mychem-discuss Mailing List for Mychem
Status: Beta
Brought to you by:
pansanel
Menu
▾
▴
mychem-discuss — Discussion of Mychem Issues
You can subscribe to this list here.
| 2009 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(2) |
Sep
(1) |
Oct
(2) |
Nov
|
Dec
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2010 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
(1) |
Oct
|
Nov
|
Dec
|
| 2012 |
Jan
(1) |
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
(8) |
| 2014 |
Jan
(4) |
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2015 |
Jan
(1) |
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
(1) |
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
| 2016 |
Jan
|
Feb
(4) |
Mar
(8) |
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
|
From: Fredrik W. <fr...@wa...> - 2016-10-20 18:34:12
|
Hi,
What versions of OpenBabel and Mychem do you use?
I also think that this question is best answered in the Mychem list so I forwarded it there.
Kind regards,
Fredrik
Skickat från min iPhone
> 20 okt. 2016 kl. 18:44 skrev Martin Morissette <mar...@ou...>:
>
> Hi, I would need some help to create a SQL query that returns hits ordered on the tanimoto coefficient of the queried smiles and the fingerprints stored in the database. So far, I was able to set the sql variable as follow :
> SET @fp = (SELECT FINGERPRINT2(SMILES_TO_MOLECULE(‘smiles')));
> Where the smiles is inserted with php from a JSME input
> Then I want to modify the current substructure search query :
> $query = "SELECT compounds.name AS No, pdt.fullname as Name FROM pdt,compounds,bin_structures WHERE pdt.name=compounds.name AND compounds.id=bin_structures.compound_id AND MATCH_SUBSTRUCT('".$_POST['smiles']."',obserialized)";
> to compute the tanimoto of @fp and bin_structures.fp2
> Whenever I try to compute TANIMOTO(@fp, fp2) from bin_structures I get a NULL value.
> I tried the TANIMOTO function examples from the documentation but I always get NULL values.
> If I use two variables @fp1 and @fp2 and set these values with 2 different smiles fingerprints, I can compute the TANIMOTO(@fp1, @fp2).
> I use a LAMP stack on Ubuntu 14.04 64 bits.
> Any help is welcome
> Thank you
> Martin
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
|
|
From: Muriel K. <mur...@gm...> - 2016-03-24 16:12:42
|
Hello, I completly deactivate AppArmor for mysql ( $ sudo aa-complain /etc/apparmor.d/usr.sbin.mysqld ) and now it is working. Thank you very much, Muriel 2016-03-24 16:51 GMT+01:00 Muriel Keribin <mur...@gm...>: > And yes I am using Ubuntu ( Ubuntu 14.04.3 LTS (GNU/Linux > 3.19.0-25-generic x86_64) ), mySQL 14.14 and openbabel 2.3.90 > > 2016-03-24 16:11 GMT+01:00 Jerome Pansanel <j.p...@pa...>: > >> Hi Muriel, >> >> Are you using Ubuntu? Did you look at: >> http://mychem.sourceforge.net/doc/apbs02.html >> >> In your case, replace /usr/lib/openbabel by /usr/local/openbabel/lib >> >> Best, >> >> Jerome >> >> Le 24/03/2016 16:05, Muriel Keribin a écrit : >> > Hello, >> > >> > I try to install mychem (I had it installed before but I update my >> > openbabel version and the command were not working anymore). >> > >> > To compile it I had to use >> > $ cmake >> > -DOPENBABEL2_INCLUDE_DIR=/usr/local/openbabel/include/openbabel-2.0/ >> > -DOPENBABEL2_LIBRARIES=/usr/local/openbabel/lib/libopenbabel.so.4 .. >> > >> > Then everything compiles and the installation is done without errors. >> > >> > Then, the >> > $ mysql -u user -p < ../src/mychemdb.sql >> > gives the following error >> > ERROR 1126 (HY000) at line 10: Can't open shared library 'libmychem.so' >> > (errno: 0 libopenbabel.so.4: cannot open shared object file: No such >> > file or directory) >> > >> > $ ldd ..../libmychem.so told me it does not find the libopenbabel.so.4 >> > So I added in the etc/ld.so.conf the complete path to the folder of the >> > openbabel.so.4 >> > then >> > $ ldd/libmychem.so >> > gives me >> > libopenbabel.so.4 => /usr/local/openbabel/lib/libopenbabel.so.4 >> > (0x00007f43d504c000) >> > >> > and I still got the same ERROR 1126 >> > >> > I restart mysql and reboot the machine... and I still have this ERROR >> > 1126... >> > >> > >> > >> > I also try the "module test enable", and all the tests failed. I looked >> > at the LastTest.log, I saw for all tests the following : >> > Error: query failed (FUNCTION mysql.molfile_to_molecule does not exist) >> > Testing molfile_to_molecule ... [FAILED] >> > >> > So I think this is because I cannot load the functions to mysql... >> > >> > >> > I wonder what I am doing wrong, and what I can do to make it works. >> > >> > Best >> > Muriel >> > >> > >> > >> > >> ------------------------------------------------------------------------------ >> > Transform Data into Opportunity. >> > Accelerate data analysis in your applications with >> > Intel Data Analytics Acceleration Library. >> > Click to learn more. >> > http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 >> > >> > >> > >> > _______________________________________________ >> > Mychem-discuss mailing list >> > Myc...@li... >> > https://lists.sourceforge.net/lists/listinfo/mychem-discuss >> > >> >> >> >> ------------------------------------------------------------------------------ >> Transform Data into Opportunity. >> Accelerate data analysis in your applications with >> Intel Data Analytics Acceleration Library. >> Click to learn more. >> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 >> _______________________________________________ >> Mychem-discuss mailing list >> Myc...@li... >> https://lists.sourceforge.net/lists/listinfo/mychem-discuss >> > > |
|
From: Jerome P. <j.p...@pa...> - 2016-03-24 15:28:37
|
Hi Muriel, Are you using Ubuntu? Did you look at: http://mychem.sourceforge.net/doc/apbs02.html In your case, replace /usr/lib/openbabel by /usr/local/openbabel/lib Best, Jerome Le 24/03/2016 16:05, Muriel Keribin a écrit : > Hello, > > I try to install mychem (I had it installed before but I update my > openbabel version and the command were not working anymore). > > To compile it I had to use > $ cmake > -DOPENBABEL2_INCLUDE_DIR=/usr/local/openbabel/include/openbabel-2.0/ > -DOPENBABEL2_LIBRARIES=/usr/local/openbabel/lib/libopenbabel.so.4 .. > > Then everything compiles and the installation is done without errors. > > Then, the > $ mysql -u user -p < ../src/mychemdb.sql > gives the following error > ERROR 1126 (HY000) at line 10: Can't open shared library 'libmychem.so' > (errno: 0 libopenbabel.so.4: cannot open shared object file: No such > file or directory) > > $ ldd ..../libmychem.so told me it does not find the libopenbabel.so.4 > So I added in the etc/ld.so.conf the complete path to the folder of the > openbabel.so.4 > then > $ ldd/libmychem.so > gives me > libopenbabel.so.4 => /usr/local/openbabel/lib/libopenbabel.so.4 > (0x00007f43d504c000) > > and I still got the same ERROR 1126 > > I restart mysql and reboot the machine... and I still have this ERROR > 1126... > > > > I also try the "module test enable", and all the tests failed. I looked > at the LastTest.log, I saw for all tests the following : > Error: query failed (FUNCTION mysql.molfile_to_molecule does not exist) > Testing molfile_to_molecule ... [FAILED] > > So I think this is because I cannot load the functions to mysql... > > > I wonder what I am doing wrong, and what I can do to make it works. > > Best > Muriel > > > > ------------------------------------------------------------------------------ > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 > > > > _______________________________________________ > Mychem-discuss mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-discuss > |
|
From: Muriel K. <mur...@gm...> - 2016-03-24 15:05:28
|
Hello, I try to install mychem (I had it installed before but I update my openbabel version and the command were not working anymore). To compile it I had to use $ cmake -DOPENBABEL2_INCLUDE_DIR=/usr/local/openbabel/include/openbabel-2.0/ -DOPENBABEL2_LIBRARIES=/usr/local/openbabel/lib/libopenbabel.so.4 .. Then everything compiles and the installation is done without errors. Then, the $ mysql -u user -p < ../src/mychemdb.sql gives the following error ERROR 1126 (HY000) at line 10: Can't open shared library 'libmychem.so' (errno: 0 libopenbabel.so.4: cannot open shared object file: No such file or directory) $ ldd ..../libmychem.so told me it does not find the libopenbabel.so.4 So I added in the etc/ld.so.conf the complete path to the folder of the openbabel.so.4 then $ ldd/libmychem.so gives me libopenbabel.so.4 => /usr/local/openbabel/lib/libopenbabel.so.4 (0x00007f43d504c000) and I still got the same ERROR 1126 I restart mysql and reboot the machine... and I still have this ERROR 1126... I also try the "module test enable", and all the tests failed. I looked at the LastTest.log, I saw for all tests the following : Error: query failed (FUNCTION mysql.molfile_to_molecule does not exist) Testing molfile_to_molecule ... [FAILED] So I think this is because I cannot load the functions to mysql... I wonder what I am doing wrong, and what I can do to make it works. Best Muriel |
|
From: JoeSox <jo...@gm...> - 2016-03-03 20:40:11
|
I appreciate the help. I did find a guide here https://sourceforge.net/projects/mychem/files/documentation/0.9.3/mychem.pdf/download -- Thank You, Joe On Thu, Mar 3, 2016 at 11:35 AM, Fredrik Wallner <fr...@wa...> wrote: > There is no database created. You have to create a database yourself > according to your needs. I believe there is a tutorial on the Mychem > website. > > Kind regards, > Fredrik > > Skickat från min iPhone > > 3 mars 2016 kl. 19:56 skrev JoeSox <jo...@gm...>: > > Fredrik, > Thanks yes, I am using 0.9.3 and unbuntu 14.04LTS. > I ran the command without error but when I log into phpMyAdmin I only see > these databases: > information_schema > mysql > performance_schema > phpmyadmin > > Should I be able to see the database using phpadmin? If so what should it > be named again? > > -- > Thank you, Joe > > On Wed, Mar 2, 2016 at 11:48 PM, Fredrik Wallner <fr...@wa...> > wrote: > >> I just look at the source forge files listing and 0.9.3 is listed there >> as well. The only thing is that sourceforge doesn’t seem to mark it as >> newest for some reason (see screenshot), is that something you can look at >> Jerome? >> >> Kind regards, >> Fredrik >> <Mychem_-_Browse__mychem_at_SourceForge_net.png> >> >> 3 mars 2016 kl. 08:45 skrev Fredrik Wallner <fr...@wa...>: >> >> Hi, >> >> The development of Mychem has moved to GitHub and the releases can be >> found here https://github.com/mychem/mychem-code/releases >> If you look at the Mychem homepage at http://mychem.sourceforge.net it >> shows the links to github under ”Download”. >> >> Anyway, after running "*mysql -u user -p < src/mychemdb.sql”* you are >> done. Your mysql database is now chemically aware. What to do next is >> entirely dependent on your use-case. >> >> Kind regards, >> Fredrik >> >> 2 mars 2016 kl. 16:49 skrev JoeSox <jo...@gm...>: >> >> Jerome and Fredrik,Thanks for the replies. >> The sourceforge website says 0.9.2 is the latest version to download >> https://sourceforge.net/projects/mychem/files >> >> I am farther now but not sure what to do after >> "*mysql -u user -p < src/mychemdb.sql" ??* >> >> that ran without error >> >> sudo apt-get install libopenbabel-dev >> sudo apt-get install libmysqlclient-dev >> sudo apt-get install pkg-config >> seemed to do the trick. >> -- >> Thank You, Joe >> >> On Wed, Mar 2, 2016 at 1:08 AM, Fredrik Wallner <fr...@wa...> >> wrote: >> >>> Hi, >>> >>> A couple of points to help you going on. First of all it seems like you >>> are using mychem 0.9.2, but I believe the latest is 0.9.3 so a first try >>> would be to download the latest version. Secondly, please make sure that >>> you have both openbabel and mysql installed, specifically you need the >>> development packages, i.e. libopenbabel-dev and libmysqlclient-dev. I would >>> also make sure that pkg-config is installed. Finally, with this in place >>> start from the beginning by deleting the build directory and let cmake do >>> its thing. >>> >>> Kind regards, >>> Fredrik >>> >>> 23 feb. 2016 kl. 21:50 skrev JoeSox <jo...@gm...>: >>> >>> Hello, >>> Not sure how active this list is but I was wondering if I could get some >>> second eyes on my installation issues with Ubuntu 14.04 32bit >>> I am not exactly sure why it is erroring out as it doesn't seem to be >>> finding the mysql installation as it states "MySQL not found"? >>> Attached is the CMakeOutput.log >>> >>> >>> I am following these instructions >>> http://mychem.sourceforge.net/doc/apas03.html >>> A.3.1.1. Standard Installation on GNU/Linux >>> -- >>> Thank You, Joe >>> <CMakeOutput.log> >>> ------------------------------------------------------------------------------ >>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>> Monitor end-to-end web transactions and take corrective actions now >>> Troubleshoot faster and improve end-user experience. Signup Now! >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ >>> Mychem-discuss mailing list >>> Myc...@li... >>> https://lists.sourceforge.net/lists/listinfo/mychem-discuss >>> >>> >>> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ >> Mychem-discuss mailing list >> Myc...@li... >> https://lists.sourceforge.net/lists/listinfo/mychem-discuss >> >> >> >> > |
|
From: Fredrik W. <fr...@wa...> - 2016-03-03 19:35:23
|
There is no database created. You have to create a database yourself according to your needs. I believe there is a tutorial on the Mychem website. Kind regards, Fredrik Skickat från min iPhone > 3 mars 2016 kl. 19:56 skrev JoeSox <jo...@gm...>: > > Fredrik, > Thanks yes, I am using 0.9.3 and unbuntu 14.04LTS. > I ran the command without error but when I log into phpMyAdmin I only see these databases: > information_schema > mysql > performance_schema > phpmyadmin > > Should I be able to see the database using phpadmin? If so what should it be named again? > > -- > Thank you, Joe > >> On Wed, Mar 2, 2016 at 11:48 PM, Fredrik Wallner <fr...@wa...> wrote: >> I just look at the source forge files listing and 0.9.3 is listed there as well. The only thing is that sourceforge doesn’t seem to mark it as newest for some reason (see screenshot), is that something you can look at Jerome? >> >> Kind regards, >> Fredrik >> <Mychem_-_Browse__mychem_at_SourceForge_net.png> >> >>> 3 mars 2016 kl. 08:45 skrev Fredrik Wallner <fr...@wa...>: >>> >>> Hi, >>> >>> The development of Mychem has moved to GitHub and the releases can be found here https://github.com/mychem/mychem-code/releases >>> If you look at the Mychem homepage at http://mychem.sourceforge.net it shows the links to github under ”Download”. >>> >>> Anyway, after running "mysql -u user -p < src/mychemdb.sql” you are done. Your mysql database is now chemically aware. What to do next is entirely dependent on your use-case. >>> >>> Kind regards, >>> Fredrik >>> >>>> 2 mars 2016 kl. 16:49 skrev JoeSox <jo...@gm...>: >>>> >>>> Jerome and Fredrik,Thanks for the replies. >>>> The sourceforge website says 0.9.2 is the latest version to download >>>> https://sourceforge.net/projects/mychem/files >>>> >>>> I am farther now but not sure what to do after >>>> "mysql -u user -p < src/mychemdb.sql" ?? >>>> >>>> that ran without error >>>> >>>> sudo apt-get install libopenbabel-dev >>>> sudo apt-get install libmysqlclient-dev >>>> sudo apt-get install pkg-config >>>> seemed to do the trick. >>>> -- >>>> Thank You, Joe >>>> >>>>> On Wed, Mar 2, 2016 at 1:08 AM, Fredrik Wallner <fr...@wa...> wrote: >>>>> Hi, >>>>> >>>>> A couple of points to help you going on. First of all it seems like you are using mychem 0.9.2, but I believe the latest is 0.9.3 so a first try would be to download the latest version. Secondly, please make sure that you have both openbabel and mysql installed, specifically you need the development packages, i.e. libopenbabel-dev and libmysqlclient-dev. I would also make sure that pkg-config is installed. Finally, with this in place start from the beginning by deleting the build directory and let cmake do its thing. >>>>> >>>>> Kind regards, >>>>> Fredrik >>>>>> 23 feb. 2016 kl. 21:50 skrev JoeSox <jo...@gm...>: >>>>>> >>>>>> Hello, >>>>>> Not sure how active this list is but I was wondering if I could get some second eyes on my installation issues with Ubuntu 14.04 32bit >>>>>> I am not exactly sure why it is erroring out as it doesn't seem to be finding the mysql installation as it states "MySQL not found"? >>>>>> Attached is the CMakeOutput.log >>>>>> >>>>>> >>>>>> I am following these instructions http://mychem.sourceforge.net/doc/apas03.html >>>>>> A.3.1.1. Standard Installation on GNU/Linux >>>>>> -- >>>>>> Thank You, Joe >>>>>> <CMakeOutput.log>------------------------------------------------------------------------------ >>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>> Monitor end-to-end web transactions and take corrective actions now >>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ >>>>>> Mychem-discuss mailing list >>>>>> Myc...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/mychem-discuss >>>> >>>> ------------------------------------------------------------------------------ >>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>> Monitor end-to-end web transactions and take corrective actions now >>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ >>>> Mychem-discuss mailing list >>>> Myc...@li... >>>> https://lists.sourceforge.net/lists/listinfo/mychem-discuss > |
|
From: JoeSox <jo...@gm...> - 2016-03-02 15:50:20
|
Jerome and Fredrik,Thanks for the replies. The sourceforge website says 0.9.2 is the latest version to download https://sourceforge.net/projects/mychem/files I am farther now but not sure what to do after "*mysql -u user -p < src/mychemdb.sql" ??* that ran without error sudo apt-get install libopenbabel-dev sudo apt-get install libmysqlclient-dev sudo apt-get install pkg-config seemed to do the trick. -- Thank You, Joe On Wed, Mar 2, 2016 at 1:08 AM, Fredrik Wallner <fr...@wa...> wrote: > Hi, > > A couple of points to help you going on. First of all it seems like you > are using mychem 0.9.2, but I believe the latest is 0.9.3 so a first try > would be to download the latest version. Secondly, please make sure that > you have both openbabel and mysql installed, specifically you need the > development packages, i.e. libopenbabel-dev and libmysqlclient-dev. I would > also make sure that pkg-config is installed. Finally, with this in place > start from the beginning by deleting the build directory and let cmake do > its thing. > > Kind regards, > Fredrik > > 23 feb. 2016 kl. 21:50 skrev JoeSox <jo...@gm...>: > > Hello, > Not sure how active this list is but I was wondering if I could get some > second eyes on my installation issues with Ubuntu 14.04 32bit > I am not exactly sure why it is erroring out as it doesn't seem to be > finding the mysql installation as it states "MySQL not found"? > Attached is the CMakeOutput.log > > > I am following these instructions > http://mychem.sourceforge.net/doc/apas03.html > A.3.1.1. Standard Installation on GNU/Linux > -- > Thank You, Joe > <CMakeOutput.log> > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ > Mychem-discuss mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-discuss > > > |
|
From: Fredrik W. <fr...@wa...> - 2016-03-02 09:27:19
|
Hi, A couple of points to help you going on. First of all it seems like you are using mychem 0.9.2, but I believe the latest is 0.9.3 so a first try would be to download the latest version. Secondly, please make sure that you have both openbabel and mysql installed, specifically you need the development packages, i.e. libopenbabel-dev and libmysqlclient-dev. I would also make sure that pkg-config is installed. Finally, with this in place start from the beginning by deleting the build directory and let cmake do its thing. Kind regards, Fredrik > 23 feb. 2016 kl. 21:50 skrev JoeSox <jo...@gm...>: > > Hello, > Not sure how active this list is but I was wondering if I could get some second eyes on my installation issues with Ubuntu 14.04 32bit > I am not exactly sure why it is erroring out as it doesn't seem to be finding the mysql installation as it states "MySQL not found"? > Attached is the CMakeOutput.log > > > I am following these instructions http://mychem.sourceforge.net/doc/apas03.html <http://mychem.sourceforge.net/doc/apas03.html> > A.3.1.1. Standard Installation on GNU/Linux > -- > Thank You, Joe > <CMakeOutput.log>------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ > Mychem-discuss mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-discuss |
|
From: Jerome P. <j.p...@pa...> - 2016-03-02 09:21:05
|
Hi Joe, Did you install yourself MySQL ? Can you install the following package on your Ubuntu : libmysqlclient-dev Cheers, Jerome Le 23/02/2016 23:03, JoeSox a écrit : > update: > I used cmake-gui to help me out with the variables but I am not sure I > am headed down the correct path. > Here is the latest output > > > root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build# > <mailto:root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build#> cmake .. > > -- The build type is RelWithDebInfo > > -- Test module disabled > > -- Using mysql-config: /etc/mysql/my.cnf > > -- MySQL Version: sh: 1: /etc/mysql/my.cnf: Permission denied > > -- MySQL Plugin Dir: > > -- Found MySQL sh: 1: /etc/mysql/my.cnf: Permission denied: > /usr/include/i386-linux-gnu, /usr/include/i386-linux-gnu > > -- Mychem installation directory: /usr/local/lib > > -- Defining dlhandler source files > > -- Configuring done > > WARNING: Target "mychem-lib" requests linking to directory > "/usr/include/i386-linux-gnu". Targets may link only to libraries. > CMake is dropping the item. > > WARNING: Target "conversion_test" requests linking to directory > "/usr/include/i386-linux-gnu". Targets may link only to libraries. > CMake is dropping the item. > > WARNING: Target "helper_test" requests linking to directory > "/usr/include/i386-linux-gnu". Targets may link only to libraries. > CMake is dropping the item. > > WARNING: Target "modification_test" requests linking to directory > "/usr/include/i386-linux-gnu". Targets may link only to libraries. > CMake is dropping the item. > > WARNING: Target "molmatch_test" requests linking to directory > "/usr/include/i386-linux-gnu". Targets may link only to libraries. > CMake is dropping the item. > > WARNING: Target "property_test" requests linking to directory > "/usr/include/i386-linux-gnu". Targets may link only to libraries. > CMake is dropping the item. > > -- Generating done > > -- Build files have been written to: /home/it/Downloads/mychem-0.9.2/build > > root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build# > <mailto:root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build#> make > > Scanning dependencies of target mychem-lib > > [ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o > > In file included from /home/it/Downloads/mychem-0.9.2/src/conversion.c:31:0: > > /home/it/Downloads/mychem-0.9.2/src/conversion.h:45:23: fatal error: > my_global.h: No such file or directory > > #include <my_global.h> > > ^ > > compilation terminated. > > make[2]: *** [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1 > > make[1]: *** [src/CMakeFiles/mychem-lib.dir/all] Error 2 > > make: *** [all] Error 2 > > root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build# > <mailto:root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build#> > > > > -- > Thanks, Joe > > ---------- Forwarded message ---------- > From: *JoeSox* <jo...@gm... <mailto:jo...@gm...>> > Date: Tue, Feb 23, 2016 at 1:07 PM > Subject: Fwd: Configuring incomplete, error occurred! > To: myc...@li... > <mailto:myc...@li...> > > > Hello, > I was wondering if I could get some second eyes on my installation > issues with Ubuntu 14.04 32bit > I am not exactly sure why it is erroring out as it doesn't seem to be > finding the mysql installation as it states "MySQL not found"? > > I am following these > instructions http://mychem.sourceforge.net/doc/apas03.html > A.3.1.1. Standard Installation on GNU/Linux > > CMake Error: The following variables are used in this project, but they > are set to NOTFOUND. > > Please set them or make sure they are set and tested correctly in the > CMake files: > > MYSQL_LIBRARIES_mysqlclient > > linked by target "mychem-lib" in directory > /home/it/Downloads/mychem-0.9.2/src > > linked by target "conversion_test" in directory > /home/it/Downloads/mychem-0.9.2/tests > > linked by target "helper_test" in directory > /home/it/Downloads/mychem-0.9.2/tests > > linked by target "modification_test" in directory > /home/it/Downloads/mychem-0.9.2/tests > > linked by target "molmatch_test" in directory > /home/it/Downloads/mychem-0.9.2/tests > > linked by target "property_test" in directory > /home/it/Downloads/mychem-0.9.2/tests > > MySQL_INCLUDE_DIR (ADVANCED) > > used as include directory in directory > /home/it/Downloads/mychem-0.9.2/src > > used as include directory in directory > /home/it/Downloads/mychem-0.9.2/tests > > used as include directory in directory > /home/it/Downloads/mychem-0.9.2/tests > > used as include directory in directory > /home/it/Downloads/mychem-0.9.2/tests > > used as include directory in directory > /home/it/Downloads/mychem-0.9.2/tests > > used as include directory in directory > /home/it/Downloads/mychem-0.9.2/tests > > > > -- Configuring incomplete, errors occurred! > > > > I am not sure which file I need to edit those variables if I am reading > that correctly. > -- > Thank You, Joe > > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > > > > _______________________________________________ > Mychem-discuss mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-discuss > |
|
From: JoeSox <jo...@gm...> - 2016-02-23 22:03:52
|
update:
I used cmake-gui to help me out with the variables but I am not sure I am
headed down the correct path.
Here is the latest output
root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build# cmake ..
-- The build type is RelWithDebInfo
-- Test module disabled
-- Using mysql-config: /etc/mysql/my.cnf
-- MySQL Version: sh: 1: /etc/mysql/my.cnf: Permission denied
-- MySQL Plugin Dir:
-- Found MySQL sh: 1: /etc/mysql/my.cnf: Permission denied:
/usr/include/i386-linux-gnu, /usr/include/i386-linux-gnu
-- Mychem installation directory: /usr/local/lib
-- Defining dlhandler source files
-- Configuring done
WARNING: Target "mychem-lib" requests linking to directory
"/usr/include/i386-linux-gnu". Targets may link only to libraries. CMake
is dropping the item.
WARNING: Target "conversion_test" requests linking to directory
"/usr/include/i386-linux-gnu". Targets may link only to libraries. CMake
is dropping the item.
WARNING: Target "helper_test" requests linking to directory
"/usr/include/i386-linux-gnu". Targets may link only to libraries. CMake
is dropping the item.
WARNING: Target "modification_test" requests linking to directory
"/usr/include/i386-linux-gnu". Targets may link only to libraries. CMake
is dropping the item.
WARNING: Target "molmatch_test" requests linking to directory
"/usr/include/i386-linux-gnu". Targets may link only to libraries. CMake
is dropping the item.
WARNING: Target "property_test" requests linking to directory
"/usr/include/i386-linux-gnu". Targets may link only to libraries. CMake
is dropping the item.
-- Generating done
-- Build files have been written to: /home/it/Downloads/mychem-0.9.2/build
root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build# make
Scanning dependencies of target mychem-lib
[ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o
In file included from /home/it/Downloads/mychem-0.9.2/src/conversion.c:31:0:
/home/it/Downloads/mychem-0.9.2/src/conversion.h:45:23: fatal error:
my_global.h: No such file or directory
#include <my_global.h>
^
compilation terminated.
make[2]: *** [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1
make[1]: *** [src/CMakeFiles/mychem-lib.dir/all] Error 2
make: *** [all] Error 2
root@it-testubuntu:/home/it/Downloads/mychem-0.9.2/build#
--
Thanks, Joe
---------- Forwarded message ----------
From: JoeSox <jo...@gm...>
Date: Tue, Feb 23, 2016 at 1:07 PM
Subject: Fwd: Configuring incomplete, error occurred!
To: myc...@li...
Hello,
I was wondering if I could get some second eyes on my installation issues
with Ubuntu 14.04 32bit
I am not exactly sure why it is erroring out as it doesn't seem to be
finding the mysql installation as it states "MySQL not found"?
I am following these instructions
http://mychem.sourceforge.net/doc/apas03.html
A.3.1.1. Standard Installation on GNU/Linux
CMake Error: The following variables are used in this project, but they are
set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake
files:
MYSQL_LIBRARIES_mysqlclient
linked by target "mychem-lib" in directory
/home/it/Downloads/mychem-0.9.2/src
linked by target "conversion_test" in directory
/home/it/Downloads/mychem-0.9.2/tests
linked by target "helper_test" in directory
/home/it/Downloads/mychem-0.9.2/tests
linked by target "modification_test" in directory
/home/it/Downloads/mychem-0.9.2/tests
linked by target "molmatch_test" in directory
/home/it/Downloads/mychem-0.9.2/tests
linked by target "property_test" in directory
/home/it/Downloads/mychem-0.9.2/tests
MySQL_INCLUDE_DIR (ADVANCED)
used as include directory in directory
/home/it/Downloads/mychem-0.9.2/src
used as include directory in directory
/home/it/Downloads/mychem-0.9.2/tests
used as include directory in directory
/home/it/Downloads/mychem-0.9.2/tests
used as include directory in directory
/home/it/Downloads/mychem-0.9.2/tests
used as include directory in directory
/home/it/Downloads/mychem-0.9.2/tests
used as include directory in directory
/home/it/Downloads/mychem-0.9.2/tests
-- Configuring incomplete, errors occurred!
I am not sure which file I need to edit those variables if I am reading
that correctly.
--
Thank You, Joe
|
|
From: JoeSox <jo...@gm...> - 2016-02-23 21:07:19
|
Hello, I was wondering if I could get some second eyes on my installation issues with Ubuntu 14.04 32bit I am not exactly sure why it is erroring out as it doesn't seem to be finding the mysql installation as it states "MySQL not found"? I am following these instructions http://mychem.sourceforge.net/doc/apas03.html A.3.1.1. Standard Installation on GNU/Linux CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: MYSQL_LIBRARIES_mysqlclient linked by target "mychem-lib" in directory /home/it/Downloads/mychem-0.9.2/src linked by target "conversion_test" in directory /home/it/Downloads/mychem-0.9.2/tests linked by target "helper_test" in directory /home/it/Downloads/mychem-0.9.2/tests linked by target "modification_test" in directory /home/it/Downloads/mychem-0.9.2/tests linked by target "molmatch_test" in directory /home/it/Downloads/mychem-0.9.2/tests linked by target "property_test" in directory /home/it/Downloads/mychem-0.9.2/tests MySQL_INCLUDE_DIR (ADVANCED) used as include directory in directory /home/it/Downloads/mychem-0.9.2/src used as include directory in directory /home/it/Downloads/mychem-0.9.2/tests used as include directory in directory /home/it/Downloads/mychem-0.9.2/tests used as include directory in directory /home/it/Downloads/mychem-0.9.2/tests used as include directory in directory /home/it/Downloads/mychem-0.9.2/tests used as include directory in directory /home/it/Downloads/mychem-0.9.2/tests -- Configuring incomplete, errors occurred! I am not sure which file I need to edit those variables if I am reading that correctly. -- Thank You, Joe |
|
From: JoeSox <jo...@gm...> - 2016-02-23 21:01:30
|
Hello, (Sorry if duplicate, but this one is without the attachment) Not sure how active this list is but I was wondering if I could get some second eyes on my installation issues with Ubuntu 14.04 32bit I am not exactly sure why it is erroring out as it doesn't seem to be finding the mysql installation as it states "MySQL not found"? below is some output from CMakeOutput.log I am following these instructions http://mychem.sourceforge.net/doc/apas03.html A.3.1.1. Standard Installation on GNU/Linux The system is: Linux - 4.2.0-27-generic - i686 Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded. Compiler: /usr/bin/cc Build flags: Id flags: The output was: 0 Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out" The C compiler identification is GNU, found in "/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/2.8.12.2/CompilerIdC/a.out " Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded. Compiler: /usr/bin/c++ Build flags: Id flags: The output was: 0 Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out" The CXX compiler identification is GNU, found in "/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/ 2.8.12.2/CompilerIdCXX/a.out" Determining if the C compiler works passed with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec1392744111/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec1392744111.dir/build.make CMakeFiles/cmTryCompileExec1392744111.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec1392744111.dir/testCCompiler.c.o /usr/bin/cc -o CMakeFiles/cmTryCompileExec1392744111.dir/testCCompiler.c.o -c /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/testCCompiler.c Linking C executable cmTryCompileExec1392744111 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1392744111.dir/link.txt --verbose=1 /usr/bin/cc CMakeFiles/cmTryCompileExec1392744111.dir/testCCompiler.c.o -o cmTryCompileExec1392744111 -rdynamic make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' Detecting C compiler ABI info compiled with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec4180922737/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec4180922737.dir/build.make CMakeFiles/cmTryCompileExec4180922737.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o /usr/bin/cc -o CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o -c /usr/share/cmake-2.8/Modules/CMakeCCompilerABI.c Linking C executable cmTryCompileExec4180922737 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec4180922737.dir/link.txt --verbose=1 /usr/bin/cc -v CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o -o cmTryCompileExec4180922737 -rdynamic Using built-in specs. COLLECT_GCC=/usr/bin/cc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.8/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04.1' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-i386 --with-arch-directory=i386 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1) COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec4180922737' '-rdynamic' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib/ld-linux.so.2 -z relro -o cmTryCompileExec4180922737 /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crt1.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/i686-linux-gnu/4.8 -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.8/../../.. CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/i686-linux-gnu/4.8/crtend.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crtn.o make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' Parsed C implicit link information from above output: link line regex: [^( *|.*[/\])(ld|([^/\]+-)?ld|collect2)[^/\]*( |$)] ignore line: [Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp] ignore line: [] ignore line: [Run Build Command:/usr/bin/make "cmTryCompileExec4180922737/fast"] ignore line: [/usr/bin/make -f CMakeFiles/cmTryCompileExec4180922737.dir/build.make CMakeFiles/cmTryCompileExec4180922737.dir/build] ignore line: [make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp'] ignore line: [/usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1] ignore line: [Building C object CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o] ignore line: [/usr/bin/cc -o CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o -c /usr/share/cmake-2.8/Modules/CMakeCCompilerABI.c] ignore line: [Linking C executable cmTryCompileExec4180922737] ignore line: [/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec4180922737.dir/link.txt --verbose=1] ignore line: [/usr/bin/cc -v CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o -o cmTryCompileExec4180922737 -rdynamic ] ignore line: [Using built-in specs.] ignore line: [COLLECT_GCC=/usr/bin/cc] ignore line: [COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.8/lto-wrapper] ignore line: [Target: i686-linux-gnu] ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04.1' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-i386 --with-arch-directory=i386 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu] ignore line: [Thread model: posix] ignore line: [gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1) ] ignore line: [COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/] ignore line: [LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../:/lib/:/usr/lib/] ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec4180922737' '-rdynamic' '-mtune=generic' '-march=i686'] link line: [ /usr/lib/gcc/i686-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib/ld-linux.so.2 -z relro -o cmTryCompileExec4180922737 /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crt1.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/i686-linux-gnu/4.8 -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.8/../../.. CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/i686-linux-gnu/4.8/crtend.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crtn.o] arg [/usr/lib/gcc/i686-linux-gnu/4.8/collect2] ==> ignore arg [--sysroot=/] ==> ignore arg [--build-id] ==> ignore arg [--eh-frame-hdr] ==> ignore arg [-m] ==> ignore arg [elf_i386] ==> ignore arg [--hash-style=gnu] ==> ignore arg [--as-needed] ==> ignore arg [-export-dynamic] ==> ignore arg [-dynamic-linker] ==> ignore arg [/lib/ld-linux.so.2] ==> ignore arg [-zrelro] ==> ignore arg [-o] ==> ignore arg [cmTryCompileExec4180922737] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crt1.o] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crti.o] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/crtbegin.o] ==> ignore arg [-L/usr/lib/gcc/i686-linux-gnu/4.8] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8] arg [-L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu] arg [-L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib] arg [-L/lib/i386-linux-gnu] ==> dir [/lib/i386-linux-gnu] arg [-L/lib/../lib] ==> dir [/lib/../lib] arg [-L/usr/lib/i386-linux-gnu] ==> dir [/usr/lib/i386-linux-gnu] arg [-L/usr/lib/../lib] ==> dir [/usr/lib/../lib] arg [-L/usr/lib/gcc/i686-linux-gnu/4.8/../../..] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../..] arg [CMakeFiles/cmTryCompileExec4180922737.dir/CMakeCCompilerABI.c.o] ==> ignore arg [-lgcc] ==> lib [gcc] arg [--as-needed] ==> ignore arg [-lgcc_s] ==> lib [gcc_s] arg [--no-as-needed] ==> ignore arg [-lc] ==> lib [c] arg [-lgcc] ==> lib [gcc] arg [--as-needed] ==> ignore arg [-lgcc_s] ==> lib [gcc_s] arg [--no-as-needed] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/crtend.o] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crtn.o] ==> ignore remove lib [gcc] remove lib [gcc_s] remove lib [gcc] remove lib [gcc_s] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8] ==> [/usr/lib/gcc/i686-linux-gnu/4.8] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu] ==> [/usr/lib/i386-linux-gnu] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib] ==> [/usr/lib] collapse library dir [/lib/i386-linux-gnu] ==> [/lib/i386-linux-gnu] collapse library dir [/lib/../lib] ==> [/lib] collapse library dir [/usr/lib/i386-linux-gnu] ==> [/usr/lib/i386-linux-gnu] collapse library dir [/usr/lib/../lib] ==> [/usr/lib] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../..] ==> [/usr/lib] implicit libs: [c] implicit dirs: [/usr/lib/gcc/i686-linux-gnu/4.8;/usr/lib/i386-linux-gnu;/usr/lib;/lib/i386-linux-gnu;/lib] implicit fwks: [] Determining if the CXX compiler works passed with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec102389692/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec102389692.dir/build.make CMakeFiles/cmTryCompileExec102389692.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building CXX object CMakeFiles/cmTryCompileExec102389692.dir/testCXXCompiler.cxx.o /usr/bin/c++ -o CMakeFiles/cmTryCompileExec102389692.dir/testCXXCompiler.cxx.o -c /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx Linking CXX executable cmTryCompileExec102389692 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec102389692.dir/link.txt --verbose=1 /usr/bin/c++ CMakeFiles/cmTryCompileExec102389692.dir/testCXXCompiler.cxx.o -o cmTryCompileExec102389692 -rdynamic make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' Detecting CXX compiler ABI info compiled with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec3170478078/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec3170478078.dir/build.make CMakeFiles/cmTryCompileExec3170478078.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building CXX object CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o /usr/bin/c++ -o CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o -c /usr/share/cmake-2.8/Modules/CMakeCXXCompilerABI.cpp Linking CXX executable cmTryCompileExec3170478078 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3170478078.dir/link.txt --verbose=1 /usr/bin/c++ -v CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o -o cmTryCompileExec3170478078 -rdynamic Using built-in specs. COLLECT_GCC=/usr/bin/c++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.8/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04.1' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-i386 --with-arch-directory=i386 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1) COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec3170478078' '-rdynamic' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib/ld-linux.so.2 -z relro -o cmTryCompileExec3170478078 /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crt1.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/i686-linux-gnu/4.8 -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.8/../../.. CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/4.8/crtend.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crtn.o make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' Parsed CXX implicit link information from above output: link line regex: [^( *|.*[/\])(ld|([^/\]+-)?ld|collect2)[^/\]*( |$)] ignore line: [Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp] ignore line: [] ignore line: [Run Build Command:/usr/bin/make "cmTryCompileExec3170478078/fast"] ignore line: [/usr/bin/make -f CMakeFiles/cmTryCompileExec3170478078.dir/build.make CMakeFiles/cmTryCompileExec3170478078.dir/build] ignore line: [make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp'] ignore line: [/usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1] ignore line: [Building CXX object CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o] ignore line: [/usr/bin/c++ -o CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o -c /usr/share/cmake-2.8/Modules/CMakeCXXCompilerABI.cpp] ignore line: [Linking CXX executable cmTryCompileExec3170478078] ignore line: [/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3170478078.dir/link.txt --verbose=1] ignore line: [/usr/bin/c++ -v CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o -o cmTryCompileExec3170478078 -rdynamic ] ignore line: [Using built-in specs.] ignore line: [COLLECT_GCC=/usr/bin/c++] ignore line: [COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.8/lto-wrapper] ignore line: [Target: i686-linux-gnu] ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04.1' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-i386 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-i386 --with-arch-directory=i386 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu] ignore line: [Thread model: posix] ignore line: [gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1) ] ignore line: [COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/] ignore line: [LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.8/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.8/../../../:/lib/:/usr/lib/] ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec3170478078' '-rdynamic' '-shared-libgcc' '-mtune=generic' '-march=i686'] link line: [ /usr/lib/gcc/i686-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib/ld-linux.so.2 -z relro -o cmTryCompileExec3170478078 /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crt1.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/i686-linux-gnu/4.8 -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.8/../../.. CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/4.8/crtend.o /usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crtn.o] arg [/usr/lib/gcc/i686-linux-gnu/4.8/collect2] ==> ignore arg [--sysroot=/] ==> ignore arg [--build-id] ==> ignore arg [--eh-frame-hdr] ==> ignore arg [-m] ==> ignore arg [elf_i386] ==> ignore arg [--hash-style=gnu] ==> ignore arg [--as-needed] ==> ignore arg [-export-dynamic] ==> ignore arg [-dynamic-linker] ==> ignore arg [/lib/ld-linux.so.2] ==> ignore arg [-zrelro] ==> ignore arg [-o] ==> ignore arg [cmTryCompileExec3170478078] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crt1.o] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crti.o] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/crtbegin.o] ==> ignore arg [-L/usr/lib/gcc/i686-linux-gnu/4.8] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8] arg [-L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu] arg [-L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib] arg [-L/lib/i386-linux-gnu] ==> dir [/lib/i386-linux-gnu] arg [-L/lib/../lib] ==> dir [/lib/../lib] arg [-L/usr/lib/i386-linux-gnu] ==> dir [/usr/lib/i386-linux-gnu] arg [-L/usr/lib/../lib] ==> dir [/usr/lib/../lib] arg [-L/usr/lib/gcc/i686-linux-gnu/4.8/../../..] ==> dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../..] arg [CMakeFiles/cmTryCompileExec3170478078.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore arg [-lstdc++] ==> lib [stdc++] arg [-lm] ==> lib [m] arg [-lgcc_s] ==> lib [gcc_s] arg [-lgcc] ==> lib [gcc] arg [-lc] ==> lib [c] arg [-lgcc_s] ==> lib [gcc_s] arg [-lgcc] ==> lib [gcc] arg [/usr/lib/gcc/i686-linux-gnu/4.8/crtend.o] ==> ignore arg [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu/crtn.o] ==> ignore remove lib [gcc_s] remove lib [gcc] remove lib [gcc_s] remove lib [gcc] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8] ==> [/usr/lib/gcc/i686-linux-gnu/4.8] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu] ==> [/usr/lib/i386-linux-gnu] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib] ==> [/usr/lib] collapse library dir [/lib/i386-linux-gnu] ==> [/lib/i386-linux-gnu] collapse library dir [/lib/../lib] ==> [/lib] collapse library dir [/usr/lib/i386-linux-gnu] ==> [/usr/lib/i386-linux-gnu] collapse library dir [/usr/lib/../lib] ==> [/usr/lib] collapse library dir [/usr/lib/gcc/i686-linux-gnu/4.8/../../..] ==> [/usr/lib] implicit libs: [stdc++;m;c] implicit dirs: [/usr/lib/gcc/i686-linux-gnu/4.8;/usr/lib/i386-linux-gnu;/usr/lib;/lib/i386-linux-gnu;/lib] implicit fwks: [] Determining if the include file stdlib.h exists passed with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec1184516468/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec1184516468.dir/build.make CMakeFiles/cmTryCompileExec1184516468.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec1184516468.dir/CheckIncludeFile.c.o /usr/bin/cc -o CMakeFiles/cmTryCompileExec1184516468.dir/CheckIncludeFile.c.o -c /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c Linking C executable cmTryCompileExec1184516468 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1184516468.dir/link.txt --verbose=1 /usr/bin/cc CMakeFiles/cmTryCompileExec1184516468.dir/CheckIncludeFile.c.o -o cmTryCompileExec1184516468 -rdynamic make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' Determining if the include file stdio.h exists passed with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec3775167972/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec3775167972.dir/build.make CMakeFiles/cmTryCompileExec3775167972.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec3775167972.dir/CheckIncludeFile.c.o /usr/bin/cc -o CMakeFiles/cmTryCompileExec3775167972.dir/CheckIncludeFile.c.o -c /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c Linking C executable cmTryCompileExec3775167972 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3775167972.dir/link.txt --verbose=1 /usr/bin/cc CMakeFiles/cmTryCompileExec3775167972.dir/CheckIncludeFile.c.o -o cmTryCompileExec3775167972 -rdynamic make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' Determining if the include file string.h exists passed with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec1801199595/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec1801199595.dir/build.make CMakeFiles/cmTryCompileExec1801199595.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec1801199595.dir/CheckIncludeFile.c.o /usr/bin/cc -o CMakeFiles/cmTryCompileExec1801199595.dir/CheckIncludeFile.c.o -c /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c Linking C executable cmTryCompileExec1801199595 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1801199595.dir/link.txt --verbose=1 /usr/bin/cc CMakeFiles/cmTryCompileExec1801199595.dir/CheckIncludeFile.c.o -o cmTryCompileExec1801199595 -rdynamic make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' Determining if the include file sstream exists passed with the following output: Change Dir: /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make "cmTryCompileExec2537652457/fast" /usr/bin/make -f CMakeFiles/cmTryCompileExec2537652457.dir/build.make CMakeFiles/cmTryCompileExec2537652457.dir/build make[1]: Entering directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building CXX object CMakeFiles/cmTryCompileExec2537652457.dir/CheckIncludeFile.cxx.o /usr/bin/c++ -o CMakeFiles/cmTryCompileExec2537652457.dir/CheckIncludeFile.cxx.o -c /home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx Linking CXX executable cmTryCompileExec2537652457 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2537652457.dir/link.txt --verbose=1 /usr/bin/c++ CMakeFiles/cmTryCompileExec2537652457.dir/CheckIncludeFile.cxx.o -o cmTryCompileExec2537652457 -rdynamic make[1]: Leaving directory `/home/it/Downloads/mychem-0.9.2/build/CMakeFiles/CMakeTmp' -- Thank You, Joe |
|
From: JoeSox <jo...@gm...> - 2016-02-23 20:50:42
|
Hello, Not sure how active this list is but I was wondering if I could get some second eyes on my installation issues with Ubuntu 14.04 32bit I am not exactly sure why it is erroring out as it doesn't seem to be finding the mysql installation as it states "MySQL not found"? Attached is the CMakeOutput.log I am following these instructions http://mychem.sourceforge.net/doc/apas03.html A.3.1.1. Standard Installation on GNU/Linux -- Thank You, Joe |
|
From: Jerome P. <j.p...@pa...> - 2015-10-27 17:42:33
|
Hi, The new version of Mychem has been released. It is mainly a bug fix. The documentation has also been completed. You can download it from : * https://sourceforge.net/projects/mychem/files/mychem/0.9.3/mychem-0.9.3.tgz/download * https://sourceforge.net/projects/mychem/files/mychem/0.9.3/mychem-0.9.3.zip/download Cheers, Jerome Pansanel |
|
From: Fredrik W. <fr...@wa...> - 2015-07-02 11:09:00
|
Hi, I think I have managed to fix the issue and I submitted a pull request on GitHub. If you would like to test it out before it is merged you could try to clone my rep at https://github.com/fredrikw/mychem-code <https://github.com/fredrikw/mychem-code> Kind regards, Fredrik > 18 jun 2015 kl. 03:32 skrev dua...@ic...: > > > Hi, > > Mychem.0.9.2 is installed and the tests are passed except two functions 'cml_to_molecule' and 'molecule_to_cml', and then the mychem database is created according to the instructions of " The Mychem Handbook". When the "select match_substruct('C=O', obserialzied ) from bin_structures " is executed, the message "ERROR 1123 (HY000): Can't initialize function 'match_substruct'; The second argument is null" is returned. substruct_ATOM_IDS() and substruct_count() functions can be executed correctly. Would you like to give me some help about the above error message? Thanks in advance. > > Best Regards > > Duan Baogen > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Mychem-discuss mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-discuss |
|
From: <dua...@ic...> - 2015-06-18 01:50:22
|
Hi,
Mychem.0.9.2 is installed and the tests are passed except two functions 'cml_to_molecule' and 'molecule_to_cml', and then the mychem database is created according to the instructions of " The Mychem Handbook". When the "select match_substruct('C=O', obserialzied ) from bin_structures " is executed, the message "ERROR 1123 (HY000): Can't initialize function 'match_substruct'; The second argument is null" is returned. substruct_ATOM_IDS() and substruct_count() functions can be executed correctly. Would you like to give me some help about the above error message? Thanks in advance.
Best Regards
Duan Baogen
|
|
From: Jerome P. <j.p...@pa...> - 2015-01-25 23:08:29
|
Hi, I did not send any news since a long time ago. First of all, I wish you a very happy new Year! I have moved the Mychem code to GitHub. If you want to retrieve the last version of the source code: git clone https://github.com/mychem/mychem-code.git If you want to contribute, you should first fork the project in your GitHub repository and then propose any modification via Pull Request. I will add you also to the GitHub project. The website remains hosted at SourceForge, as the official source packages. The last official version of Mychem is 0.9.2: https://sourceforge.net/projects/mychem/files/mychem/0.9.2/ This release contains a fix for bug #15 (https://sourceforge.net/p/mychem/bugs/15/) Cheers, Jerome |
|
From: Taka S. <ser...@gm...> - 2014-01-25 02:17:47
|
Dear Jerome. Thank you for your quick reply and advice. Yes I use ubunts 12.04 64bit. I tried your advice. But I got same error . Thanks. 2014/1/24 Jerome Pansanel <j.p...@pa...> > Dear Takyuki, > > Are you using Ubuntu? Did you apply the fix for AppArmor as described > on: > http://mychem.sourceforge.net/doc/apbs02.html > > Best regards, > > Jerome > > Le jeudi 23 janvier 2014 à 06:33 +0900, Taka Seri a écrit : > > Dear all. > > > > > > I tried to install mychem but it was faild. > > > > I checked error.log file, and I got following messages. > > > > It seems to that my system failed to open libmychem.so . > > I was wondering if anyone might have same advices or suggestion to me? > > > > Best regards. > > > > > > Takyuki > > > > key_buffer_size=16777216 > > read_buffer_size=131072 > > max_used_connections=1 > > max_threads=151 > > thread_count=1 > > connection_count=1 > > It is possible that mysqld could use up to > > key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = > > 346700 K bytes of memory > > Hope that's ok; if not, decrease some variables in the equation. > > > > Thread pointer: 0x7f03dfa46a20 > > Attempting backtrace. You can use the following information to find > > out > > where mysqld died. If you see no messages after this, something went > > terribly wrong... > > 140120 19:50:41 [Warning] Using unique option prefix myisam-recover > > instead of myisam-recover-options is deprecated and will be removed in > > a future release. Please use the full name instead. > > 140120 19:50:41 [Note] Plugin 'FEDERATED' is disabled. > > 140120 19:50:41 InnoDB: The InnoDB memory heap is disabled > > 140120 19:50:41 InnoDB: Mutexes and rw_locks use GCC atomic builtins > > 140120 19:50:41 InnoDB: Compressed tables use zlib 1.2.3.4 > > 140120 19:50:41 InnoDB: Initializing buffer pool, size = 128.0M > > 140120 19:50:41 InnoDB: Completed initialization of buffer pool > > 140120 19:50:41 InnoDB: highest supported file format is Barracuda. > > InnoDB: The log sequence number in ibdata files does not match > > InnoDB: the log sequence number in the ib_logfiles! > > 140120 19:50:41 InnoDB: Database was not shut down normally! > > InnoDB: Starting crash recovery. > > InnoDB: Reading tablespace information from the .ibd files... > > InnoDB: Restoring possible half-written data pages from the > > doublewrite > > InnoDB: buffer... > > 140120 19:50:41 InnoDB: Waiting for the background threads to start > > 140120 19:50:42 InnoDB: 5.5.34 started; log sequence number 3528273 > > 140120 19:50:42 [Note] Server hostname (bind-address): '127.0.0.1'; > > port: 3306 > > 140120 19:50:42 [Note] - '127.0.0.1' resolves to '127.0.0.1'; > > 140120 19:50:42 [Note] Server socket created on IP: '127.0.0.1'. > > 140120 19:50:42 [ERROR] Can't open shared library > > 'libmychem.so' (errno: 0 /usr/lib/mysql/plugin/libmychem.so: undefined > > symbol: _ZN9OpenBabel5OBMol7AddAtomERNS_6OBAtomEb) > > 140120 19:50:42 [Note] Event Scheduler: Loaded 0 events > > 140120 19:50:42 [Note] /usr/sbin/mysqld: ready for connections. > > Version: '5.5.34-0ubuntu0.12.04.1' socket: > > '/var/run/mysqld/mysqld.sock' port: 3306 (Ubuntu) > > > > > ------------------------------------------------------------------------------ > > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > > Learn Why More Businesses Are Choosing CenturyLink Cloud For > > Critical Workloads, Development Environments & Everything In Between. > > Get a Quote or Start a Free Trial Today. > > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > > _______________________________________________ > > Mychem-discuss mailing list > > Myc...@li... > > https://lists.sourceforge.net/lists/listinfo/mychem-discuss > > > |
|
From: Jerome P. <j.p...@pa...> - 2014-01-23 22:20:55
|
Dear Takyuki, Are you using Ubuntu? Did you apply the fix for AppArmor as described on: http://mychem.sourceforge.net/doc/apbs02.html Best regards, Jerome Le jeudi 23 janvier 2014 à 06:33 +0900, Taka Seri a écrit : > Dear all. > > > I tried to install mychem but it was faild. > > I checked error.log file, and I got following messages. > > It seems to that my system failed to open libmychem.so . > I was wondering if anyone might have same advices or suggestion to me? > > Best regards. > > > Takyuki > > key_buffer_size=16777216 > read_buffer_size=131072 > max_used_connections=1 > max_threads=151 > thread_count=1 > connection_count=1 > It is possible that mysqld could use up to > key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = > 346700 K bytes of memory > Hope that's ok; if not, decrease some variables in the equation. > > Thread pointer: 0x7f03dfa46a20 > Attempting backtrace. You can use the following information to find > out > where mysqld died. If you see no messages after this, something went > terribly wrong... > 140120 19:50:41 [Warning] Using unique option prefix myisam-recover > instead of myisam-recover-options is deprecated and will be removed in > a future release. Please use the full name instead. > 140120 19:50:41 [Note] Plugin 'FEDERATED' is disabled. > 140120 19:50:41 InnoDB: The InnoDB memory heap is disabled > 140120 19:50:41 InnoDB: Mutexes and rw_locks use GCC atomic builtins > 140120 19:50:41 InnoDB: Compressed tables use zlib 1.2.3.4 > 140120 19:50:41 InnoDB: Initializing buffer pool, size = 128.0M > 140120 19:50:41 InnoDB: Completed initialization of buffer pool > 140120 19:50:41 InnoDB: highest supported file format is Barracuda. > InnoDB: The log sequence number in ibdata files does not match > InnoDB: the log sequence number in the ib_logfiles! > 140120 19:50:41 InnoDB: Database was not shut down normally! > InnoDB: Starting crash recovery. > InnoDB: Reading tablespace information from the .ibd files... > InnoDB: Restoring possible half-written data pages from the > doublewrite > InnoDB: buffer... > 140120 19:50:41 InnoDB: Waiting for the background threads to start > 140120 19:50:42 InnoDB: 5.5.34 started; log sequence number 3528273 > 140120 19:50:42 [Note] Server hostname (bind-address): '127.0.0.1'; > port: 3306 > 140120 19:50:42 [Note] - '127.0.0.1' resolves to '127.0.0.1'; > 140120 19:50:42 [Note] Server socket created on IP: '127.0.0.1'. > 140120 19:50:42 [ERROR] Can't open shared library > 'libmychem.so' (errno: 0 /usr/lib/mysql/plugin/libmychem.so: undefined > symbol: _ZN9OpenBabel5OBMol7AddAtomERNS_6OBAtomEb) > 140120 19:50:42 [Note] Event Scheduler: Loaded 0 events > 140120 19:50:42 [Note] /usr/sbin/mysqld: ready for connections. > Version: '5.5.34-0ubuntu0.12.04.1' socket: > '/var/run/mysqld/mysqld.sock' port: 3306 (Ubuntu) > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Mychem-discuss mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-discuss |
|
From: Taka S. <ser...@gm...> - 2014-01-22 21:33:11
|
Dear all. I tried to install mychem but it was faild. I checked error.log file, and I got following messages. It seems to that my system failed to open libmychem.so . I was wondering if anyone might have same advices or suggestion to me? Best regards. Takyuki key_buffer_size=16777216 read_buffer_size=131072 max_used_connections=1 max_threads=151 thread_count=1 connection_count=1 It is possible that mysqld could use up to key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 346700 K bytes of memory Hope that's ok; if not, decrease some variables in the equation. Thread pointer: 0x7f03dfa46a20 Attempting backtrace. You can use the following information to find out where mysqld died. If you see no messages after this, something went terribly wrong... 140120 19:50:41 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead. 140120 19:50:41 [Note] Plugin 'FEDERATED' is disabled. 140120 19:50:41 InnoDB: The InnoDB memory heap is disabled 140120 19:50:41 InnoDB: Mutexes and rw_locks use GCC atomic builtins 140120 19:50:41 InnoDB: Compressed tables use zlib 1.2.3.4 140120 19:50:41 InnoDB: Initializing buffer pool, size = 128.0M 140120 19:50:41 InnoDB: Completed initialization of buffer pool 140120 19:50:41 InnoDB: highest supported file format is Barracuda. InnoDB: The log sequence number in ibdata files does not match InnoDB: the log sequence number in the ib_logfiles! 140120 19:50:41 InnoDB: Database was not shut down normally! InnoDB: Starting crash recovery. InnoDB: Reading tablespace information from the .ibd files... InnoDB: Restoring possible half-written data pages from the doublewrite InnoDB: buffer... 140120 19:50:41 InnoDB: Waiting for the background threads to start 140120 19:50:42 InnoDB: 5.5.34 started; log sequence number 3528273 140120 19:50:42 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306 140120 19:50:42 [Note] - '127.0.0.1' resolves to '127.0.0.1'; 140120 19:50:42 [Note] Server socket created on IP: '127.0.0.1'. 140120 19:50:42 [ERROR] Can't open shared library 'libmychem.so' (errno: 0 /usr/lib/mysql/plugin/libmychem.so: undefined symbol: _ZN9OpenBabel5OBMol7AddAtomERNS_6OBAtomEb) 140120 19:50:42 [Note] Event Scheduler: Loaded 0 events 140120 19:50:42 [Note] /usr/sbin/mysqld: ready for connections. Version: '5.5.34-0ubuntu0.12.04.1' socket: '/var/run/mysqld/mysqld.sock' port: 3306 (Ubuntu) |
|
From: Taka S. <ser...@gm...> - 2014-01-20 13:10:53
|
Dear all. This is my first post to the mailinglist. I'm interested in mychem and tried to build it. After build, I could found libmychem.so in /etc/mysql/plugin. But I could not find mychem-plugin from mysql. I was wondering if you could give some advice to me. OS: ubuntu 12.04 Install log is follows. -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- The build type is RelWithDebInfo -- Test module disabled -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig -- OPENBABEL_MINI_FOUND <TRUE> -- Found OpenBabel2: /usr/local/lib/libopenbabel.so -- Open Babel Exe: /usr/local/bin/babel -- Using mysql-config: /usr/bin/mysql_config -- MySQL Version: 5.5.34 -- MySQL Plugin Dir: /usr/lib/mysql/plugin -- Found MySQL 5.5.34: /usr/include/mysql, /usr/lib/x86_64-linux-gnu/libmysqlclient.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libdl.so -- Mychem installation directory: /usr/lib/mysql/plugin -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for stdio.h -- Looking for stdio.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Defining dlhandler source files -- Configuring done -- Generating done -- Build files have been written to: /home/serizawatf/discus-deploy/mychem-build Scanning dependencies of target conversion_test Scanning dependencies of target modification_test Scanning dependencies of target helper_test [ 3%] [ 7%] [ 11%] Building CXX object tests/CMakeFiles/modification_test.dir/modification_test.cpp.o Building CXX object tests/CMakeFiles/helper_test.dir/helper_test.cpp.o Building CXX object tests/CMakeFiles/conversion_test.dir/conversion_test.cpp.o Scanning dependencies of target mychem-lib [ 14%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o [ 18%] Building CXX object tests/CMakeFiles/helper_test.dir/mysql_handler.cpp.o [ 22%] Building CXX object tests/CMakeFiles/modification_test.dir/mysql_handler.cpp.o [ 25%] Building CXX object src/CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o [ 29%] [ 33%] Building CXX object tests/CMakeFiles/modification_test.dir/test_functions.cpp.o Building CXX object tests/CMakeFiles/helper_test.dir/test_functions.cpp.o [ 37%] Building CXX object tests/CMakeFiles/conversion_test.dir/mysql_handler.cpp.o [ 40%] Building CXX object tests/CMakeFiles/conversion_test.dir/test_functions.cpp.o Linking CXX executable helper_test [ 40%] Built target helper_test Linking CXX executable modification_test Scanning dependencies of target molmatch_test [ 44%] Building CXX object tests/CMakeFiles/molmatch_test.dir/molmatch_test.cpp.o [ 44%] Built target modification_test Scanning dependencies of target property_test [ 48%] Building CXX object tests/CMakeFiles/property_test.dir/property_test.cpp.o [ 51%] Building CXX object tests/CMakeFiles/molmatch_test.dir/mysql_handler.cpp.o Linking CXX executable conversion_test [ 51%] Built target conversion_test [ 55%] Building CXX object tests/CMakeFiles/molmatch_test.dir/test_functions.cpp.o [ 59%] Building CXX object tests/CMakeFiles/property_test.dir/mysql_handler.cpp.o [ 62%] Building C object src/CMakeFiles/mychem-lib.dir/helper.c.o [ 66%] Building CXX object src/CMakeFiles/mychem-lib.dir/helper_wrapper.cpp.o [ 70%] [ 74%] Building C object src/CMakeFiles/mychem-lib.dir/modification.c.o Building CXX object tests/CMakeFiles/property_test.dir/test_functions.cpp.o [ 77%] Building CXX object src/CMakeFiles/mychem-lib.dir/modification_wrapper.cpp.o [ 81%] Building C object src/CMakeFiles/mychem-lib.dir/molmatch.c.o [ 85%] Building CXX object src/CMakeFiles/mychem-lib.dir/molmatch_wrapper.cpp.o Linking CXX executable molmatch_test [ 85%] Built target molmatch_test [ 88%] Building C object src/CMakeFiles/mychem-lib.dir/property.c.o Linking CXX executable property_test [ 92%] Building CXX object src/CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o [ 92%] Built target property_test [ 96%] Building CXX object src/CMakeFiles/mychem-lib.dir/serialization.cpp.o [100%] Building CXX object src/CMakeFiles/mychem-lib.dir/dlhandler_unix.cpp.o Linking CXX shared library libmychem.so [100%] Built target mychem-lib -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- The build type is RelWithDebInfo -- Test module disabled -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig -- OPENBABEL_MINI_FOUND <TRUE> -- Found OpenBabel2: /usr/local/lib/libopenbabel.so -- Open Babel Exe: /usr/local/bin/babel -- Using mysql-config: /usr/bin/mysql_config -- MySQL Version: 5.5.34 -- MySQL Plugin Dir: /usr/lib/mysql/plugin -- Found MySQL 5.5.34: /usr/include/mysql, /usr/lib/x86_64-linux-gnu/libmysqlclient.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libdl.so -- Mychem installation directory: /usr/lib/mysql/plugin -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for stdio.h -- Looking for stdio.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Defining dlhandler source files -- Configuring done -- Generating done -- Build files have been written to: /home/serizawatf/discus-deploy/mychem-build Scanning dependencies of target conversion_test Scanning dependencies of target helper_test Scanning dependencies of target modification_test [ 3%] [ 7%] [ 11%] Building CXX object tests/CMakeFiles/conversion_test.dir/conversion_test.cpp.o Building CXX object tests/CMakeFiles/modification_test.dir/modification_test.cpp.o Scanning dependencies of target mychem-lib Building CXX object tests/CMakeFiles/helper_test.dir/helper_test.cpp.o [ 14%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o [ 18%] Building CXX object tests/CMakeFiles/helper_test.dir/mysql_handler.cpp.o [ 22%] Building CXX object tests/CMakeFiles/modification_test.dir/mysql_handler.cpp.o [ 25%] Building CXX object src/CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o [ 29%] Building CXX object tests/CMakeFiles/helper_test.dir/test_functions.cpp.o [ 33%] Building CXX object tests/CMakeFiles/modification_test.dir/test_functions.cpp.o [ 37%] Building CXX object tests/CMakeFiles/conversion_test.dir/mysql_handler.cpp.o [ 40%] Building CXX object tests/CMakeFiles/conversion_test.dir/test_functions.cpp.o Linking CXX executable helper_test Linking CXX executable modification_test [ 40%] Built target helper_test Scanning dependencies of target molmatch_test [ 44%] Building CXX object tests/CMakeFiles/molmatch_test.dir/molmatch_test.cpp.o [ 44%] Built target modification_test Scanning dependencies of target property_test [ 48%] Building CXX object tests/CMakeFiles/property_test.dir/property_test.cpp.o Linking CXX executable conversion_test [ 51%] Building CXX object tests/CMakeFiles/molmatch_test.dir/mysql_handler.cpp.o [ 51%] Built target conversion_test [ 55%] Building C object src/CMakeFiles/mychem-lib.dir/helper.c.o [ 59%] Building CXX object src/CMakeFiles/mychem-lib.dir/helper_wrapper.cpp.o [ 62%] Building CXX object tests/CMakeFiles/property_test.dir/mysql_handler.cpp.o [ 66%] Building CXX object tests/CMakeFiles/molmatch_test.dir/test_functions.cpp.o [ 70%] Building C object src/CMakeFiles/mychem-lib.dir/modification.c.o [ 74%] Building CXX object tests/CMakeFiles/property_test.dir/test_functions.cpp.o [ 77%] Building CXX object src/CMakeFiles/mychem-lib.dir/modification_wrapper.cpp.o [ 81%] Building C object src/CMakeFiles/mychem-lib.dir/molmatch.c.o [ 85%] Building CXX object src/CMakeFiles/mychem-lib.dir/molmatch_wrapper.cpp.o Linking CXX executable molmatch_test [ 85%] Built target molmatch_test [ 88%] Building C object src/CMakeFiles/mychem-lib.dir/property.c.o [ 92%] Building CXX object src/CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o Linking CXX executable property_test [ 92%] Built target property_test [ 96%] Building CXX object src/CMakeFiles/mychem-lib.dir/serialization.cpp.o [100%] Building CXX object src/CMakeFiles/mychem-lib.dir/dlhandler_unix.cpp.o Linking CXX shared library libmychem.so [100%] Built target mychem-lib Best Regards. Takayuki |
|
From: Li, L. <le...@gm...> - 2013-12-17 19:06:06
|
Dear Martin, Thank you for your email. It works now by using your approach! Cheers! Leon On Tue, Dec 17, 2013 at 1:32 PM, Wettig, Martin <Mar...@ch...>wrote: > > Dear Leon, > > do you try to install MyChem on a 64-Bit Ubuntu? Your error message looks > similar to which we got. > > Jerome's following solution helped us: > > > > > The problem has appear with recent version of GCC. In order to compile > > Mychem, remove the '-std=iso9899:1990' entry from the CMakeLists.txt at > > the root of the project directory. > > Kind Regards, > > Martin > > ________________________________________ > Von: Li, Leon [le...@gm...] > Gesendet: Dienstag, 17. Dezember 2013 03:35 > An: myc...@li... > Betreff: [Mychem-discuss] install mychem in Ubuntu > > Dear all, > > I met the following problem when I tried to install mychem in Ubuntu. > Could anybody shed a light on this? > > Thanks in advance, > Leon > > ============================================== > > Scanning dependencies of target mychem-lib > [ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o > In file included from /usr/include/mysql/my_global.h:77:0, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/my_config.h:501:6: warning: "_MSC_VER" is not defined > [-Wundef] > #if (_MSC_VER > 1310) > ^ > /usr/include/mysql/my_config.h:592:6: warning: > "WITH_NDBCLUSTER_STORAGE_ENGINE" is not defined [-Wundef] > #if (WITH_NDBCLUSTER_STORAGE_ENGINE) && !defined(EMBEDDED_LIBRARY) > ^ > In file included from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45:0, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/my_global.h:694:6: warning: "_MSC_VER" is not defined > [-Wundef] > #if (_MSC_VER) > ^ > In file included from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45:0, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/my_global.h:1426:5: warning: "__STDC_VERSION__" is not > defined [-Wundef] > #if __STDC_VERSION__ < 199901L > ^ > In file included from /usr/include/mysql/my_pthread.h:832:0, > from /usr/include/mysql/my_sys.h:44, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/mysql/psi/mysql_thread.h:551:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_mutex_init( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:575:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_mutex_destroy( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:596:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_mutex_lock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:626:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_mutex_trylock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:656:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_mutex_unlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:676:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_rwlock_init( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:695:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_prlock_init( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:711:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_rwlock_destroy( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:725:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_prlock_destroy( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:739:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_rwlock_rdlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:767:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_prlock_rdlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:795:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_rwlock_wrlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:823:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_prlock_wrlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:851:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_rwlock_tryrdlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:878:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_rwlock_trywrlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:905:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_rwlock_unlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:918:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_prlock_unlock( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:931:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_cond_init( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:947:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_cond_destroy( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:960:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_cond_wait( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:988:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_cond_timedwait( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:1017:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_cond_signal( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:1029:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_cond_broadcast( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:1042:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’ > static inline int inline_mysql_thread_create( > ^ > /usr/include/mysql/mysql/psi/mysql_thread.h:1055:15: error: expected ‘=’, > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’ > static inline void inline_mysql_thread_set_psi_id(ulong id) > ^ > In file included from /usr/include/mysql/my_sys.h:46:0, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/m_ctype.h:366:1: error: unknown type name ‘inline’ > static inline my_bool > ^ > /usr/include/mysql/m_ctype.h:367:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ > or ‘__attribute__’ before ‘my_cs_have_contractions’ > my_cs_have_contractions(CHARSET_INFO *cs) > ^ > /usr/include/mysql/m_ctype.h:372:1: error: unknown type name ‘inline’ > static inline my_bool > ^ > /usr/include/mysql/m_ctype.h:373:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ > or ‘__attribute__’ before ‘my_cs_can_be_contraction_head’ > my_cs_can_be_contraction_head(CHARSET_INFO *cs, my_wc_t wc) > ^ > /usr/include/mysql/m_ctype.h:378:1: error: unknown type name ‘inline’ > static inline my_bool > ^ > /usr/include/mysql/m_ctype.h:379:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ > or ‘__attribute__’ before ‘my_cs_can_be_contraction_tail’ > my_cs_can_be_contraction_tail(CHARSET_INFO *cs, my_wc_t wc) > ^ > /usr/include/mysql/m_ctype.h:384:1: error: unknown type name ‘inline’ > static inline uint16* > ^ > /usr/include/mysql/m_ctype.h:384:21: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ > or ‘__attribute__’ before ‘*’ token > static inline uint16* > ^ > In file included from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46:0, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/my_sys.h:815:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ > or ‘__attribute__’ before ‘char’ > static inline char *safe_strdup_root(MEM_ROOT *root, const char *str) > ^ > In file included from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:50:0, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/m_string.h:63:50: warning: "HAVE_DECL_BZERO" is not > defined [-Wundef] > #if !defined(bzero) && (!defined(HAVE_BZERO) || !HAVE_DECL_BZERO || > defined(_AIX)) > ^ > In file included from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:50:0, > from > /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31: > /usr/include/mysql/m_string.h:266:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ > or ‘__attribute__’ before ‘const’ > static inline const uchar *skip_trailing_space(const uchar *ptr,size_t > len) > ^ > /usr/include/mysql/m_string.h:292:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ > or ‘__attribute__’ before ‘void’ > static inline void lex_string_set(LEX_STRING *lex_str, const char *c_str) > ^ > make[2]: *** [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1 > make[1]: *** [src/CMakeFiles/mychem-lib.dir/all] Error 2 > make: *** [all] Error 2 > > |
|
From: Wettig, M. <Mar...@ch...> - 2013-12-17 18:34:45
|
Dear Leon,
do you try to install MyChem on a 64-Bit Ubuntu? Your error message looks similar to which we got.
Jerome's following solution helped us:
>
> The problem has appear with recent version of GCC. In order to compile
> Mychem, remove the '-std=iso9899:1990' entry from the CMakeLists.txt at
> the root of the project directory.
Kind Regards,
Martin
________________________________________
Von: Li, Leon [le...@gm...]
Gesendet: Dienstag, 17. Dezember 2013 03:35
An: myc...@li...
Betreff: [Mychem-discuss] install mychem in Ubuntu
Dear all,
I met the following problem when I tried to install mychem in Ubuntu. Could anybody shed a light on this?
Thanks in advance,
Leon
==============================================
Scanning dependencies of target mychem-lib
[ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o
In file included from /usr/include/mysql/my_global.h:77:0,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_config.h:501:6: warning: "_MSC_VER" is not defined [-Wundef]
#if (_MSC_VER > 1310)
^
/usr/include/mysql/my_config.h:592:6: warning: "WITH_NDBCLUSTER_STORAGE_ENGINE" is not defined [-Wundef]
#if (WITH_NDBCLUSTER_STORAGE_ENGINE) && !defined(EMBEDDED_LIBRARY)
^
In file included from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45:0,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_global.h:694:6: warning: "_MSC_VER" is not defined [-Wundef]
#if (_MSC_VER)
^
In file included from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45:0,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_global.h:1426:5: warning: "__STDC_VERSION__" is not defined [-Wundef]
#if __STDC_VERSION__ < 199901L
^
In file included from /usr/include/mysql/my_pthread.h:832:0,
from /usr/include/mysql/my_sys.h:44,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/mysql/psi/mysql_thread.h:551:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:575:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:596:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_lock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:626:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_trylock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:656:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_unlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:676:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:695:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:711:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:725:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:739:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_rdlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:767:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_rdlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:795:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_wrlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:823:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_wrlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:851:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_tryrdlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:878:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_trywrlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:905:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_unlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:918:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_unlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:931:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:947:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:960:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_wait(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:988:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_timedwait(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1017:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_signal(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1029:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_broadcast(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1042:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_thread_create(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1055:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’
static inline void inline_mysql_thread_set_psi_id(ulong id)
^
In file included from /usr/include/mysql/my_sys.h:46:0,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/m_ctype.h:366:1: error: unknown type name ‘inline’
static inline my_bool
^
/usr/include/mysql/m_ctype.h:367:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘my_cs_have_contractions’
my_cs_have_contractions(CHARSET_INFO *cs)
^
/usr/include/mysql/m_ctype.h:372:1: error: unknown type name ‘inline’
static inline my_bool
^
/usr/include/mysql/m_ctype.h:373:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘my_cs_can_be_contraction_head’
my_cs_can_be_contraction_head(CHARSET_INFO *cs, my_wc_t wc)
^
/usr/include/mysql/m_ctype.h:378:1: error: unknown type name ‘inline’
static inline my_bool
^
/usr/include/mysql/m_ctype.h:379:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘my_cs_can_be_contraction_tail’
my_cs_can_be_contraction_tail(CHARSET_INFO *cs, my_wc_t wc)
^
/usr/include/mysql/m_ctype.h:384:1: error: unknown type name ‘inline’
static inline uint16*
^
/usr/include/mysql/m_ctype.h:384:21: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
static inline uint16*
^
In file included from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46:0,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_sys.h:815:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘char’
static inline char *safe_strdup_root(MEM_ROOT *root, const char *str)
^
In file included from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:50:0,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/m_string.h:63:50: warning: "HAVE_DECL_BZERO" is not defined [-Wundef]
#if !defined(bzero) && (!defined(HAVE_BZERO) || !HAVE_DECL_BZERO || defined(_AIX))
^
In file included from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:50:0,
from /home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/m_string.h:266:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘const’
static inline const uchar *skip_trailing_space(const uchar *ptr,size_t len)
^
/usr/include/mysql/m_string.h:292:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’
static inline void lex_string_set(LEX_STRING *lex_str, const char *c_str)
^
make[2]: *** [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1
make[1]: *** [src/CMakeFiles/mychem-lib.dir/all] Error 2
make: *** [all] Error 2
|
|
From: björn <bjo...@ch...> - 2013-12-17 08:44:26
|
Dear all,
I try to calculate the tanimoto for different fingerprints. For a new
project of mine I have to switch to a 64bit mysql version by using
ubuntu as operating system.
On the previous 32bit version the tanimoto calculation works well for
different kind of fingerprint. I use for example the integrated
fingerprint2/4 but also for example MDL. To use the tanimoto function
for this one I transform the fingerprint into bytes and upload this one
into the blob column. It works well.
Now I do the same without changing anything in my script for the new
64bit version. If there are more than one fingerprint in the table I get
for all tanimoto comparisons "NULL". If I compare the compound only with
itself I get the error message: "lost connection to mysql server during
query".
I checked the thread_stack variable. size:"196608" by using the
following command: "show variables where `Variable_name` = 'thread_stack';"
By the way, the tanimoto function works well if I create the
fingerprints by the integrated fingerprint functions.
FINGERPRINT2("molfile")
I also export the fingerprint calculated by the FINGERPRINT2("molfile")
command and upload this one in byte formate. But also this is not working.
Hope sombody can help me.
Best regards
Björn
--
_____________________________
Björn-O. Gohlke
Structural Bioinformatics Group
Charité - Universitätsmedizin Berlin
Lindenberger Weg 80
13125 Berlin
Germany
Tel: +49 30 450 540 755
bjo...@ch...
|
|
From: Li, L. <le...@gm...> - 2013-12-17 02:36:14
|
Dear all,
I met the following problem when I tried to install mychem in Ubuntu. Could
anybody shed a light on this?
Thanks in advance,
Leon
==============================================
Scanning dependencies of target mychem-lib
[ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o
In file included from /usr/include/mysql/my_global.h:77:0,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_config.h:501:6: warning: "_MSC_VER" is not defined
[-Wundef]
#if (_MSC_VER > 1310)
^
/usr/include/mysql/my_config.h:592:6: warning:
"WITH_NDBCLUSTER_STORAGE_ENGINE" is not defined [-Wundef]
#if (WITH_NDBCLUSTER_STORAGE_ENGINE) && !defined(EMBEDDED_LIBRARY)
^
In file included from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45:0,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_global.h:694:6: warning: "_MSC_VER" is not defined
[-Wundef]
#if (_MSC_VER)
^
In file included from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:45:0,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_global.h:1426:5: warning: "__STDC_VERSION__" is not
defined [-Wundef]
#if __STDC_VERSION__ < 199901L
^
In file included from /usr/include/mysql/my_pthread.h:832:0,
from /usr/include/mysql/my_sys.h:44,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/mysql/psi/mysql_thread.h:551:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:575:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:596:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_lock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:626:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_trylock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:656:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_mutex_unlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:676:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:695:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:711:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:725:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:739:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_rdlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:767:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_rdlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:795:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_wrlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:823:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_wrlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:851:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_tryrdlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:878:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_trywrlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:905:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_rwlock_unlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:918:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_prlock_unlock(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:931:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_init(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:947:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_destroy(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:960:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_wait(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:988:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_timedwait(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1017:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_signal(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1029:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_cond_broadcast(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1042:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
static inline int inline_mysql_thread_create(
^
/usr/include/mysql/mysql/psi/mysql_thread.h:1055:15: error: expected ‘=’,
‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’
static inline void inline_mysql_thread_set_psi_id(ulong id)
^
In file included from /usr/include/mysql/my_sys.h:46:0,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/m_ctype.h:366:1: error: unknown type name ‘inline’
static inline my_bool
^
/usr/include/mysql/m_ctype.h:367:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘my_cs_have_contractions’
my_cs_have_contractions(CHARSET_INFO *cs)
^
/usr/include/mysql/m_ctype.h:372:1: error: unknown type name ‘inline’
static inline my_bool
^
/usr/include/mysql/m_ctype.h:373:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘my_cs_can_be_contraction_head’
my_cs_can_be_contraction_head(CHARSET_INFO *cs, my_wc_t wc)
^
/usr/include/mysql/m_ctype.h:378:1: error: unknown type name ‘inline’
static inline my_bool
^
/usr/include/mysql/m_ctype.h:379:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘my_cs_can_be_contraction_tail’
my_cs_can_be_contraction_tail(CHARSET_INFO *cs, my_wc_t wc)
^
/usr/include/mysql/m_ctype.h:384:1: error: unknown type name ‘inline’
static inline uint16*
^
/usr/include/mysql/m_ctype.h:384:21: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
or ‘__attribute__’ before ‘*’ token
static inline uint16*
^
In file included from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:46:0,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/my_sys.h:815:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘char’
static inline char *safe_strdup_root(MEM_ROOT *root, const char *str)
^
In file included from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:50:0,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/m_string.h:63:50: warning: "HAVE_DECL_BZERO" is not
defined [-Wundef]
#if !defined(bzero) && (!defined(HAVE_BZERO) || !HAVE_DECL_BZERO ||
defined(_AIX))
^
In file included from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.h:50:0,
from
/home/leonqli/Downloads/mychem/mychem-0.9.1/src/conversion.c:31:
/usr/include/mysql/m_string.h:266:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
or ‘__attribute__’ before ‘const’
static inline const uchar *skip_trailing_space(const uchar *ptr,size_t len)
^
/usr/include/mysql/m_string.h:292:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
or ‘__attribute__’ before ‘void’
static inline void lex_string_set(LEX_STRING *lex_str, const char *c_str)
^
make[2]: *** [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1
make[1]: *** [src/CMakeFiles/mychem-lib.dir/all] Error 2
make: *** [all] Error 2
|