web: http://schatzlab.cshl.edu > > > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > > > > > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > <mailto:AMO...@li...><mailto:AMO...@li... > <mailto:AMO...@li...>> > https://lists.sourceforge.net/lists/listinfo/amos-devel > > > > > > -- > > Assistant Professor of Quantitative Biology > Cold Spring Harbor Laboratory > > One Bungtown Road > Koch Building #1119 > Cold Spring Harbor, NY 11724 > phone: 703-966-1987 > email: ms...@cs... <mailto:ms...@cs...> > web: http://schatzlab.cshl.edu > |
From: Michael S. <ms...@cs...> - 2011-08-05 03:13:51
|
Hi Florent, I fixed the warnings (it was complaining about using char * foo = "string" instead of const char * foo = "string") and touched up the qt4 automake support. I posted the AMOS 3.1.0 on the website. If there are any show stoppers, of course we should fix them, otherwise we can fold any new changes into a 3.1.1 (or 3.2) release. Thanks! Mike On Thu, Aug 4, 2011 at 8:08 PM, Florent Angly <flo...@gm...>wrote: > Hi Mike, > > Excellent! The build process works fine for me now, with a very simple > './configure' command. > > In addition to the deprecated header warnings from before, the only > noteworthy glitch is the presence of a new warning related to Hawkeye I > think: > > In file included from main.cc:8:0: > icons/AAI.xpm:549:803: warning: deprecated conversion from string constant > to ‘char*’ [-Wwrite-strings] > > In file included from main.cc:9:0: > icons/Hawkeye.xpm:562:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from LaunchPadBase.cc:32:0: > icons/Hawkeye.xpm:562:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from MainWindow.cc:25:0: > icons/fontdecrease.xpm:23:21: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from MainWindow.cc:26:0: > icons/fontincrease.xpm:23:21: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:27:0: > icons/rangebar_horiz.xpm:37:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:28:0: > icons/rangebar_vert.xpm:37:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:29:0: > icons/rangegroove_horiz.xpm:29:1: warning: deprecated conversion from > string constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:30:0: > icons/rangegroove_vert.xpm:29:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:31:0: > icons/rangearrow_left.xpm:47:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:32:0: > icons/rangearrow_right.xpm:47:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:33:0: > icons/rangearrow_up.xpm:47:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:34:0: > icons/rangearrow_down.xpm:47:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:35:0: > icons/rangegrip_left.xpm:35:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:36:0: > icons/rangegrip_right.xpm:35:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:37:0: > icons/rangegrip_up.xpm:25:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > In file included from RangeScrollBar.cc:38:0: > icons/rangegrip_down.xpm:25:1: warning: deprecated conversion from string > constant to ‘char*’ [-Wwrite-strings] > > Thanks, > > Florent > > > > On 05/08/11 06:55, Michael Schatz wrote: > I just posted AMOS 3.1.0-rc2 that reworks the configure script to detect > Qt4. It should work out-of-the-box on most any system if you have Qt > installed in a standard way. If you have Qt installed to a non-standard > location, use --with-qmake-qt4=<PATH> and set the path to the command > 'qmake'. The configure script will then call qmake to figure out what the > correct build flags should be. > > http://sourceforge.net/projects/amos/files/amos/3.1.0/ > > I also "fixed" the broken warning saying that Perl was missing. This > warning is actually emitted from a broken check for Python (not Perl), and > didn't do anything useful so I completely removed it. > > Finally, I posted a tarball with the tutorial dataset described in the AMOS > protocols paper to the sample_data directory (renamed from test_data): > http://sourceforge.net/projects/amos/files/sample_data/ > > Mike > > > > > On Thu, Aug 4, 2011 at 10:34 AM, <br...@cs...<mailto: > br...@cs...>> wrote: > > > > we've been scratching our head about the Qt4 stuff as well - we are > > putting together an automated test harness and the results have > > been unpredictable as far as Qt was concerned (e.g., works on > > centos but not ubuntu). Now that I see your logs I think I know > > what's going on. The AMOS config files are looking for > > ${Qt4_dir}/lib, however it appears that the corresponding > > libraries are in /usr/lib/qt4 on some systems. > > > > Dan and Bryan, can you guys check if that's the problem? > > Qt4 directory has different structures on different operating systems. > Below are detailed structures on ubuntu, fedora and centos. > > 1) on Ubuntu 10.10: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/include/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > bin doc include mkspecs plugins q3porting.xml translations > > $ ls /usr/lib/qt4 > plugins > > -> there isn't a qt4/lib directory > > 2) on Fedora15: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > translations > > $ ls /usr/lib/qt4 > bin import mkspecs phrasebooks plugins q3porting.xml > > -> there is a qt4/lib directory > > 3) on Cent os: > $ whereis qt4 > qt4: /usr/lib/qt4 > > $ ls /usr/lib/qt4 > bin include lib mkspecs phrasebooks plugins q3porting.xml translation > > $ ls /usr/lib/qt4/lib > many .prl and .so files > > -> there is a qt4/lib directory containing many files. > > Bryan > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > _______________________________________________ > AMOS-devel mailing list > AMO...@li...<mailto:AMO...@li...> > https://lists.sourceforge.net/lists/listinfo/amos-devel > > > > -- > > Assistant Professor of Quantitative Biology > Cold Spring Harbor Laboratory > > One Bungtown Road > Koch Building #1119 > Cold Spring Harbor, NY 11724 > phone: 703-966-1987 > email: ms...@cs...<mailto:ms...@cs...> > web: http://schatzlab.cshl.edu > > > > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > > > > > _______________________________________________ > AMOS-devel mailing list > AMO...@li...<mailto:AMO...@li...> > https://lists.sourceforge.net/lists/listinfo/amos-devel > > > -- Assistant Professor of Quantitative Biology Cold Spring Harbor Laboratory One Bungtown Road Koch Building #1119 Cold Spring Harbor, NY 11724 phone: 703-966-1987 email: ms...@cs... web: http://schatzlab.cshl.edu |
From: Florent A. <flo...@gm...> - 2011-08-05 00:09:38
|
Hi Mike, Excellent! The build process works fine for me now, with a very simple './configure' command. In addition to the deprecated header warnings from before, the only noteworthy glitch is the presence of a new warning related to Hawkeye I think: > In file included from main.cc:8:0: > icons/AAI.xpm:549:803: warning: deprecated conversion from string > constant to 'char*' [-Wwrite-strings] > > In file included from main.cc:9:0: > icons/Hawkeye.xpm:562:1: warning: deprecated conversion from string > constant to 'char*' [-Wwrite-strings] > > In file included from LaunchPadBase.cc:32:0: > icons/Hawkeye.xpm:562:1: warning: deprecated conversion from string > constant to 'char*' [-Wwrite-strings] > > In file included from MainWindow.cc:25:0: > icons/fontdecrease.xpm:23:21: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from MainWindow.cc:26:0: > icons/fontincrease.xpm:23:21: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:27:0: > icons/rangebar_horiz.xpm:37:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:28:0: > icons/rangebar_vert.xpm:37:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:29:0: > icons/rangegroove_horiz.xpm:29:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:30:0: > icons/rangegroove_vert.xpm:29:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:31:0: > icons/rangearrow_left.xpm:47:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:32:0: > icons/rangearrow_right.xpm:47:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:33:0: > icons/rangearrow_up.xpm:47:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:34:0: > icons/rangearrow_down.xpm:47:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:35:0: > icons/rangegrip_left.xpm:35:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:36:0: > icons/rangegrip_right.xpm:35:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:37:0: > icons/rangegrip_up.xpm:25:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] > > In file included from RangeScrollBar.cc:38:0: > icons/rangegrip_down.xpm:25:1: warning: deprecated conversion from > string constant to 'char*' [-Wwrite-strings] Thanks, Florent On 05/08/11 06:55, Michael Schatz wrote: > I just posted AMOS 3.1.0-rc2 that reworks the configure script to > detect Qt4. It should work out-of-the-box on most any system if you > have Qt installed in a standard way. If you have Qt installed to a > non-standard location, use --with-qmake-qt4=<PATH> and set the path to > the command 'qmake'. The configure script will then call qmake to > figure out what the correct build flags should be. > > http://sourceforge.net/projects/amos/files/amos/3.1.0/ > > I also "fixed" the broken warning saying that Perl was missing. This > warning is actually emitted from a broken check for Python (not Perl), > and didn't do anything useful so I completely removed it. > > Finally, I posted a tarball with the tutorial dataset described in the > AMOS protocols paper to the sample_data directory (renamed from > test_data): > http://sourceforge.net/projects/amos/files/sample_data/ > > Mike > > > > > On Thu, Aug 4, 2011 at 10:34 AM, <br...@cs... > <mailto:br...@cs...>> wrote: > > > > > we've been scratching our head about the Qt4 stuff as well > - we are > > putting together an automated test harness and the results have > > been unpredictable as far as Qt was concerned (e.g., works on > > centos but not ubuntu). Now that I see your logs I think I know > > what's going on. The AMOS config files are looking for > > ${Qt4_dir}/lib, however it appears that the corresponding > > libraries are in /usr/lib/qt4 on some systems. > > > > Dan and Bryan, can you guys check if that's the problem? > > Qt4 directory has different structures on different operating systems. > Below are detailed structures on ubuntu, fedora and centos. > > 1) on Ubuntu 10.10: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/include/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > bin doc include mkspecs plugins q3porting.xml translations > > $ ls /usr/lib/qt4 > plugins > > -> there isn't a qt4/lib directory > > 2) on Fedora15: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > translations > > $ ls /usr/lib/qt4 > bin import mkspecs phrasebooks plugins q3porting.xml > > -> there is a qt4/lib directory > > 3) on Cent os: > $ whereis qt4 > qt4: /usr/lib/qt4 > > $ ls /usr/lib/qt4 > bin include lib mkspecs phrasebooks plugins q3porting.xml translation > > $ ls /usr/lib/qt4/lib > many .prl and .so files > > -> there is a qt4/lib directory containing many files. > > Bryan > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > <mailto:AMO...@li...> > https://lists.sourceforge.net/lists/listinfo/amos-devel > > > > > -- > > Assistant Professor of Quantitative Biology > Cold Spring Harbor Laboratory > > One Bungtown Road > Koch Building #1119 > Cold Spring Harbor, NY 11724 > phone: 703-966-1987 > email: ms...@cs... <mailto:ms...@cs...> > web: http://schatzlab.cshl.edu > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos& much more. Register early& save! > http://p.sf.net/sfu/rim-blackberry-1 > > > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-devel |
From: Michael S. <ms...@cs...> - 2011-08-04 20:56:19
|
I just posted AMOS 3.1.0-rc2 that reworks the configure script to detect Qt4. It should work out-of-the-box on most any system if you have Qt installed in a standard way. If you have Qt installed to a non-standard location, use --with-qmake-qt4=<PATH> and set the path to the command 'qmake'. The configure script will then call qmake to figure out what the correct build flags should be. http://sourceforge.net/projects/amos/files/amos/3.1.0/ I also "fixed" the broken warning saying that Perl was missing. This warning is actually emitted from a broken check for Python (not Perl), and didn't do anything useful so I completely removed it. Finally, I posted a tarball with the tutorial dataset described in the AMOS protocols paper to the sample_data directory (renamed from test_data): http://sourceforge.net/projects/amos/files/sample_data/ Mike On Thu, Aug 4, 2011 at 10:34 AM, <br...@cs...> wrote: > > > > we've been scratching our head about the Qt4 stuff as well - we are > > putting together an automated test harness and the results have > > been unpredictable as far as Qt was concerned (e.g., works on > > centos but not ubuntu). Now that I see your logs I think I know > > what's going on. The AMOS config files are looking for > > ${Qt4_dir}/lib, however it appears that the corresponding > > libraries are in /usr/lib/qt4 on some systems. > > > > Dan and Bryan, can you guys check if that's the problem? > > Qt4 directory has different structures on different operating systems. > Below are detailed structures on ubuntu, fedora and centos. > > 1) on Ubuntu 10.10: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/include/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > bin doc include mkspecs plugins q3porting.xml translations > > $ ls /usr/lib/qt4 > plugins > > -> there isn't a qt4/lib directory > > 2) on Fedora15: > $ whereis qt4 > qt4: /usr/lib/qt4 /usr/share/qt4 > > $ ls /usr/share/qt4 > translations > > $ ls /usr/lib/qt4 > bin import mkspecs phrasebooks plugins q3porting.xml > > -> there is a qt4/lib directory > > 3) on Cent os: > $ whereis qt4 > qt4: /usr/lib/qt4 > > $ ls /usr/lib/qt4 > bin include lib mkspecs phrasebooks plugins q3porting.xml translation > > $ ls /usr/lib/qt4/lib > many .prl and .so files > > -> there is a qt4/lib directory containing many files. > > Bryan > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-devel > -- Assistant Professor of Quantitative Biology Cold Spring Harbor Laboratory One Bungtown Road Koch Building #1119 Cold Spring Harbor, NY 11724 phone: 703-966-1987 email: ms...@cs... web: http://schatzlab.cshl.edu |
From: <br...@cs...> - 2011-08-04 14:34:12
|
> > we've been scratching our head about the Qt4 stuff as well - we are > putting together an automated test harness and the results have > been unpredictable as far as Qt was concerned (e.g., works on > centos but not ubuntu). Now that I see your logs I think I know > what's going on. The AMOS config files are looking for > ${Qt4_dir}/lib, however it appears that the corresponding > libraries are in /usr/lib/qt4 on some systems. > > Dan and Bryan, can you guys check if that's the problem? Qt4 directory has different structures on different operating systems. Below are detailed structures on ubuntu, fedora and centos. 1) on Ubuntu 10.10: $ whereis qt4 qt4: /usr/lib/qt4 /usr/include/qt4 /usr/share/qt4 $ ls /usr/share/qt4 bin doc include mkspecs plugins q3porting.xml translations $ ls /usr/lib/qt4 plugins -> there isn't a qt4/lib directory 2) on Fedora15: $ whereis qt4 qt4: /usr/lib/qt4 /usr/share/qt4 $ ls /usr/share/qt4 translations $ ls /usr/lib/qt4 bin import mkspecs phrasebooks plugins q3porting.xml -> there is a qt4/lib directory 3) on Cent os: $ whereis qt4 qt4: /usr/lib/qt4 $ ls /usr/lib/qt4 bin include lib mkspecs phrasebooks plugins q3porting.xml translation $ ls /usr/lib/qt4/lib many .prl and .so files -> there is a qt4/lib directory containing many files. Bryan |
From: Michael S. <ms...@cs...> - 2011-08-04 04:19:04
|
I see the problem. The link flags and libraries needed for building Qt apps are different on every OS, and the automake scripts were tuned for centos/redhat. The immediate workaround is to build AMOS without hawkeye and then build hawkeye separately: cd amos ./configure (Qt fails) make make install cd src/hawkeye/ qmake make cp hawkeye ../../bin I have an idea on how to integrate this into the automake system, but isn't a 5 minute job. The basic idea is to include a minimal example in the configure script, and call qmake on it to generate the OS specific Makefile, and then grab the appropriate defines from the generated Makefile. I will try to implement this tomorrow. Mike On Wed, Aug 3, 2011 at 11:00 PM, Florent Angly <flo...@gm...>wrote: > On 04/08/11 12:12, Mihai Pop wrote: > > how'bout /usr/lib/qt4/lib? On RedHat that directory has .so files. > > > > Mihai > > Ok, here are some more attempts on my system: > > $ locate libQtCore.so > /usr/lib/libQtCore.so.4 > /usr/lib/libQtCore.so.4.7 > /usr/lib/libQtCore.so.4.7.3 > /usr/lib32/libQtCore.so.4 > /usr/lib32/libQtCore.so.4.6 > /usr/lib32/libQtCore.so.4.6.3 > > $ ls -1 /usr/share/qt4 > bin > doc > include > mkspecs > plugins > q3porting.xml > translations > > ./configure --with-Qt4-dir=/usr/share/qt4 --with-Qt4-lib=/usr/lib > --with-Qt4-include-dir=/usr/share/qt4/include > --with-Qt4-bin-dir=/usr/share/qt4/bin > > WARNING! Qt4 toolkit was not found > > ./configure --with-Qt4-lib=/usr/lib > --with-Qt4-include-dir=/usr/share/qt4/include > --with-Qt4-bin-dir=/usr/share/qt4/bin > > WARNING! Qt4 toolkit malfunctioning > > ./configure --with-Qt4-lib=/usr/lib > > WARNING! Qt4 toolkit malfunctioning > > ./configure --with-Qt4-lib-dir=/usr/lib > > WARNING! Qt4 toolkit was not found > > ./configure --with-Qt4-lib-dir=/usr/lib --with-Qt4-dir=/usr/share/qt4 > > WARNING! Qt4 toolkit malfunctioning > > ./configure --with-Qt4-lib=/usr/lib --with-Qt4-dir=/usr/share/qt4 > > WARNING! Qt4 toolkit was not found but is required > > So, sometimes, Qt4 is found but not working... > Does that help? > > Florent > -- Assistant Professor of Quantitative Biology Cold Spring Harbor Laboratory One Bungtown Road Koch Building #1119 Cold Spring Harbor, NY 11724 phone: 703-966-1987 email: ms...@cs... web: http://schatzlab.cshl.edu |
From: Florent A. <flo...@gm...> - 2011-08-04 03:00:55
|
On 04/08/11 12:12, Mihai Pop wrote: > how'bout /usr/lib/qt4/lib? On RedHat that directory has .so files. > > Mihai Ok, here are some more attempts on my system: $ locate libQtCore.so /usr/lib/libQtCore.so.4 /usr/lib/libQtCore.so.4.7 /usr/lib/libQtCore.so.4.7.3 /usr/lib32/libQtCore.so.4 /usr/lib32/libQtCore.so.4.6 /usr/lib32/libQtCore.so.4.6.3 $ ls -1 /usr/share/qt4 bin doc include mkspecs plugins q3porting.xml translations ./configure --with-Qt4-dir=/usr/share/qt4 --with-Qt4-lib=/usr/lib --with-Qt4-include-dir=/usr/share/qt4/include --with-Qt4-bin-dir=/usr/share/qt4/bin WARNING! Qt4 toolkit was not found ./configure --with-Qt4-lib=/usr/lib --with-Qt4-include-dir=/usr/share/qt4/include --with-Qt4-bin-dir=/usr/share/qt4/bin WARNING! Qt4 toolkit malfunctioning ./configure --with-Qt4-lib=/usr/lib WARNING! Qt4 toolkit malfunctioning ./configure --with-Qt4-lib-dir=/usr/lib WARNING! Qt4 toolkit was not found ./configure --with-Qt4-lib-dir=/usr/lib --with-Qt4-dir=/usr/share/qt4 WARNING! Qt4 toolkit malfunctioning ./configure --with-Qt4-lib=/usr/lib --with-Qt4-dir=/usr/share/qt4 WARNING! Qt4 toolkit was not found but is required So, sometimes, Qt4 is found but not working... Does that help? Florent |
From: Florent A. <flo...@gm...> - 2011-08-04 02:37:03
|
Could you name some of the *.so files Qt4 needs? I'll run the 'locate' command to see if and where they are on my harddrive, or if they don't exist, I could try to find which package provides them. Thanks, Florent On 04/08/11 12:12, Mihai Pop wrote: > how'bout /usr/lib/qt4/lib? On RedHat that directory has .so files. > > Mihai |
From: Mihai P. <mp...@um...> - 2011-08-04 02:12:49
|
how'bout /usr/lib/qt4/lib? On RedHat that directory has .so files. Mihai |
From: Daniel S. <ds...@um...> - 2011-08-04 02:02:11
|
There aren't any lib or .so files under /usr/lib/qt4 just a directory called plugins. -Dan On Wed, Aug 3, 2011 at 9:25 PM, Mihai Pop <mp...@um...> wrote: > Florent, > > we've been scratching our head about the Qt4 stuff as well - we are putting > together an automated test harness and the results have been unpredictable > as far as Qt was concerned (e.g., works on centos but not ubuntu). Now that > I see your logs I think I know what's going on. The AMOS config files are > looking for ${Qt4_dir}/lib, however it appears that the corresponding > libraries are in /usr/lib/qt4 on some systems. > > Dan and Bryan, can you guys check if that's the problem? > > Also, the Perl thing is a problem for me as well on cygwin - the log file > indicates it found it but then it promptly forgets about it. Again > something we need to figure out. > > Mihai > > > > On 8/3/2011 8:25 PM, Florent Angly wrote: > > Hi Mike, > > Thanks for this RC1 version. I gave it a spin on my Debian-based system and > here are my comments: > > 1/ My first issue is with a warning about missing Perl although Perl is > installed and the configure step already looked and found Perl: > > ./configure > ... > checking for blat... /usr/local/bin/blat > configure: WARNING: could not find perl > checking for perl module Statistics::Descriptive... ok > ... > > More on that error in config.log: > ... > configure:4522: checking for perl > configure:4540: found /usr/bin/perl > configure:4553: result: /usr/bin/perl > configure:4563: checking for python > configure:4581: found /usr/bin/python > configure:4594: result: /usr/bin/python > configure:4604: checking for nucmer > configure:4622: found /usr/bin/nucmer > configure:4635: result: /usr/bin/nucmer > configure:4645: checking for delta-filter > configure:4663: found /usr/bin/delta-filter > configure:4676: result: /usr/bin/delta-filter > configure:4686: checking for show-coords > configure:4704: found /usr/bin/show-coords > configure:4717: result: /usr/bin/show-coords > configure:4727: checking for blat > configure:4745: found /usr/local/bin/blat > configure:4758: result: /usr/local/bin/blat > configure:4808: WARNING: could not find perl > configure:4858: checking for perl module Statistics::Descriptive > configure:4868: result: ok > configure:4930: checking for perl module XML::Parser > configure:4940: result: ok > configure:5002: checking for perl module DBI > configure:5012: result: ok > ... > > 2/ But I also get trouble because of Qt4 > -- AMOS Assembler 3.1.0-rc1 Configuration Results -- > C compiler: gcc -g -O2 > C++ compiler: g++ -g -O2 > GCC version: gcc (Debian 4.6.1-4) 4.6.1 > Host System type: x86_64-unknown-linux-gnu > Install prefix: /home/floflooo/Downloads/amos-3.1.0-rc1 > Install eprefix: ${prefix} > > See config.h for further configuration information. > Email <amo...@li...> with questions and bug reports. > > WARNING! Qt4 toolkit was not found but is required to run AMOS GUIs > install Qt4 or locate Qt4 with configure to build GUIs > see config.log for more information on what went wrong > > So, I did: sudo apt-get install libqt4-dev libqt4-core libqt4-gui > > And Qt4 was still not found by configure. > > 3/ Then I tried the old trick documented on the Wiki > (https://sourceforge.net/apps/mediawiki/amos/index.php?title=Debian_installation): > > ./configure --with-Qt-dir=/usr/share/qt4 > configure: WARNING: unrecognized options: --with-Qt-dir > > Old trick did not work anymore... But now I RTFM'd and realized that the > option is called --with-Qt4-dir. Since there is no support for Qt3 anymore, > I suggest that this --with-Qt4-dir is renamed --with-Qt-dir for consistency > with previous versions of AMOS > > 4/ Using --with-Qt4-dir, I tried to configure again, using my /usr/share/qt4 > directory: > > $ ls -al /usr/share/qt4 > total 360 > drwxr-xr-x 6 root root 4096 Aug 4 09:35 . > drwxr-xr-x 375 root root 12288 Aug 2 16:39 .. > drwxr-xr-x 2 root root 4096 Aug 4 09:35 bin > drwxr-xr-x 3 root root 4096 Aug 4 09:34 doc > lrwxrwxrwx 1 root root 17 Jul 6 11:43 include -> ../../include/qt4 > drwxr-xr-x 99 root root 4096 Aug 4 09:35 mkspecs > lrwxrwxrwx 1 root root 21 Jul 6 11:43 plugins -> > ../../lib/qt4/plugins > -rw-r--r-- 1 root root 333214 Mar 30 15:16 q3porting.xml > drwxr-xr-x 2 root root 4096 Jul 19 11:29 translations > > ./configure --with-Qt4-dir=/usr/share/qt4 > > I got the same warning as before: > WARNING! Qt4 toolkit was not found... > > Am I missing some Qt4 files? If so, which ones should I be looking for? > > 5/ Ok, so without Qt4, I proceeded with the installation: > > make > > And I got the following warnings: > > Making all in AMOS > make[3]: Entering directory > `/home/floflooo_mint/Downloads/amos-3.1.0-rc1/src/AMOS' > g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT libAMOS_a-BankStream_AMOS.o > -MD -MP -MF .deps/libAMOS_a-BankStream_AMOS.Tpo -c -o > libAMOS_a-BankStream_AMOS.o `test -f 'BankStream_AMOS.cc' || echo > './'`BankStream_AMOS.cc > In file included from /usr/include/c++/4.6/ext/hash_map:61:0, > from utility_AMOS.hh:48, > from Bank_AMOS.hh:22, > from BankStream_AMOS.hh:13, > from BankStream_AMOS.cc:10: > /usr/include/c++/4.6/backward/backward_warning.h:33:2: warning: #warning > This file includes at least one deprecated or antiquated header which may be > removed without further notice at a future date. Please use a non-deprecated > interface with equivalent functionality instead. For a listing of > replacement headers and interfaces, consult the file backward_warning.h. To > disable this warning use -Wno-deprecated. [-Wcpp] > mv -f .deps/libAMOS_a-BankStream_AMOS.Tpo .deps/libAMOS_a-BankStream_AMOS.Po > g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT libAMOS_a-Bank_AMOS.o -MD -MP > -MF .deps/libAMOS_a-Bank_AMOS.Tpo -c -o libAMOS_a-Bank_AMOS.o `test -f > 'Bank_AMOS.cc' || echo './'`Bank_AMOS.cc > In file included from /usr/include/c++/4.6/ext/hash_map:61:0, > from utility_AMOS.hh:48, > from Bank_AMOS.hh:22, > from Bank_AMOS.cc:10: > /usr/include/c++/4.6/backward/backward_warning.h:33:2: warning: #warning > This file includes at least one deprecated or antiquated header which may be > removed without further notice at a future date. Please use a non-deprecated > interface with equivalent functionality instead. For a listing of > replacement headers and interfaces, consult the file backward_warning.h. To > disable this warning use -Wno-deprecated. [-Wcpp] > mv -f .deps/libAMOS_a-Bank_AMOS.Tpo .deps/libAMOS_a-Bank_AMOS.Po > > Dan has commented earlier on this issue: > "This is because <ext/hash_map> is not part of the standard C++ library and > should be changed to include <unorder_map> instead. This shouldn't be a > problem though and is a warning. I didn't change this in the release as I > am not sure of all the effects this could have on the core AMOS libraries > (bugs, performance, etc)." > > Maybe it's time to take the plunge and fix and test this? > > 6/ Test files > It is nice to have large data files be distributed separately from the AMOS > code so that the AMOS package is not too large. But where can users find the > tutorial files that were created for the recent paper that Todd wrote? > > 7/ In the Changelog, you can decide if you want to add: > The make-consensus module now handles ambiguous N bases (reported by Mark > Rose). > > This is a seemingly small change, but the consequences can be large since Ns > were previously removed from the sequence, potentially creating frameshifts. > > Looking forward to the new release! > Best, > > Florent > > > On 03/08/11 16:42, Michael Schatz wrote: > > Hi AMOS Developers, > I just posted a release candidate of AMOS 3.1.0 to sourceforge (and tagged > in git as AMOS_3_1_0_rc1): > http://sourceforge.net/projects/amos/files/amos/3.1.0/ > Can a few of you download, compile and see if anything is terribly broken? > I also posted a couple sample banks to: > http://sourceforge.net/projects/amos/files/test_data/ > > > Also, does anyone have any major changes they want to include in the > changelog? Here is what I have so far: > Version 3.1.0 - August 2011 > * Versioning of AMOS Banks -- all old banks require rebulding > * Added FRCurve pipeline for comparing multiple assemblies of the same > data: http://amos.sf.net/frcurve/ > * New version of Hawkeye using Qt 4 (removed Qt 3 version completely) > * Moved undocumented/prototype code into Experimental directory. Use > configure -enable-Experimental to build > * Many small updates and bug fixes > Version 3.0.0 - December 2010 > * New version of the scaffolder, Bambus 2.0 > * New lightweight, parametrable assembler based on Minimus, Minimo > * Experimental support for Qt 4 in Hawkeye > * Updated unitigger for Minimus, Unitigger > * Compute the complexity of a genome with genome-complexity > (http://www.biomedcentral.com/1471-2105/11/21) > * Utility that can convert large fastq files into a bank, fast2amos > * Ability to build only core AMOS binaries with Autoconf > * Support for writing SAM format in bank2contig > * toAmos now automatically reads mate pairs in FASTA files (reads > ending in /1 or .1) > * libSlice - correctly compute consensus even with very deep coverage > * Many small updates and bug fixes > Thanks! > Mike > > > -- > > Assistant Professor of Quantitative Biology > Cold Spring Harbor Laboratory > > One Bungtown Road > Koch Building #1119 > Cold Spring Harbor, NY 11724 > phone: 703-966-1987 > email: ms...@cs... > web: http://schatzlab.cshl.edu > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-devel > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-devel > > |
From: Mihai P. <mp...@um...> - 2011-08-04 01:25:49
|
<html> <head> <meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#FFFFFF" text="#000000"> Florent,<br> <br> we've been scratching our head about the Qt4 stuff as well - we are putting together an automated test harness and the results have been unpredictable as far as Qt was concerned (e.g., works on centos but not ubuntu). Now that I see your logs I think I know what's going on. The AMOS config files are looking for ${Qt4_dir}/lib, however it appears that the corresponding libraries are in /usr/lib/qt4 on some systems. <br> <br> Dan and Bryan, can you guys check if that's the problem?<br> <br> Also, the Perl thing is a problem for me as well on cygwin - the log file indicates it found it but then it promptly forgets about it. Again something we need to figure out.<br> <br> Mihai<br> <br> <br> <br> On 8/3/2011 8:25 PM, Florent Angly wrote: <blockquote type="cite"> <meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> Hi Mike,<br> <br> Thanks for this RC1 version. I gave it a spin on my Debian-based system and here are my comments:<br> <br> 1/ My first issue is with a warning about missing Perl although Perl is installed and the configure step already looked and found Perl:<br> <br> ./configure<br> ...<br> checking for blat... /usr/local/bin/blat<br> configure: WARNING: could not find perl<br> checking for perl module Statistics::Descriptive... ok<br> ...<br> <br> More on that error in config.log:<br> ...<br> configure:4522: checking for perl<br> configure:4540: found /usr/bin/perl<br> configure:4553: result: /usr/bin/perl<br> configure:4563: checking for python<br> configure:4581: found /usr/bin/python<br> configure:4594: result: /usr/bin/python<br> configure:4604: checking for nucmer<br> configure:4622: found /usr/bin/nucmer<br> configure:4635: result: /usr/bin/nucmer<br> configure:4645: checking for delta-filter<br> configure:4663: found /usr/bin/delta-filter<br> configure:4676: result: /usr/bin/delta-filter<br> configure:4686: checking for show-coords<br> configure:4704: found /usr/bin/show-coords<br> configure:4717: result: /usr/bin/show-coords<br> configure:4727: checking for blat<br> configure:4745: found /usr/local/bin/blat<br> configure:4758: result: /usr/local/bin/blat<br> configure:4808: WARNING: could not find perl<br> configure:4858: checking for perl module Statistics::Descriptive<br> configure:4868: result: ok<br> configure:4930: checking for perl module XML::Parser<br> configure:4940: result: ok<br> configure:5002: checking for perl module DBI<br> configure:5012: result: ok<br> ...<br> <br> 2/ But I also get trouble because of Qt4<br> -- AMOS Assembler 3.1.0-rc1 Configuration Results --<br> C compiler: gcc -g -O2<br> C++ compiler: g++ -g -O2<br> GCC version: gcc (Debian 4.6.1-4) 4.6.1<br> Host System type: x86_64-unknown-linux-gnu<br> Install prefix: /home/floflooo/Downloads/amos-3.1.0-rc1<br> Install eprefix: ${prefix}<br> <br> See config.h for further configuration information.<br> Email <a class="moz-txt-link-rfc2396E" href="mailto:amo...@li..."><amo...@li...></a> with questions and bug reports.<br> <br> WARNING! Qt4 toolkit was not found but is required to run AMOS GUIs<br> install Qt4 or locate Qt4 with configure to build GUIs<br> see config.log for more information on what went wrong<br> <br> So, I did: sudo apt-get install libqt4-dev libqt4-core libqt4-gui<br> <br> And Qt4 was still not found by configure.<br> <br> 3/ Then I tried the old trick documented on the Wiki (<a class="moz-txt-link-freetext" href="https://sourceforge.net/apps/mediawiki/amos/index.php?title=Debian_installation">https://sourceforge.net/apps/mediawiki/amos/index.php?title=Debian_installation</a>):<br> <br> ./configure --with-Qt-dir=/usr/share/qt4<br> configure: WARNING: unrecognized options: --with-Qt-dir<br> <br> Old trick did not work anymore... But now I RTFM'd and realized that the option is called --with-Qt4-dir. Since there is no support for Qt3 anymore, I suggest that this --with-Qt4-dir is renamed --with-Qt-dir for consistency with previous versions of AMOS<br> <br> 4/ Using --with-Qt4-dir, I tried to configure again, using my /usr/share/qt4 directory:<br> <br> $ ls -al /usr/share/qt4<br> total 360<br> drwxr-xr-x 6 root root 4096 Aug 4 09:35 .<br> drwxr-xr-x 375 root root 12288 Aug 2 16:39 ..<br> drwxr-xr-x 2 root root 4096 Aug 4 09:35 bin<br> drwxr-xr-x 3 root root 4096 Aug 4 09:34 doc<br> lrwxrwxrwx 1 root root 17 Jul 6 11:43 include -> ../../include/qt4<br> drwxr-xr-x 99 root root 4096 Aug 4 09:35 mkspecs<br> lrwxrwxrwx 1 root root 21 Jul 6 11:43 plugins -> ../../lib/qt4/plugins<br> -rw-r--r-- 1 root root 333214 Mar 30 15:16 q3porting.xml<br> drwxr-xr-x 2 root root 4096 Jul 19 11:29 translations<br> <br> ./configure --with-Qt4-dir=/usr/share/qt4<br> <br> I got the same warning as before:<br> WARNING! Qt4 toolkit was not found...<br> <br> Am I missing some Qt4 files? If so, which ones should I be looking for?<br> <br> 5/ Ok, so without Qt4, I proceeded with the installation:<br> <br> make<br> <br> And I got the following warnings:<br> <br> Making all in AMOS<br> make[3]: Entering directory `/home/floflooo_mint/Downloads/amos-3.1.0-rc1/src/AMOS'<br> g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT libAMOS_a-BankStream_AMOS.o -MD -MP -MF .deps/libAMOS_a-BankStream_AMOS.Tpo -c -o libAMOS_a-BankStream_AMOS.o `test -f 'BankStream_AMOS.cc' || echo './'`BankStream_AMOS.cc<br> In file included from /usr/include/c++/4.6/ext/hash_map:61:0,<br> from utility_AMOS.hh:48,<br> from Bank_AMOS.hh:22,<br> from BankStream_AMOS.hh:13,<br> from BankStream_AMOS.cc:10:<br> /usr/include/c++/4.6/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]<br> mv -f .deps/libAMOS_a-BankStream_AMOS.Tpo .deps/libAMOS_a-BankStream_AMOS.Po<br> g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT libAMOS_a-Bank_AMOS.o -MD -MP -MF .deps/libAMOS_a-Bank_AMOS.Tpo -c -o libAMOS_a-Bank_AMOS.o `test -f 'Bank_AMOS.cc' || echo './'`Bank_AMOS.cc<br> In file included from /usr/include/c++/4.6/ext/hash_map:61:0,<br> from utility_AMOS.hh:48,<br> from Bank_AMOS.hh:22,<br> from Bank_AMOS.cc:10:<br> /usr/include/c++/4.6/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]<br> mv -f .deps/libAMOS_a-Bank_AMOS.Tpo .deps/libAMOS_a-Bank_AMOS.Po<br> <br> Dan has commented earlier on this issue: <br> "This is because <ext/hash_map> is not part of the standard C++ library and should be changed to include <unorder_map> instead. This shouldn't be a problem though and is a warning. I didn't change this in the release as I am not sure of all the effects this could have on the core AMOS libraries (bugs, performance, etc)."<br> <br> Maybe it's time to take the plunge and fix and test this?<br> <br> 6/ Test files<br> It is nice to have large data files be distributed separately from the AMOS code so that the AMOS package is not too large. But where can users find the tutorial files that were created for the recent paper that Todd wrote?<br> <br> 7/ In the Changelog, you can decide if you want to add:<br> The make-consensus module now handles ambiguous N bases (reported by Mark Rose).<br> <br> This is a seemingly small change, but the consequences can be large since Ns were previously removed from the sequence, potentially creating frameshifts.<br> <br> Looking forward to the new release!<br> Best,<br> <br> Florent<br> <br> <br> On 03/08/11 16:42, Michael Schatz wrote: <blockquote cite="mid:CAHs-QZrLCvqQK3tU3454G0i-DsQooRsCokJs=+2XCmgA=S4...@ma..." type="cite">Hi AMOS Developers, <div><br> </div> <div>I just posted a release candidate of AMOS 3.1.0 to sourceforge (and tagged in git as AMOS_3_1_0_rc1):</div> <div><a moz-do-not-send="true" href="http://sourceforge.net/projects/amos/files/amos/3.1.0/">http://sourceforge.net/projects/amos/files/amos/3.1.0/</a></div> <div><br> </div> <div>Can a few of you download, compile and see if anything is terribly broken?</div> <div><br> </div> <div>I also posted a couple sample banks to:</div> <div><a moz-do-not-send="true" href="http://sourceforge.net/projects/amos/files/test_data/">http://sourceforge.net/projects/amos/files/test_data/</a></div> <div><br> </div> <div><br> </div> <div><br> </div> <div>Also, does anyone have any major changes they want to include in the changelog? Here is what I have so far:</div> <div><br> </div> <div> <div>Version 3.1.0 - August 2011</div> <div> * Versioning of AMOS Banks -- all old banks require rebulding</div> <div> * Added FRCurve pipeline for comparing multiple assemblies of the same data: <a moz-do-not-send="true" href="http://amos.sf.net/frcurve/">http://amos.sf.net/frcurve/</a></div> <div> * New version of Hawkeye using Qt 4 (removed Qt 3 version completely)</div> <div> * Moved undocumented/prototype code into Experimental directory. Use configure -enable-Experimental to build</div> <div> * Many small updates and bug fixes</div> <div><br> </div> <div>Version 3.0.0 - December 2010</div> <div><br> </div> <div> * New version of the scaffolder, Bambus 2.0</div> <div> * New lightweight, parametrable assembler based on Minimus, Minimo</div> <div> * Experimental support for Qt 4 in Hawkeye</div> <div> * Updated unitigger for Minimus, Unitigger</div> <div> * Compute the complexity of a genome with genome-complexity (<a moz-do-not-send="true" href="http://www.biomedcentral.com/1471-2105/11/21">http://www.biomedcentral.com/1471-2105/11/21</a>)</div> <div> * Utility that can convert large fastq files into a bank, fast2amos</div> <div> * Ability to build only core AMOS binaries with Autoconf</div> <div> * Support for writing SAM format in bank2contig</div> <div> * toAmos now automatically reads mate pairs in FASTA files (reads ending in /1 or .1)</div> <div> * libSlice - correctly compute consensus even with very deep coverage</div> <div> * Many small updates and bug fixes</div> </div> <div><br> </div> <div>Thanks!</div> <div><br> </div> <div>Mike</div> <div><br> </div> <div><br clear="all"> <br> -- <br> <br> Assistant Professor of Quantitative Biology<br> Cold Spring Harbor Laboratory<br> <br> One Bungtown Road<br> Koch Building #1119<br> Cold Spring Harbor, NY 11724<br> phone: 703-966-1987<br> email: <a moz-do-not-send="true" href="mailto:ms...@cs..." target="_blank">ms...@cs...</a><br> web: <a moz-do-not-send="true" href="http://schatzlab.cshl.edu" target="_blank">http://schatzlab.cshl.edu</a><br> <br> </div> <pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset> ------------------------------------------------------------------------------ BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. Connect with experts. Get tools for creating Super Apps. See the latest technologies. Sessions, hands-on labs, demos & much more. Register early & save! <a class="moz-txt-link-freetext" href="http://p.sf.net/sfu/rim-blackberry-1">http://p.sf.net/sfu/rim-blackberry-1</a></pre> <pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset> _______________________________________________ AMOS-devel mailing list <a class="moz-txt-link-abbreviated" href="mailto:AMO...@li...">AMO...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/amos-devel">https://lists.sourceforge.net/lists/listinfo/amos-devel</a> </pre> </blockquote> <br> <br> <fieldset class="mimeAttachmentHeader"></fieldset> <br> <pre wrap="">------------------------------------------------------------------------------ BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. Connect with experts. Get tools for creating Super Apps. See the latest technologies. Sessions, hands-on labs, demos & much more. Register early & save! <a class="moz-txt-link-freetext" href="http://p.sf.net/sfu/rim-blackberry-1">http://p.sf.net/sfu/rim-blackberry-1</a></pre> <br> <fieldset class="mimeAttachmentHeader"></fieldset> <br> <pre wrap="">_______________________________________________ AMOS-devel mailing list <a class="moz-txt-link-abbreviated" href="mailto:AMO...@li...">AMO...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/amos-devel">https://lists.sourceforge.net/lists/listinfo/amos-devel</a> </pre> </blockquote> <br> </body> </html> |
From: Florent A. <flo...@gm...> - 2011-08-04 00:26:19
|
Hi Mike, Thanks for this RC1 version. I gave it a spin on my Debian-based system and here are my comments: 1/ My first issue is with a warning about missing Perl although Perl is installed and the configure step already looked and found Perl: ./configure ... checking for blat... /usr/local/bin/blat configure: WARNING: could not find perl checking for perl module Statistics::Descriptive... ok ... More on that error in config.log: ... configure:4522: checking for perl configure:4540: found /usr/bin/perl configure:4553: result: /usr/bin/perl configure:4563: checking for python configure:4581: found /usr/bin/python configure:4594: result: /usr/bin/python configure:4604: checking for nucmer configure:4622: found /usr/bin/nucmer configure:4635: result: /usr/bin/nucmer configure:4645: checking for delta-filter configure:4663: found /usr/bin/delta-filter configure:4676: result: /usr/bin/delta-filter configure:4686: checking for show-coords configure:4704: found /usr/bin/show-coords configure:4717: result: /usr/bin/show-coords configure:4727: checking for blat configure:4745: found /usr/local/bin/blat configure:4758: result: /usr/local/bin/blat configure:4808: WARNING: could not find perl configure:4858: checking for perl module Statistics::Descriptive configure:4868: result: ok configure:4930: checking for perl module XML::Parser configure:4940: result: ok configure:5002: checking for perl module DBI configure:5012: result: ok ... 2/ But I also get trouble because of Qt4 -- AMOS Assembler 3.1.0-rc1 Configuration Results -- C compiler: gcc -g -O2 C++ compiler: g++ -g -O2 GCC version: gcc (Debian 4.6.1-4) 4.6.1 Host System type: x86_64-unknown-linux-gnu Install prefix: /home/floflooo/Downloads/amos-3.1.0-rc1 Install eprefix: ${prefix} See config.h for further configuration information. Email <amo...@li...> with questions and bug reports. WARNING! Qt4 toolkit was not found but is required to run AMOS GUIs install Qt4 or locate Qt4 with configure to build GUIs see config.log for more information on what went wrong So, I did: sudo apt-get install libqt4-dev libqt4-core libqt4-gui And Qt4 was still not found by configure. 3/ Then I tried the old trick documented on the Wiki (https://sourceforge.net/apps/mediawiki/amos/index.php?title=Debian_installation): ./configure --with-Qt-dir=/usr/share/qt4 configure: WARNING: unrecognized options: --with-Qt-dir Old trick did not work anymore... But now I RTFM'd and realized that the option is called --with-Qt4-dir. Since there is no support for Qt3 anymore, I suggest that this --with-Qt4-dir is renamed --with-Qt-dir for consistency with previous versions of AMOS 4/ Using --with-Qt4-dir, I tried to configure again, using my /usr/share/qt4 directory: $ ls -al /usr/share/qt4 total 360 drwxr-xr-x 6 root root 4096 Aug 4 09:35 . drwxr-xr-x 375 root root 12288 Aug 2 16:39 .. drwxr-xr-x 2 root root 4096 Aug 4 09:35 bin drwxr-xr-x 3 root root 4096 Aug 4 09:34 doc lrwxrwxrwx 1 root root 17 Jul 6 11:43 include -> ../../include/qt4 drwxr-xr-x 99 root root 4096 Aug 4 09:35 mkspecs lrwxrwxrwx 1 root root 21 Jul 6 11:43 plugins -> ../../lib/qt4/plugins -rw-r--r-- 1 root root 333214 Mar 30 15:16 q3porting.xml drwxr-xr-x 2 root root 4096 Jul 19 11:29 translations ./configure --with-Qt4-dir=/usr/share/qt4 I got the same warning as before: WARNING! Qt4 toolkit was not found... Am I missing some Qt4 files? If so, which ones should I be looking for? 5/ Ok, so without Qt4, I proceeded with the installation: make And I got the following warnings: Making all in AMOS make[3]: Entering directory `/home/floflooo_mint/Downloads/amos-3.1.0-rc1/src/AMOS' g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT libAMOS_a-BankStream_AMOS.o -MD -MP -MF .deps/libAMOS_a-BankStream_AMOS.Tpo -c -o libAMOS_a-BankStream_AMOS.o `test -f 'BankStream_AMOS.cc' || echo './'`BankStream_AMOS.cc In file included from /usr/include/c++/4.6/ext/hash_map:61:0, from utility_AMOS.hh:48, from Bank_AMOS.hh:22, from BankStream_AMOS.hh:13, from BankStream_AMOS.cc:10: /usr/include/c++/4.6/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] mv -f .deps/libAMOS_a-BankStream_AMOS.Tpo .deps/libAMOS_a-BankStream_AMOS.Po g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT libAMOS_a-Bank_AMOS.o -MD -MP -MF .deps/libAMOS_a-Bank_AMOS.Tpo -c -o libAMOS_a-Bank_AMOS.o `test -f 'Bank_AMOS.cc' || echo './'`Bank_AMOS.cc In file included from /usr/include/c++/4.6/ext/hash_map:61:0, from utility_AMOS.hh:48, from Bank_AMOS.hh:22, from Bank_AMOS.cc:10: /usr/include/c++/4.6/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] mv -f .deps/libAMOS_a-Bank_AMOS.Tpo .deps/libAMOS_a-Bank_AMOS.Po Dan has commented earlier on this issue: "This is because <ext/hash_map> is not part of the standard C++ library and should be changed to include <unorder_map> instead. This shouldn't be a problem though and is a warning. I didn't change this in the release as I am not sure of all the effects this could have on the core AMOS libraries (bugs, performance, etc)." Maybe it's time to take the plunge and fix and test this? 6/ Test files It is nice to have large data files be distributed separately from the AMOS code so that the AMOS package is not too large. But where can users find the tutorial files that were created for the recent paper that Todd wrote? 7/ In the Changelog, you can decide if you want to add: The make-consensus module now handles ambiguous N bases (reported by Mark Rose). This is a seemingly small change, but the consequences can be large since Ns were previously removed from the sequence, potentially creating frameshifts. Looking forward to the new release! Best, Florent On 03/08/11 16:42, Michael Schatz wrote: > Hi AMOS Developers, > > I just posted a release candidate of AMOS 3.1.0 to sourceforge (and > tagged in git as AMOS_3_1_0_rc1): > http://sourceforge.net/projects/amos/files/amos/3.1.0/ > > Can a few of you download, compile and see if anything is terribly broken? > > I also posted a couple sample banks to: > http://sourceforge.net/projects/amos/files/test_data/ > > > > Also, does anyone have any major changes they want to include in the > changelog? Here is what I have so far: > > Version 3.1.0 - August 2011 > * Versioning of AMOS Banks -- all old banks require rebulding > * Added FRCurve pipeline for comparing multiple assemblies of the > same data: http://amos.sf.net/frcurve/ > * New version of Hawkeye using Qt 4 (removed Qt 3 version completely) > * Moved undocumented/prototype code into Experimental directory. > Use configure -enable-Experimental to build > * Many small updates and bug fixes > > Version 3.0.0 - December 2010 > > * New version of the scaffolder, Bambus 2.0 > * New lightweight, parametrable assembler based on Minimus, Minimo > * Experimental support for Qt 4 in Hawkeye > * Updated unitigger for Minimus, Unitigger > * Compute the complexity of a genome with genome-complexity > (http://www.biomedcentral.com/1471-2105/11/21) > * Utility that can convert large fastq files into a bank, fast2amos > * Ability to build only core AMOS binaries with Autoconf > * Support for writing SAM format in bank2contig > * toAmos now automatically reads mate pairs in FASTA files (reads > ending in /1 or .1) > * libSlice - correctly compute consensus even with very deep coverage > * Many small updates and bug fixes > > Thanks! > > Mike > > > > -- > > Assistant Professor of Quantitative Biology > Cold Spring Harbor Laboratory > > One Bungtown Road > Koch Building #1119 > Cold Spring Harbor, NY 11724 > phone: 703-966-1987 > email: ms...@cs... <mailto:ms...@cs...> > web: http://schatzlab.cshl.edu > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos& much more. Register early& save! > http://p.sf.net/sfu/rim-blackberry-1 > > > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-devel |
From: Michael S. <ms...@cs...> - 2011-08-03 06:43:15
|
Hi AMOS Developers, I just posted a release candidate of AMOS 3.1.0 to sourceforge (and tagged in git as AMOS_3_1_0_rc1): http://sourceforge.net/projects/amos/files/amos/3.1.0/ Can a few of you download, compile and see if anything is terribly broken? I also posted a couple sample banks to: http://sourceforge.net/projects/amos/files/test_data/ Also, does anyone have any major changes they want to include in the changelog? Here is what I have so far: Version 3.1.0 - August 2011 * Versioning of AMOS Banks -- all old banks require rebulding * Added FRCurve pipeline for comparing multiple assemblies of the same data: http://amos.sf.net/frcurve/ * New version of Hawkeye using Qt 4 (removed Qt 3 version completely) * Moved undocumented/prototype code into Experimental directory. Use configure -enable-Experimental to build * Many small updates and bug fixes Version 3.0.0 - December 2010 * New version of the scaffolder, Bambus 2.0 * New lightweight, parametrable assembler based on Minimus, Minimo * Experimental support for Qt 4 in Hawkeye * Updated unitigger for Minimus, Unitigger * Compute the complexity of a genome with genome-complexity ( http://www.biomedcentral.com/1471-2105/11/21) * Utility that can convert large fastq files into a bank, fast2amos * Ability to build only core AMOS binaries with Autoconf * Support for writing SAM format in bank2contig * toAmos now automatically reads mate pairs in FASTA files (reads ending in /1 or .1) * libSlice - correctly compute consensus even with very deep coverage * Many small updates and bug fixes Thanks! Mike -- Assistant Professor of Quantitative Biology Cold Spring Harbor Laboratory One Bungtown Road Koch Building #1119 Cold Spring Harbor, NY 11724 phone: 703-966-1987 email: ms...@cs... web: http://schatzlab.cshl.edu |
From: Michael S. <mic...@gm...> - 2011-07-29 20:34:53
|
So can you build using qmake & make? Mike On Fri, Jul 29, 2011 at 4:24 PM, <br...@cs...> wrote: > Actually, after I installed qt4 and used --with-Qt4-dir, the building > process failed at the "make" step at the top level rather than the "make" > step in /src/hawkeye. Before qt4 was installed, the building process > completed successfully. > > Bryan > > Hi Bryan, > > > > These are all AMOS libraries: > > > > /usr/bin/ld: cannot find -lDataStore > > /usr/bin/ld: cannot find -lAMOS > > /usr/bin/ld: cannot find -lCommon > > /usr/bin/ld: cannot find -lread > > > > If you build AMOS from the top level first, you should then be able to go > > into the hawkeye directory and build hawkeye using qmake & make. Once we > > get > > hawkeye built using qmake & make, we can try to figure out how to better > > integrate hawkeye into the toplevel autoconf system. > > > > Mike > > > > > > On Fri, Jul 29, 2011 at 3:43 PM, <br...@cs...> wrote: > > > >> The second option is just my thought. It is not on the wiki. > >> Could you please tell me which packages I should install to remove those > >> errors as well as the qt4 warning notice that I mentioned in my first > >> email? > >> > >> Thanks for your help. > >> Bryan > >> > >> > Hi Bryan, > >> > > >> > Ideally they should both work (they do on my mac), although it is next > >> to > >> > impossible to integrate Qt into autoconf. As such, the second option > >> > should > >> > be more reliable because it uses the native Qt build system rather > >> than > >> > the > >> > autoconf system. Although now I see the second option is missing a > >> make. > >> > Where is this on the wiki? I will fix it. > >> > > >> > 2. "./bootstrap > >> > ./configure > >> > make <<--- add me > >> > cd src/hawkeye > >> > qmake > >> > make > >> > cd .. > >> > cd .. > >> > make install" > >> > > >> > Mike > >> > > >> > > >> > > >> > On Fri, Jul 29, 2011 at 3:20 PM, <br...@cs...> wrote: > >> > > >> >> Hi Mike, > >> >> > >> >> I used ubuntu package manager to install libzzip-dev and > >> libzip-dev(??) > >> >> instead of libz-devel since I could not find out libz-devel in ubuntu > >> >> synaptic package manager. The previous error ("cannot find -lz") > >> seems > >> >> to > >> >> be fixed, but there are other errors > >> >> > >> >> /usr/bin/ld: cannot find -lDataStore > >> >> /usr/bin/ld: cannot find -lAMOS > >> >> /usr/bin/ld: cannot find -lCommon > >> >> /usr/bin/ld: cannot find -lread > >> >> collect2: ld returned 1 exit status > >> >> make: *** [hawkeye] Error 1 > >> >> > >> >> I wonder where I can find the official guide to build AMOS. The > >> current > >> >> guide on AMOS wiki page will not work. Now I am a little bit confused > >> >> between 2 options below > >> >> > >> >> 1. "./bootstrap > >> >> ./configure > >> >> make > >> >> make install" > >> >> > >> >> 2. "./bootstrap > >> >> ./configure > >> >> cd src/hawkeye > >> >> qmake > >> >> make > >> >> cd .. > >> >> cd .. > >> >> make install" > >> >> > >> >> Which one did you follow? > >> >> > >> >> Thanks, > >> >> Bryan > >> >> > Hi Byran, > >> >> > > >> >> > Looks like libz (the compression library) is not installed by > >> default > >> >> on > >> >> > ubuntu. Can you installing libz-devel and try 'cd src/hawkeye && > >> qmake > >> >> && > >> >> > make' again? > >> >> > > >> >> > Thanks, > >> >> > > >> >> > Mike > >> >> > > >> >> > > >> >> > > >> >> > On Fri, Jul 29, 2011 at 2:23 PM, <br...@cs...> wrote: > >> >> > > >> >> >> Hi Mike, > >> >> >> > >> >> >> I have just tested building AMOS with qt4 on ubuntu 10.10, ubuntu > >> >> 11.04, > >> >> >> fedora 15 and cent OS 5.5. All machines failed at "make" step. On > >> >> ubuntu > >> >> >> 11.04, I cd into src/hawkeye and then run "qmake; make" but got > >> the > >> >> >> following error: > >> >> >> ".... > >> >> >> /usr/bin/ld: cannot find -lz > >> >> >> collect2: ld returned 1 exit status > >> >> >> make: *** [hawkeye] Error 1" > >> >> >> > >> >> >> These are the steps I followed to build AMOS: > >> >> >> > >> >> >> ./bootstrap > >> >> >> ./configure --with-Qt4-dir=/usr/share/qt4 --prefix=/usr/local/AMOS > >> >> >> make [*** got errors here and then I run "qmake; make" inside > >> >> >> src/hawkeye] > >> >> >> make install > >> >> >> > >> >> >> Also, although qt4 was already installed > >> >> >> (libqt4-core/libqt4-dev/libqt4-gui for ubuntu, > >> >> qt4.i686/qt4-devel.i686 > >> >> >> for > >> >> >> fedora), it has this notice "WARNING! Qt4 toolkit was not found > >> but > >> >> is > >> >> >> required to run AMOS GUIs" > >> >> >> > >> >> >> So, Would it be possible that you could provide me with more > >> detailed > >> >> >> instruction to build AMOS with qt4? > >> >> >> > >> >> >> Thanks, > >> >> >> Bryan > >> >> >> > >> >> >> > Hi Everyone, > >> >> >> > > >> >> >> > I added hawkeye back into the build system, and updated the > >> >> autoconf > >> >> >> to > >> >> >> > check for Qt 4 instead of Qt 3. I've tested it on my mac and on > >> >> some > >> >> >> linux > >> >> >> > workstations at CBCB, and everything checks out. > >> >> >> > > >> >> >> > For mac, the preferred route is to install the precompiled > >> >> libraries > >> >> >> as > >> >> >> > frameworks into /Library/Frameworks/Qt*.frameworks -- once done, > >> it > >> >> >> should > >> >> >> > automagically find them without needing any special flags. If > >> you > >> >> >> > installed > >> >> >> > them someplace else use --with-Qt4-dir=/path/to/Frameworks (and > >> >> >> > --with-Qt4-bin-dir=/path/to/bin/moc if moc is not in your path) > >> >> >> > > >> >> >> > For linux, you should be able to use --with-Qt4-dir to point to > >> the > >> >> >> top > >> >> >> > level install directory. If you use a recent version of Qt, the > >> >> path > >> >> >> will > >> >> >> > look something like this: > >> >> >> > /path/to/packages/QtSDK/Desktop/Qt/473/gcc > >> >> >> > > >> >> >> > and inside will be bin/moc, include/Qt/*, lib/libQtCore.* > >> >> >> > > >> >> >> > On linux, it is possible that the automake version will fail > >> >> because > >> >> >> Qt > >> >> >> > requires some different libraries than expected. In this case, > >> you > >> >> can > >> >> >> cd > >> >> >> > into src/hawkeye and manually run 'qmake; make' there > >> separately. > >> >> >> > > >> >> >> > Please let me know if you have any questions or problems with > >> it. > >> >> >> > > >> >> >> > Mike > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > On Tue, Jun 14, 2011 at 11:07 PM, Michael Schatz > >> >> >> > <mic...@gm...>wrote: > >> >> >> > > >> >> >> >> Hi Florent, > >> >> >> >> > >> >> >> >> I just committed a patch to update Hawkeye/Qt4 to support > >> sorting > >> >> >> >> contigs > >> >> >> >> by coverage, importing AFG files, and a few other clean ups. I > >> >> >> reviewed > >> >> >> >> the > >> >> >> >> changelog for the QT3 version, and I believe these are all of > >> the > >> >> >> >> outstanding features, but please let me know if you spot any > >> >> others. > >> >> >> >> > >> >> >> >> Thanks! > >> >> >> >> > >> >> >> >> Mike > >> >> >> >> > >> >> >> >> > >> >> >> >> On Tue, Jun 14, 2011 at 12:01 AM, Florent Angly > >> >> >> >> <flo...@gm...>wrote: > >> >> >> >> > >> >> >> >>> Hi Mike, > >> >> >> >>> > >> >> >> >>> Thanks for your work on making Hawkeye work with QT4! I'll be > >> >> happy > >> >> >> to > >> >> >> >>> test it when you think it's ready. > >> >> >> >>> > >> >> >> >>> Can I ask you a favour and ask you that you have a look at > >> what > >> >> >> >>> features > >> >> >> >>> were added to Hawkeye QT3 that were not added to Hawkeye QT4? > >> I > >> >> know > >> >> >> >>> for > >> >> >> >>> sure that I added support for sorting contigs by coverage (in > >> >> >> addition > >> >> >> >>> to > >> >> >> >>> length and number of reads) in the QT3 version and not the QT4 > >> >> >> version > >> >> >> >>> (that > >> >> >> >>> I was unaware of). Other developers may also have added > >> features > >> >> >> that > >> >> >> >>> need > >> >> >> >>> to be brought to the QT4 version. > >> >> >> >>> > >> >> >> >>> Thanks, > >> >> >> >>> > >> >> >> >>> Florent > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> On 14/06/11 01:56, Daniel Sommer wrote: > >> >> >> >>> > >> >> >> >>> Mike, I went ahead and removed hawkeye from the current > >> automake > >> >> >> build > >> >> >> >>> system so it will not get built. Whenever you are ready feel > >> >> free > >> >> >> to > >> >> >> >>> add it > >> >> >> >>> back in. > >> >> >> >>> Thanks, Dan > >> >> >> >>> > >> >> >> >>> PS, I CC'd anyone that I thought might add it back so that > >> they > >> >> >> would > >> >> >> >>> know not to. > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> On Wed, Jun 8, 2011 at 8:21 PM, Michael Schatz > >> >> >> >>> <mic...@gm...>wrote: > >> >> >> >>> > >> >> >> >>>> Hi Dan, > >> >> >> >>>> > >> >> >> >>>> I am in the middle of revamping hawkeye to use qt4 and add > >> some > >> >> >> new > >> >> >> >>>> features. I removed the old version (using qt3) from CVS in > >> >> >> >>>> amos/src/bankviewer and now the only version lives in > >> >> >> amos/src/hawkeye > >> >> >> >>>> and > >> >> >> >>>> uses qt4. I didnt add it into the automake build system, > >> because > >> >> I > >> >> >> >>>> havent > >> >> >> >>>> had a chance to update it for qt4 but it looks like someone > >> else > >> >> >> >>>> already > >> >> >> >>>> did. Can you coordinate the update to the automake system or > >> >> should > >> >> >> I? > >> >> >> >>>> > >> >> >> >>>> Thanks, > >> >> >> >>>> > >> >> >> >>>> Mike > >> >> >> >>>> > >> >> >> >>>> > >> >> >> >>>> On Jun 8, 2011, at 5:10 PM, Daniel Sommer > >> >> <ds...@um...> > >> >> >> >>>> wrote: > >> >> >> >>>> > >> >> >> >>>> Mike, The latest hawkeye checkin doesn't build correctly. > >> >> Could > >> >> >> >>>> you > >> >> >> >>>> take a look at it? We have a new project that is testing the > >> >> AMOS > >> >> >> >>>> builds > >> >> >> >>>> and they are reporting errors with hawkeye. I also am having > >> >> >> problems > >> >> >> >>>> building hawkeye. > >> >> >> >>>> > >> >> >> >>>> Thanks, Dan > >> >> >> >>>> > >> >> >> >>>> > >> >> >> >>>> ---------- Forwarded message ---------- > >> >> >> >>>> From: <br...@cs...> > >> >> >> >>>> Date: Wed, Jun 8, 2011 at 11:04 AM > >> >> >> >>>> Subject: Re: build errors > >> >> >> >>>> To: Daniel Sommer <ds...@um...> > >> >> >> >>>> Cc: Mihai Pop <mp...@um...>, at...@cs... > >> >> >> >>>> > >> >> >> >>>> > >> >> >> >>>> Hi Dan, > >> >> >> >>>> > >> >> >> >>>> Here is the error when I build AMOS on Ubuntu 10.10 > >> >> >> >>>> > >> >> >> >>>> Making all in hawkeye > >> >> >> >>>> make[3]: Entering directory `/home/bryanta/AMOS/src/hawkeye' > >> >> >> >>>> make[3]: *** No rule to make target `all'. Stop. > >> >> >> >>>> make[3]: Leaving directory `/home/bryanta/AMOS/src/hawkeye' > >> >> >> >>>> make[2]: *** [all-recursive] Error 1 > >> >> >> >>>> make[2]: Leaving directory `/home/bryanta/AMOS/src' > >> >> >> >>>> make[1]: *** [all-recursive] Error 1 > >> >> >> >>>> make[1]: Leaving directory `/home/bryanta/AMOS' > >> >> >> >>>> make: *** [all] Error 2 > >> >> >> >>>> > >> >> >> >>>> I installed qt3. > >> >> >> >>>> > >> >> >> >>>> And I also got a warning about BLAT that is required to use > >> >> >> >>>> minimus2-blat. > >> >> >> >>>> > >> >> >> >>>> Could you please tell me where I can get BLAT? I searched for > >> it > >> >> >> but > >> >> >> >>>> could > >> >> >> >>>> not get it. > >> >> >> >>>> > >> >> >> >>>> Thanks, > >> >> >> >>>> Bryan > >> >> >> >>>> > Hi, Were you able to recreate the build errors you were > >> >> getting > >> >> >> >>>> with > >> >> >> >>>> the > >> >> >> >>>> > latest AMOS code? When you get errors building AMOS just > >> >> email > >> >> >> me > >> >> >> >>>> the > >> >> >> >>>> > error > >> >> >> >>>> > output and I will make sure the right developers get them. > >> >> Later > >> >> >> we > >> >> >> >>>> > should > >> >> >> >>>> > have the automated tests email the amos-developer list so > >> >> >> everyone > >> >> >> >>>> working > >> >> >> >>>> > on AMOS can be notified of build errors. > >> >> >> >>>> > > >> >> >> >>>> > Dan > >> >> >> >>>> > > >> >> >> >>>> > >> >> >> >>>> > >> >> >> >>>> > >> >> >> >>>> > >> >> >> >>> > >> >> >> >>> > >> >> >> >> > >> >> >> > > >> >> >> > >> >> >> > >> >> >> > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > >> > > > > > |
From: Michael S. <mic...@gm...> - 2011-07-29 19:51:26
|
Hi Bryan, These are all AMOS libraries: /usr/bin/ld: cannot find -lDataStore /usr/bin/ld: cannot find -lAMOS /usr/bin/ld: cannot find -lCommon /usr/bin/ld: cannot find -lread If you build AMOS from the top level first, you should then be able to go into the hawkeye directory and build hawkeye using qmake & make. Once we get hawkeye built using qmake & make, we can try to figure out how to better integrate hawkeye into the toplevel autoconf system. Mike On Fri, Jul 29, 2011 at 3:43 PM, <br...@cs...> wrote: > The second option is just my thought. It is not on the wiki. > Could you please tell me which packages I should install to remove those > errors as well as the qt4 warning notice that I mentioned in my first > email? > > Thanks for your help. > Bryan > > > Hi Bryan, > > > > Ideally they should both work (they do on my mac), although it is next to > > impossible to integrate Qt into autoconf. As such, the second option > > should > > be more reliable because it uses the native Qt build system rather than > > the > > autoconf system. Although now I see the second option is missing a make. > > Where is this on the wiki? I will fix it. > > > > 2. "./bootstrap > > ./configure > > make <<--- add me > > cd src/hawkeye > > qmake > > make > > cd .. > > cd .. > > make install" > > > > Mike > > > > > > > > On Fri, Jul 29, 2011 at 3:20 PM, <br...@cs...> wrote: > > > >> Hi Mike, > >> > >> I used ubuntu package manager to install libzzip-dev and libzip-dev(??) > >> instead of libz-devel since I could not find out libz-devel in ubuntu > >> synaptic package manager. The previous error ("cannot find -lz") seems > >> to > >> be fixed, but there are other errors > >> > >> /usr/bin/ld: cannot find -lDataStore > >> /usr/bin/ld: cannot find -lAMOS > >> /usr/bin/ld: cannot find -lCommon > >> /usr/bin/ld: cannot find -lread > >> collect2: ld returned 1 exit status > >> make: *** [hawkeye] Error 1 > >> > >> I wonder where I can find the official guide to build AMOS. The current > >> guide on AMOS wiki page will not work. Now I am a little bit confused > >> between 2 options below > >> > >> 1. "./bootstrap > >> ./configure > >> make > >> make install" > >> > >> 2. "./bootstrap > >> ./configure > >> cd src/hawkeye > >> qmake > >> make > >> cd .. > >> cd .. > >> make install" > >> > >> Which one did you follow? > >> > >> Thanks, > >> Bryan > >> > Hi Byran, > >> > > >> > Looks like libz (the compression library) is not installed by default > >> on > >> > ubuntu. Can you installing libz-devel and try 'cd src/hawkeye && qmake > >> && > >> > make' again? > >> > > >> > Thanks, > >> > > >> > Mike > >> > > >> > > >> > > >> > On Fri, Jul 29, 2011 at 2:23 PM, <br...@cs...> wrote: > >> > > >> >> Hi Mike, > >> >> > >> >> I have just tested building AMOS with qt4 on ubuntu 10.10, ubuntu > >> 11.04, > >> >> fedora 15 and cent OS 5.5. All machines failed at "make" step. On > >> ubuntu > >> >> 11.04, I cd into src/hawkeye and then run "qmake; make" but got the > >> >> following error: > >> >> ".... > >> >> /usr/bin/ld: cannot find -lz > >> >> collect2: ld returned 1 exit status > >> >> make: *** [hawkeye] Error 1" > >> >> > >> >> These are the steps I followed to build AMOS: > >> >> > >> >> ./bootstrap > >> >> ./configure --with-Qt4-dir=/usr/share/qt4 --prefix=/usr/local/AMOS > >> >> make [*** got errors here and then I run "qmake; make" inside > >> >> src/hawkeye] > >> >> make install > >> >> > >> >> Also, although qt4 was already installed > >> >> (libqt4-core/libqt4-dev/libqt4-gui for ubuntu, > >> qt4.i686/qt4-devel.i686 > >> >> for > >> >> fedora), it has this notice "WARNING! Qt4 toolkit was not found but > >> is > >> >> required to run AMOS GUIs" > >> >> > >> >> So, Would it be possible that you could provide me with more detailed > >> >> instruction to build AMOS with qt4? > >> >> > >> >> Thanks, > >> >> Bryan > >> >> > >> >> > Hi Everyone, > >> >> > > >> >> > I added hawkeye back into the build system, and updated the > >> autoconf > >> >> to > >> >> > check for Qt 4 instead of Qt 3. I've tested it on my mac and on > >> some > >> >> linux > >> >> > workstations at CBCB, and everything checks out. > >> >> > > >> >> > For mac, the preferred route is to install the precompiled > >> libraries > >> >> as > >> >> > frameworks into /Library/Frameworks/Qt*.frameworks -- once done, it > >> >> should > >> >> > automagically find them without needing any special flags. If you > >> >> > installed > >> >> > them someplace else use --with-Qt4-dir=/path/to/Frameworks (and > >> >> > --with-Qt4-bin-dir=/path/to/bin/moc if moc is not in your path) > >> >> > > >> >> > For linux, you should be able to use --with-Qt4-dir to point to the > >> >> top > >> >> > level install directory. If you use a recent version of Qt, the > >> path > >> >> will > >> >> > look something like this: > >> >> > /path/to/packages/QtSDK/Desktop/Qt/473/gcc > >> >> > > >> >> > and inside will be bin/moc, include/Qt/*, lib/libQtCore.* > >> >> > > >> >> > On linux, it is possible that the automake version will fail > >> because > >> >> Qt > >> >> > requires some different libraries than expected. In this case, you > >> can > >> >> cd > >> >> > into src/hawkeye and manually run 'qmake; make' there separately. > >> >> > > >> >> > Please let me know if you have any questions or problems with it. > >> >> > > >> >> > Mike > >> >> > > >> >> > > >> >> > > >> >> > On Tue, Jun 14, 2011 at 11:07 PM, Michael Schatz > >> >> > <mic...@gm...>wrote: > >> >> > > >> >> >> Hi Florent, > >> >> >> > >> >> >> I just committed a patch to update Hawkeye/Qt4 to support sorting > >> >> >> contigs > >> >> >> by coverage, importing AFG files, and a few other clean ups. I > >> >> reviewed > >> >> >> the > >> >> >> changelog for the QT3 version, and I believe these are all of the > >> >> >> outstanding features, but please let me know if you spot any > >> others. > >> >> >> > >> >> >> Thanks! > >> >> >> > >> >> >> Mike > >> >> >> > >> >> >> > >> >> >> On Tue, Jun 14, 2011 at 12:01 AM, Florent Angly > >> >> >> <flo...@gm...>wrote: > >> >> >> > >> >> >>> Hi Mike, > >> >> >>> > >> >> >>> Thanks for your work on making Hawkeye work with QT4! I'll be > >> happy > >> >> to > >> >> >>> test it when you think it's ready. > >> >> >>> > >> >> >>> Can I ask you a favour and ask you that you have a look at what > >> >> >>> features > >> >> >>> were added to Hawkeye QT3 that were not added to Hawkeye QT4? I > >> know > >> >> >>> for > >> >> >>> sure that I added support for sorting contigs by coverage (in > >> >> addition > >> >> >>> to > >> >> >>> length and number of reads) in the QT3 version and not the QT4 > >> >> version > >> >> >>> (that > >> >> >>> I was unaware of). Other developers may also have added features > >> >> that > >> >> >>> need > >> >> >>> to be brought to the QT4 version. > >> >> >>> > >> >> >>> Thanks, > >> >> >>> > >> >> >>> Florent > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> On 14/06/11 01:56, Daniel Sommer wrote: > >> >> >>> > >> >> >>> Mike, I went ahead and removed hawkeye from the current automake > >> >> build > >> >> >>> system so it will not get built. Whenever you are ready feel > >> free > >> >> to > >> >> >>> add it > >> >> >>> back in. > >> >> >>> Thanks, Dan > >> >> >>> > >> >> >>> PS, I CC'd anyone that I thought might add it back so that they > >> >> would > >> >> >>> know not to. > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> On Wed, Jun 8, 2011 at 8:21 PM, Michael Schatz > >> >> >>> <mic...@gm...>wrote: > >> >> >>> > >> >> >>>> Hi Dan, > >> >> >>>> > >> >> >>>> I am in the middle of revamping hawkeye to use qt4 and add some > >> >> new > >> >> >>>> features. I removed the old version (using qt3) from CVS in > >> >> >>>> amos/src/bankviewer and now the only version lives in > >> >> amos/src/hawkeye > >> >> >>>> and > >> >> >>>> uses qt4. I didnt add it into the automake build system, because > >> I > >> >> >>>> havent > >> >> >>>> had a chance to update it for qt4 but it looks like someone else > >> >> >>>> already > >> >> >>>> did. Can you coordinate the update to the automake system or > >> should > >> >> I? > >> >> >>>> > >> >> >>>> Thanks, > >> >> >>>> > >> >> >>>> Mike > >> >> >>>> > >> >> >>>> > >> >> >>>> On Jun 8, 2011, at 5:10 PM, Daniel Sommer > >> <ds...@um...> > >> >> >>>> wrote: > >> >> >>>> > >> >> >>>> Mike, The latest hawkeye checkin doesn't build correctly. > >> Could > >> >> >>>> you > >> >> >>>> take a look at it? We have a new project that is testing the > >> AMOS > >> >> >>>> builds > >> >> >>>> and they are reporting errors with hawkeye. I also am having > >> >> problems > >> >> >>>> building hawkeye. > >> >> >>>> > >> >> >>>> Thanks, Dan > >> >> >>>> > >> >> >>>> > >> >> >>>> ---------- Forwarded message ---------- > >> >> >>>> From: <br...@cs...> > >> >> >>>> Date: Wed, Jun 8, 2011 at 11:04 AM > >> >> >>>> Subject: Re: build errors > >> >> >>>> To: Daniel Sommer <ds...@um...> > >> >> >>>> Cc: Mihai Pop <mp...@um...>, at...@cs... > >> >> >>>> > >> >> >>>> > >> >> >>>> Hi Dan, > >> >> >>>> > >> >> >>>> Here is the error when I build AMOS on Ubuntu 10.10 > >> >> >>>> > >> >> >>>> Making all in hawkeye > >> >> >>>> make[3]: Entering directory `/home/bryanta/AMOS/src/hawkeye' > >> >> >>>> make[3]: *** No rule to make target `all'. Stop. > >> >> >>>> make[3]: Leaving directory `/home/bryanta/AMOS/src/hawkeye' > >> >> >>>> make[2]: *** [all-recursive] Error 1 > >> >> >>>> make[2]: Leaving directory `/home/bryanta/AMOS/src' > >> >> >>>> make[1]: *** [all-recursive] Error 1 > >> >> >>>> make[1]: Leaving directory `/home/bryanta/AMOS' > >> >> >>>> make: *** [all] Error 2 > >> >> >>>> > >> >> >>>> I installed qt3. > >> >> >>>> > >> >> >>>> And I also got a warning about BLAT that is required to use > >> >> >>>> minimus2-blat. > >> >> >>>> > >> >> >>>> Could you please tell me where I can get BLAT? I searched for it > >> >> but > >> >> >>>> could > >> >> >>>> not get it. > >> >> >>>> > >> >> >>>> Thanks, > >> >> >>>> Bryan > >> >> >>>> > Hi, Were you able to recreate the build errors you were > >> getting > >> >> >>>> with > >> >> >>>> the > >> >> >>>> > latest AMOS code? When you get errors building AMOS just > >> email > >> >> me > >> >> >>>> the > >> >> >>>> > error > >> >> >>>> > output and I will make sure the right developers get them. > >> Later > >> >> we > >> >> >>>> > should > >> >> >>>> > have the automated tests email the amos-developer list so > >> >> everyone > >> >> >>>> working > >> >> >>>> > on AMOS can be notified of build errors. > >> >> >>>> > > >> >> >>>> > Dan > >> >> >>>> > > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>> > >> >> >>> > >> >> >> > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > >> > > > > > |
From: Michael S. <mic...@gm...> - 2011-07-29 19:34:09
|
Hi Bryan, Ideally they should both work (they do on my mac), although it is next to impossible to integrate Qt into autoconf. As such, the second option should be more reliable because it uses the native Qt build system rather than the autoconf system. Although now I see the second option is missing a make. Where is this on the wiki? I will fix it. 2. "./bootstrap ./configure make <<--- add me cd src/hawkeye qmake make cd .. cd .. make install" Mike On Fri, Jul 29, 2011 at 3:20 PM, <br...@cs...> wrote: > Hi Mike, > > I used ubuntu package manager to install libzzip-dev and libzip-dev(??) > instead of libz-devel since I could not find out libz-devel in ubuntu > synaptic package manager. The previous error ("cannot find -lz") seems to > be fixed, but there are other errors > > /usr/bin/ld: cannot find -lDataStore > /usr/bin/ld: cannot find -lAMOS > /usr/bin/ld: cannot find -lCommon > /usr/bin/ld: cannot find -lread > collect2: ld returned 1 exit status > make: *** [hawkeye] Error 1 > > I wonder where I can find the official guide to build AMOS. The current > guide on AMOS wiki page will not work. Now I am a little bit confused > between 2 options below > > 1. "./bootstrap > ./configure > make > make install" > > 2. "./bootstrap > ./configure > cd src/hawkeye > qmake > make > cd .. > cd .. > make install" > > Which one did you follow? > > Thanks, > Bryan > > Hi Byran, > > > > Looks like libz (the compression library) is not installed by default on > > ubuntu. Can you installing libz-devel and try 'cd src/hawkeye && qmake && > > make' again? > > > > Thanks, > > > > Mike > > > > > > > > On Fri, Jul 29, 2011 at 2:23 PM, <br...@cs...> wrote: > > > >> Hi Mike, > >> > >> I have just tested building AMOS with qt4 on ubuntu 10.10, ubuntu 11.04, > >> fedora 15 and cent OS 5.5. All machines failed at "make" step. On ubuntu > >> 11.04, I cd into src/hawkeye and then run "qmake; make" but got the > >> following error: > >> ".... > >> /usr/bin/ld: cannot find -lz > >> collect2: ld returned 1 exit status > >> make: *** [hawkeye] Error 1" > >> > >> These are the steps I followed to build AMOS: > >> > >> ./bootstrap > >> ./configure --with-Qt4-dir=/usr/share/qt4 --prefix=/usr/local/AMOS > >> make [*** got errors here and then I run "qmake; make" inside > >> src/hawkeye] > >> make install > >> > >> Also, although qt4 was already installed > >> (libqt4-core/libqt4-dev/libqt4-gui for ubuntu, qt4.i686/qt4-devel.i686 > >> for > >> fedora), it has this notice "WARNING! Qt4 toolkit was not found but is > >> required to run AMOS GUIs" > >> > >> So, Would it be possible that you could provide me with more detailed > >> instruction to build AMOS with qt4? > >> > >> Thanks, > >> Bryan > >> > >> > Hi Everyone, > >> > > >> > I added hawkeye back into the build system, and updated the autoconf > >> to > >> > check for Qt 4 instead of Qt 3. I've tested it on my mac and on some > >> linux > >> > workstations at CBCB, and everything checks out. > >> > > >> > For mac, the preferred route is to install the precompiled libraries > >> as > >> > frameworks into /Library/Frameworks/Qt*.frameworks -- once done, it > >> should > >> > automagically find them without needing any special flags. If you > >> > installed > >> > them someplace else use --with-Qt4-dir=/path/to/Frameworks (and > >> > --with-Qt4-bin-dir=/path/to/bin/moc if moc is not in your path) > >> > > >> > For linux, you should be able to use --with-Qt4-dir to point to the > >> top > >> > level install directory. If you use a recent version of Qt, the path > >> will > >> > look something like this: > >> > /path/to/packages/QtSDK/Desktop/Qt/473/gcc > >> > > >> > and inside will be bin/moc, include/Qt/*, lib/libQtCore.* > >> > > >> > On linux, it is possible that the automake version will fail because > >> Qt > >> > requires some different libraries than expected. In this case, you can > >> cd > >> > into src/hawkeye and manually run 'qmake; make' there separately. > >> > > >> > Please let me know if you have any questions or problems with it. > >> > > >> > Mike > >> > > >> > > >> > > >> > On Tue, Jun 14, 2011 at 11:07 PM, Michael Schatz > >> > <mic...@gm...>wrote: > >> > > >> >> Hi Florent, > >> >> > >> >> I just committed a patch to update Hawkeye/Qt4 to support sorting > >> >> contigs > >> >> by coverage, importing AFG files, and a few other clean ups. I > >> reviewed > >> >> the > >> >> changelog for the QT3 version, and I believe these are all of the > >> >> outstanding features, but please let me know if you spot any others. > >> >> > >> >> Thanks! > >> >> > >> >> Mike > >> >> > >> >> > >> >> On Tue, Jun 14, 2011 at 12:01 AM, Florent Angly > >> >> <flo...@gm...>wrote: > >> >> > >> >>> Hi Mike, > >> >>> > >> >>> Thanks for your work on making Hawkeye work with QT4! I'll be happy > >> to > >> >>> test it when you think it's ready. > >> >>> > >> >>> Can I ask you a favour and ask you that you have a look at what > >> >>> features > >> >>> were added to Hawkeye QT3 that were not added to Hawkeye QT4? I know > >> >>> for > >> >>> sure that I added support for sorting contigs by coverage (in > >> addition > >> >>> to > >> >>> length and number of reads) in the QT3 version and not the QT4 > >> version > >> >>> (that > >> >>> I was unaware of). Other developers may also have added features > >> that > >> >>> need > >> >>> to be brought to the QT4 version. > >> >>> > >> >>> Thanks, > >> >>> > >> >>> Florent > >> >>> > >> >>> > >> >>> > >> >>> > >> >>> On 14/06/11 01:56, Daniel Sommer wrote: > >> >>> > >> >>> Mike, I went ahead and removed hawkeye from the current automake > >> build > >> >>> system so it will not get built. Whenever you are ready feel free > >> to > >> >>> add it > >> >>> back in. > >> >>> Thanks, Dan > >> >>> > >> >>> PS, I CC'd anyone that I thought might add it back so that they > >> would > >> >>> know not to. > >> >>> > >> >>> > >> >>> > >> >>> On Wed, Jun 8, 2011 at 8:21 PM, Michael Schatz > >> >>> <mic...@gm...>wrote: > >> >>> > >> >>>> Hi Dan, > >> >>>> > >> >>>> I am in the middle of revamping hawkeye to use qt4 and add some > >> new > >> >>>> features. I removed the old version (using qt3) from CVS in > >> >>>> amos/src/bankviewer and now the only version lives in > >> amos/src/hawkeye > >> >>>> and > >> >>>> uses qt4. I didnt add it into the automake build system, because I > >> >>>> havent > >> >>>> had a chance to update it for qt4 but it looks like someone else > >> >>>> already > >> >>>> did. Can you coordinate the update to the automake system or should > >> I? > >> >>>> > >> >>>> Thanks, > >> >>>> > >> >>>> Mike > >> >>>> > >> >>>> > >> >>>> On Jun 8, 2011, at 5:10 PM, Daniel Sommer <ds...@um...> > >> >>>> wrote: > >> >>>> > >> >>>> Mike, The latest hawkeye checkin doesn't build correctly. Could > >> >>>> you > >> >>>> take a look at it? We have a new project that is testing the AMOS > >> >>>> builds > >> >>>> and they are reporting errors with hawkeye. I also am having > >> problems > >> >>>> building hawkeye. > >> >>>> > >> >>>> Thanks, Dan > >> >>>> > >> >>>> > >> >>>> ---------- Forwarded message ---------- > >> >>>> From: <br...@cs...> > >> >>>> Date: Wed, Jun 8, 2011 at 11:04 AM > >> >>>> Subject: Re: build errors > >> >>>> To: Daniel Sommer <ds...@um...> > >> >>>> Cc: Mihai Pop <mp...@um...>, at...@cs... > >> >>>> > >> >>>> > >> >>>> Hi Dan, > >> >>>> > >> >>>> Here is the error when I build AMOS on Ubuntu 10.10 > >> >>>> > >> >>>> Making all in hawkeye > >> >>>> make[3]: Entering directory `/home/bryanta/AMOS/src/hawkeye' > >> >>>> make[3]: *** No rule to make target `all'. Stop. > >> >>>> make[3]: Leaving directory `/home/bryanta/AMOS/src/hawkeye' > >> >>>> make[2]: *** [all-recursive] Error 1 > >> >>>> make[2]: Leaving directory `/home/bryanta/AMOS/src' > >> >>>> make[1]: *** [all-recursive] Error 1 > >> >>>> make[1]: Leaving directory `/home/bryanta/AMOS' > >> >>>> make: *** [all] Error 2 > >> >>>> > >> >>>> I installed qt3. > >> >>>> > >> >>>> And I also got a warning about BLAT that is required to use > >> >>>> minimus2-blat. > >> >>>> > >> >>>> Could you please tell me where I can get BLAT? I searched for it > >> but > >> >>>> could > >> >>>> not get it. > >> >>>> > >> >>>> Thanks, > >> >>>> Bryan > >> >>>> > Hi, Were you able to recreate the build errors you were getting > >> >>>> with > >> >>>> the > >> >>>> > latest AMOS code? When you get errors building AMOS just email > >> me > >> >>>> the > >> >>>> > error > >> >>>> > output and I will make sure the right developers get them. Later > >> we > >> >>>> > should > >> >>>> > have the automated tests email the amos-developer list so > >> everyone > >> >>>> working > >> >>>> > on AMOS can be notified of build errors. > >> >>>> > > >> >>>> > Dan > >> >>>> > > >> >>>> > >> >>>> > >> >>>> > >> >>>> > >> >>> > >> >>> > >> >> > >> > > >> > >> > >> > > > > > |
From: Michael S. <mic...@gm...> - 2011-07-29 18:30:55
|
Hi Byran, Looks like libz (the compression library) is not installed by default on ubuntu. Can you installing libz-devel and try 'cd src/hawkeye && qmake && make' again? Thanks, Mike On Fri, Jul 29, 2011 at 2:23 PM, <br...@cs...> wrote: > Hi Mike, > > I have just tested building AMOS with qt4 on ubuntu 10.10, ubuntu 11.04, > fedora 15 and cent OS 5.5. All machines failed at "make" step. On ubuntu > 11.04, I cd into src/hawkeye and then run "qmake; make" but got the > following error: > ".... > /usr/bin/ld: cannot find -lz > collect2: ld returned 1 exit status > make: *** [hawkeye] Error 1" > > These are the steps I followed to build AMOS: > > ./bootstrap > ./configure --with-Qt4-dir=/usr/share/qt4 --prefix=/usr/local/AMOS > make [*** got errors here and then I run "qmake; make" inside src/hawkeye] > make install > > Also, although qt4 was already installed > (libqt4-core/libqt4-dev/libqt4-gui for ubuntu, qt4.i686/qt4-devel.i686 for > fedora), it has this notice "WARNING! Qt4 toolkit was not found but is > required to run AMOS GUIs" > > So, Would it be possible that you could provide me with more detailed > instruction to build AMOS with qt4? > > Thanks, > Bryan > > > Hi Everyone, > > > > I added hawkeye back into the build system, and updated the autoconf to > > check for Qt 4 instead of Qt 3. I've tested it on my mac and on some > linux > > workstations at CBCB, and everything checks out. > > > > For mac, the preferred route is to install the precompiled libraries as > > frameworks into /Library/Frameworks/Qt*.frameworks -- once done, it > should > > automagically find them without needing any special flags. If you > > installed > > them someplace else use --with-Qt4-dir=/path/to/Frameworks (and > > --with-Qt4-bin-dir=/path/to/bin/moc if moc is not in your path) > > > > For linux, you should be able to use --with-Qt4-dir to point to the top > > level install directory. If you use a recent version of Qt, the path will > > look something like this: > > /path/to/packages/QtSDK/Desktop/Qt/473/gcc > > > > and inside will be bin/moc, include/Qt/*, lib/libQtCore.* > > > > On linux, it is possible that the automake version will fail because Qt > > requires some different libraries than expected. In this case, you can cd > > into src/hawkeye and manually run 'qmake; make' there separately. > > > > Please let me know if you have any questions or problems with it. > > > > Mike > > > > > > > > On Tue, Jun 14, 2011 at 11:07 PM, Michael Schatz > > <mic...@gm...>wrote: > > > >> Hi Florent, > >> > >> I just committed a patch to update Hawkeye/Qt4 to support sorting > >> contigs > >> by coverage, importing AFG files, and a few other clean ups. I reviewed > >> the > >> changelog for the QT3 version, and I believe these are all of the > >> outstanding features, but please let me know if you spot any others. > >> > >> Thanks! > >> > >> Mike > >> > >> > >> On Tue, Jun 14, 2011 at 12:01 AM, Florent Angly > >> <flo...@gm...>wrote: > >> > >>> Hi Mike, > >>> > >>> Thanks for your work on making Hawkeye work with QT4! I'll be happy to > >>> test it when you think it's ready. > >>> > >>> Can I ask you a favour and ask you that you have a look at what > >>> features > >>> were added to Hawkeye QT3 that were not added to Hawkeye QT4? I know > >>> for > >>> sure that I added support for sorting contigs by coverage (in addition > >>> to > >>> length and number of reads) in the QT3 version and not the QT4 version > >>> (that > >>> I was unaware of). Other developers may also have added features that > >>> need > >>> to be brought to the QT4 version. > >>> > >>> Thanks, > >>> > >>> Florent > >>> > >>> > >>> > >>> > >>> On 14/06/11 01:56, Daniel Sommer wrote: > >>> > >>> Mike, I went ahead and removed hawkeye from the current automake build > >>> system so it will not get built. Whenever you are ready feel free to > >>> add it > >>> back in. > >>> Thanks, Dan > >>> > >>> PS, I CC'd anyone that I thought might add it back so that they would > >>> know not to. > >>> > >>> > >>> > >>> On Wed, Jun 8, 2011 at 8:21 PM, Michael Schatz > >>> <mic...@gm...>wrote: > >>> > >>>> Hi Dan, > >>>> > >>>> I am in the middle of revamping hawkeye to use qt4 and add some new > >>>> features. I removed the old version (using qt3) from CVS in > >>>> amos/src/bankviewer and now the only version lives in amos/src/hawkeye > >>>> and > >>>> uses qt4. I didnt add it into the automake build system, because I > >>>> havent > >>>> had a chance to update it for qt4 but it looks like someone else > >>>> already > >>>> did. Can you coordinate the update to the automake system or should I? > >>>> > >>>> Thanks, > >>>> > >>>> Mike > >>>> > >>>> > >>>> On Jun 8, 2011, at 5:10 PM, Daniel Sommer <ds...@um...> > >>>> wrote: > >>>> > >>>> Mike, The latest hawkeye checkin doesn't build correctly. Could > >>>> you > >>>> take a look at it? We have a new project that is testing the AMOS > >>>> builds > >>>> and they are reporting errors with hawkeye. I also am having problems > >>>> building hawkeye. > >>>> > >>>> Thanks, Dan > >>>> > >>>> > >>>> ---------- Forwarded message ---------- > >>>> From: <br...@cs...> > >>>> Date: Wed, Jun 8, 2011 at 11:04 AM > >>>> Subject: Re: build errors > >>>> To: Daniel Sommer <ds...@um...> > >>>> Cc: Mihai Pop <mp...@um...>, at...@cs... > >>>> > >>>> > >>>> Hi Dan, > >>>> > >>>> Here is the error when I build AMOS on Ubuntu 10.10 > >>>> > >>>> Making all in hawkeye > >>>> make[3]: Entering directory `/home/bryanta/AMOS/src/hawkeye' > >>>> make[3]: *** No rule to make target `all'. Stop. > >>>> make[3]: Leaving directory `/home/bryanta/AMOS/src/hawkeye' > >>>> make[2]: *** [all-recursive] Error 1 > >>>> make[2]: Leaving directory `/home/bryanta/AMOS/src' > >>>> make[1]: *** [all-recursive] Error 1 > >>>> make[1]: Leaving directory `/home/bryanta/AMOS' > >>>> make: *** [all] Error 2 > >>>> > >>>> I installed qt3. > >>>> > >>>> And I also got a warning about BLAT that is required to use > >>>> minimus2-blat. > >>>> > >>>> Could you please tell me where I can get BLAT? I searched for it but > >>>> could > >>>> not get it. > >>>> > >>>> Thanks, > >>>> Bryan > >>>> > Hi, Were you able to recreate the build errors you were getting > >>>> with > >>>> the > >>>> > latest AMOS code? When you get errors building AMOS just email me > >>>> the > >>>> > error > >>>> > output and I will make sure the right developers get them. Later we > >>>> > should > >>>> > have the automated tests email the amos-developer list so everyone > >>>> working > >>>> > on AMOS can be notified of build errors. > >>>> > > >>>> > Dan > >>>> > > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >> > > > > > |
From: Michael S. <mic...@gm...> - 2011-07-25 18:20:19
|
Also, I just created a new 'Experimental' directory in the source tree and moved in several unpublished/one-off programs and utilities. This directory is only built if you specify --enable-Experimental in the configure script. Feel free to move other experimental programs in there as well. Cheers, Mike On Mon, Jul 25, 2011 at 2:48 AM, Michael Schatz <mic...@gm...>wrote: > Hi Everyone, > > I added hawkeye back into the build system, and updated the autoconf to > check for Qt 4 instead of Qt 3. I've tested it on my mac and on some linux > workstations at CBCB, and everything checks out. > > For mac, the preferred route is to install the precompiled libraries as > frameworks into /Library/Frameworks/Qt*.frameworks -- once done, it should > automagically find them without needing any special flags. If you installed > them someplace else use --with-Qt4-dir=/path/to/Frameworks (and > --with-Qt4-bin-dir=/path/to/bin/moc if moc is not in your path) > > For linux, you should be able to use --with-Qt4-dir to point to the top > level install directory. If you use a recent version of Qt, the path will > look something like this: > /path/to/packages/QtSDK/Desktop/Qt/473/gcc > > and inside will be bin/moc, include/Qt/*, lib/libQtCore.* > > On linux, it is possible that the automake version will fail because Qt > requires some different libraries than expected. In this case, you can cd > into src/hawkeye and manually run 'qmake; make' there separately. > > Please let me know if you have any questions or problems with it. > > Mike > > > > On Tue, Jun 14, 2011 at 11:07 PM, Michael Schatz <mic...@gm... > > wrote: > >> Hi Florent, >> >> I just committed a patch to update Hawkeye/Qt4 to support sorting contigs >> by coverage, importing AFG files, and a few other clean ups. I reviewed the >> changelog for the QT3 version, and I believe these are all of the >> outstanding features, but please let me know if you spot any others. >> >> Thanks! >> >> Mike >> >> >> On Tue, Jun 14, 2011 at 12:01 AM, Florent Angly <flo...@gm...>wrote: >> >>> Hi Mike, >>> >>> Thanks for your work on making Hawkeye work with QT4! I'll be happy to >>> test it when you think it's ready. >>> >>> Can I ask you a favour and ask you that you have a look at what features >>> were added to Hawkeye QT3 that were not added to Hawkeye QT4? I know for >>> sure that I added support for sorting contigs by coverage (in addition to >>> length and number of reads) in the QT3 version and not the QT4 version (that >>> I was unaware of). Other developers may also have added features that need >>> to be brought to the QT4 version. >>> >>> Thanks, >>> >>> Florent >>> >>> >>> >>> >>> On 14/06/11 01:56, Daniel Sommer wrote: >>> >>> Mike, I went ahead and removed hawkeye from the current automake build >>> system so it will not get built. Whenever you are ready feel free to add it >>> back in. >>> Thanks, Dan >>> >>> PS, I CC'd anyone that I thought might add it back so that they would >>> know not to. >>> >>> >>> >>> On Wed, Jun 8, 2011 at 8:21 PM, Michael Schatz <mic...@gm... >>> > wrote: >>> >>>> Hi Dan, >>>> >>>> I am in the middle of revamping hawkeye to use qt4 and add some new >>>> features. I removed the old version (using qt3) from CVS in >>>> amos/src/bankviewer and now the only version lives in amos/src/hawkeye and >>>> uses qt4. I didnt add it into the automake build system, because I havent >>>> had a chance to update it for qt4 but it looks like someone else already >>>> did. Can you coordinate the update to the automake system or should I? >>>> >>>> Thanks, >>>> >>>> Mike >>>> >>>> >>>> On Jun 8, 2011, at 5:10 PM, Daniel Sommer <ds...@um...> >>>> wrote: >>>> >>>> Mike, The latest hawkeye checkin doesn't build correctly. Could you >>>> take a look at it? We have a new project that is testing the AMOS builds >>>> and they are reporting errors with hawkeye. I also am having problems >>>> building hawkeye. >>>> >>>> Thanks, Dan >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: <br...@cs...> >>>> Date: Wed, Jun 8, 2011 at 11:04 AM >>>> Subject: Re: build errors >>>> To: Daniel Sommer <ds...@um...> >>>> Cc: Mihai Pop <mp...@um...>, at...@cs... >>>> >>>> >>>> Hi Dan, >>>> >>>> Here is the error when I build AMOS on Ubuntu 10.10 >>>> >>>> Making all in hawkeye >>>> make[3]: Entering directory `/home/bryanta/AMOS/src/hawkeye' >>>> make[3]: *** No rule to make target `all'. Stop. >>>> make[3]: Leaving directory `/home/bryanta/AMOS/src/hawkeye' >>>> make[2]: *** [all-recursive] Error 1 >>>> make[2]: Leaving directory `/home/bryanta/AMOS/src' >>>> make[1]: *** [all-recursive] Error 1 >>>> make[1]: Leaving directory `/home/bryanta/AMOS' >>>> make: *** [all] Error 2 >>>> >>>> I installed qt3. >>>> >>>> And I also got a warning about BLAT that is required to use >>>> minimus2-blat. >>>> >>>> Could you please tell me where I can get BLAT? I searched for it but >>>> could >>>> not get it. >>>> >>>> Thanks, >>>> Bryan >>>> > Hi, Were you able to recreate the build errors you were getting >>>> with the >>>> > latest AMOS code? When you get errors building AMOS just email me the >>>> > error >>>> > output and I will make sure the right developers get them. Later we >>>> > should >>>> > have the automated tests email the amos-developer list so everyone >>>> working >>>> > on AMOS can be notified of build errors. >>>> > >>>> > Dan >>>> > >>>> >>>> >>>> >>>> >>> >>> >> > |
From: Michael S. <mic...@gm...> - 2011-07-25 06:48:28
|
Hi Everyone, I added hawkeye back into the build system, and updated the autoconf to check for Qt 4 instead of Qt 3. I've tested it on my mac and on some linux workstations at CBCB, and everything checks out. For mac, the preferred route is to install the precompiled libraries as frameworks into /Library/Frameworks/Qt*.frameworks -- once done, it should automagically find them without needing any special flags. If you installed them someplace else use --with-Qt4-dir=/path/to/Frameworks (and --with-Qt4-bin-dir=/path/to/bin/moc if moc is not in your path) For linux, you should be able to use --with-Qt4-dir to point to the top level install directory. If you use a recent version of Qt, the path will look something like this: /path/to/packages/QtSDK/Desktop/Qt/473/gcc and inside will be bin/moc, include/Qt/*, lib/libQtCore.* On linux, it is possible that the automake version will fail because Qt requires some different libraries than expected. In this case, you can cd into src/hawkeye and manually run 'qmake; make' there separately. Please let me know if you have any questions or problems with it. Mike On Tue, Jun 14, 2011 at 11:07 PM, Michael Schatz <mic...@gm...>wrote: > Hi Florent, > > I just committed a patch to update Hawkeye/Qt4 to support sorting contigs > by coverage, importing AFG files, and a few other clean ups. I reviewed the > changelog for the QT3 version, and I believe these are all of the > outstanding features, but please let me know if you spot any others. > > Thanks! > > Mike > > > On Tue, Jun 14, 2011 at 12:01 AM, Florent Angly <flo...@gm...>wrote: > >> Hi Mike, >> >> Thanks for your work on making Hawkeye work with QT4! I'll be happy to >> test it when you think it's ready. >> >> Can I ask you a favour and ask you that you have a look at what features >> were added to Hawkeye QT3 that were not added to Hawkeye QT4? I know for >> sure that I added support for sorting contigs by coverage (in addition to >> length and number of reads) in the QT3 version and not the QT4 version (that >> I was unaware of). Other developers may also have added features that need >> to be brought to the QT4 version. >> >> Thanks, >> >> Florent >> >> >> >> >> On 14/06/11 01:56, Daniel Sommer wrote: >> >> Mike, I went ahead and removed hawkeye from the current automake build >> system so it will not get built. Whenever you are ready feel free to add it >> back in. >> Thanks, Dan >> >> PS, I CC'd anyone that I thought might add it back so that they would >> know not to. >> >> >> >> On Wed, Jun 8, 2011 at 8:21 PM, Michael Schatz <mic...@gm...>wrote: >> >>> Hi Dan, >>> >>> I am in the middle of revamping hawkeye to use qt4 and add some new >>> features. I removed the old version (using qt3) from CVS in >>> amos/src/bankviewer and now the only version lives in amos/src/hawkeye and >>> uses qt4. I didnt add it into the automake build system, because I havent >>> had a chance to update it for qt4 but it looks like someone else already >>> did. Can you coordinate the update to the automake system or should I? >>> >>> Thanks, >>> >>> Mike >>> >>> >>> On Jun 8, 2011, at 5:10 PM, Daniel Sommer <ds...@um...> >>> wrote: >>> >>> Mike, The latest hawkeye checkin doesn't build correctly. Could you >>> take a look at it? We have a new project that is testing the AMOS builds >>> and they are reporting errors with hawkeye. I also am having problems >>> building hawkeye. >>> >>> Thanks, Dan >>> >>> >>> ---------- Forwarded message ---------- >>> From: <br...@cs...> >>> Date: Wed, Jun 8, 2011 at 11:04 AM >>> Subject: Re: build errors >>> To: Daniel Sommer <ds...@um...> >>> Cc: Mihai Pop <mp...@um...>, at...@cs... >>> >>> >>> Hi Dan, >>> >>> Here is the error when I build AMOS on Ubuntu 10.10 >>> >>> Making all in hawkeye >>> make[3]: Entering directory `/home/bryanta/AMOS/src/hawkeye' >>> make[3]: *** No rule to make target `all'. Stop. >>> make[3]: Leaving directory `/home/bryanta/AMOS/src/hawkeye' >>> make[2]: *** [all-recursive] Error 1 >>> make[2]: Leaving directory `/home/bryanta/AMOS/src' >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory `/home/bryanta/AMOS' >>> make: *** [all] Error 2 >>> >>> I installed qt3. >>> >>> And I also got a warning about BLAT that is required to use >>> minimus2-blat. >>> >>> Could you please tell me where I can get BLAT? I searched for it but >>> could >>> not get it. >>> >>> Thanks, >>> Bryan >>> > Hi, Were you able to recreate the build errors you were getting with >>> the >>> > latest AMOS code? When you get errors building AMOS just email me the >>> > error >>> > output and I will make sure the right developers get them. Later we >>> > should >>> > have the automated tests email the amos-developer list so everyone >>> working >>> > on AMOS can be notified of build errors. >>> > >>> > Dan >>> > >>> >>> >>> >>> >> >> > |
From: Michael S. <ms...@cs...> - 2011-07-25 00:14:30
|
Thanks Dan, I updated the AMOS programmers guide on the wiki: http://sourceforge.net/apps/mediawiki/amos/index.php?title=Programmer%27s_guide And added a mini tutorial on how to commit changes locally and push them back to the repo. Also- I plan to cut a AMOS 3.1 release around August 1st, so please commit any outstanding changes this week. Best, Mike On Fri, Jul 22, 2011 at 1:28 PM, Daniel Sommer <ds...@um...>wrote: > Guys, With the switch to git all the amos documentation that mentions > using cvs to checkout the AMOS code is now outdated. I am going to > try to update things but most likely will miss some so if you see > anything that mentions cvs please change to git. > > Thanks, > Dan > > On Fri, Jul 22, 2011 at 1:17 PM, Daniel Sommer <ds...@um...> > wrote: > > Everything is now switched over to git and cvs is disabled. > > Everything switched over relatively smoothly. The revision history, > > tags and branches all look good. git handles usernames differently > > than cvs so some of usernames on the old commits have been converted > > to a default user. I am looking into fixing this but it shouldn't > > effect users going forward. > > > > I put an archive of the entire cvsroot in /fs/szdevel/amos-cvsroot.tgz. > > > > Dan Sommer > > > > > > On Fri, Jul 22, 2011 at 12:58 PM, Michael Schatz <ms...@cs...> > wrote: > >> Hi Dan, > >> How did the transfer go? I'm planning to do some AMOS/Hawkeye > development > >> this weekend and am hoping to use git for this. > >> Mike > >> > >> On Wed, Jul 20, 2011 at 7:35 PM, Florent Angly <flo...@gm... > > > >> wrote: > >>> > >>> Hi Daniel, > >>> > >>> I have wished for quite some time that AMOS would be under git control > >>> rather than cvs. So, thanks so much for making the transition Dan! I > >>> don't have any outstanding commits, so as far as I am concerned, go > ahead. > >>> > >>> Regarding hosting the project on Sourceforge vs Github, the advantage > of > >>> Github I think is the ability to make a fork of a project. That fork is > >>> hosted on Github and the changes on this fork can later be pushed to > the > >>> original repository. That makes is very easy for people that aren't > >>> official developers of the project to contribute code. On Sourceforge, > >>> if you are not a maintainer of a project, you can obviously clone the > >>> repository on your local harddrive, but how can you contribute your > >>> changes back to the official project? > >>> > >>> Cheers, > >>> > >>> Florent > >>> > >>> > >>> > >>> On 21/07/11 02:11, Daniel Sommer wrote: > >>> > We are going to stick with sourceforge for now. I believe moving to > >>> > github would require new user accounts, moving the help forum and > >>> > wiki/webpages. > >>> > > >>> > I am good with turning off cvs immediately. Since the switch over > was > >>> > happening on short notice I was going to give people time but > everyone > >>> > seems to be good with switching now. I will turn off cvs. > >>> > > >>> > BTW, Git and CVS repositories can run in parallel since in git every > >>> > working tree contains a repository with a full copy of the project > >>> > history. It can be setup so git just looks at the main cvs > repository > >>> > as just another working tree. But this would require some daily > >>> > manual syncing by me so I am glad to turn off cvs. > >>> > > >>> > > >>> > Dan > >>> > > >>> > > >>> > On Wed, Jul 20, 2011 at 11:24 AM, Michael Schatz<ms...@cs...> > >>> > wrote: > >>> >> Hi Dan, > >>> >> I suggest we turn off cvs immediately after copying to git so we > don't > >>> >> accidentally commit to the wrong repo. Also, where will the new git > repo be > >>> >> housed: at sourceforge or at another site (github)? > >>> >> Thanks! > >>> >> Mike > >>> >> > >>> >> On Wed, Jul 20, 2011 at 10:52 AM, Daniel Sommer< > ds...@um...> > >>> >> wrote: > >>> >>> The AMOS project is moving to git for source control from cvs. > >>> >>> Soureforge support of cvs has been getting worse. It is down more > often > >>> >>> and always the last source control back up after an outage. Also > git should > >>> >>> give us some new needed functionality. There are many good > tutorials online > >>> >>> for git and "cvs to git" tutorials. Main git documentation site: > >>> >>> git-scm.com/documentation<http://git-scm.com/documentation>. > There will be > >>> >>> a small downtime tomorrow night when I copy over the cvs logs over > to git. > >>> >>> If you have changes to amos you can commit them or just submit > them once we > >>> >>> move over to git. We can run cvs and git in parallel for small > amount of > >>> >>> time but cvs will be turned off in the near future. > >>> >>> > >>> >>> Thanks, Dan Sommer > >>> >>> > >>> >> > >>> >> > >>> >> -- > >>> >> > >>> >> Assistant Professor of Quantitative Biology > >>> >> Cold Spring Harbor Laboratory > >>> >> > >>> >> One Bungtown Road > >>> >> Koch Building #1119 > >>> >> Cold Spring Harbor, NY 11724 > >>> >> phone: 703-966-1987 > >>> >> email: ms...@cs... > >>> >> web: http://schatzlab.cshl.edu > >>> >> > >>> > >>> > >>> > >>> > ------------------------------------------------------------------------------ > >>> 10 Tips for Better Web Security > >>> Learn 10 ways to better secure your business today. Topics covered > >>> include: > >>> Web security, SSL, hacker attacks & Denial of Service (DoS), private > keys, > >>> security Microsoft Exchange, secure Instant Messaging, and much more. > >>> http://www.accelacomm.com/jaw/sfnl/114/51426210/ > >>> _______________________________________________ > >>> AMOS-devel mailing list > >>> AMO...@li... > >>> https://lists.sourceforge.net/lists/listinfo/amos-devel > >> > >> > >> > >> -- > >> > >> Assistant Professor of Quantitative Biology > >> Cold Spring Harbor Laboratory > >> > >> One Bungtown Road > >> Koch Building #1119 > >> Cold Spring Harbor, NY 11724 > >> phone: 703-966-1987 > >> email: ms...@cs... > >> web: http://schatzlab.cshl.edu > >> > >> > > > > > ------------------------------------------------------------------------------ > 10 Tips for Better Web Security > Learn 10 ways to better secure your business today. Topics covered include: > Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, > security Microsoft Exchange, secure Instant Messaging, and much more. > http://www.accelacomm.com/jaw/sfnl/114/51426210/ > _______________________________________________ > AMOS-devel mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-devel > -- Assistant Professor of Quantitative Biology Cold Spring Harbor Laboratory One Bungtown Road Koch Building #1119 Cold Spring Harbor, NY 11724 phone: 703-966-1987 email: ms...@cs... web: http://schatzlab.cshl.edu |