Hi Galt! Finally!!! I could install the BLAT, here is the answer
http://defsci.blogspot.com/2011/02/compile-blat-on-x8664-ubuntu-1004.html You right, this has to do with the blatSrc/inc/common.mk file, only edit the 17 line: | HG_WARN_ERR = -DJK_WARN -Wall -Werror |to | HG_WARN_ERR = -DJK_WARN -Wall| After days I can be more quiet. Thank you very very much. Daniel Antonio Fernández Ugaz On 10/26/2011 07:17 PM, Galt Barber wrote: > > Hi, Daniel! > > Since you must be using gcc 4.6 whereas we use only 4.1, > it is stricter about warnings. > > Probably the quickest way to get it to work is to remove > all instances of "-Werror" from > /home/dnl/Genetics/Tools/BLAT/blatSrc/inc/common.mk > > Then try re-compiling and it will no longer treat errors as warnings. > > -Galt > > On 10/26/11 15:33, Daniel Fernández wrote: >> Hi Galt, >> >> I saw that link and I try to understand, I don't know a lot of of >> programming. Can you explain to me how I would do that?. >> >> I edit the chainBlock.c, I remove the two lines with "bestLeaf", but >> now the terminal says a other ERROR, the cheapcgi.c file (see in the >> end) >> >> Then I thought maybe I had something bad in the beginning, so read >> again the instruction (attached) >> MACHTYPE=i686 >> export MACHTYPE >> I create the /home/user/bin/$MACHTYPE file ("$MACHTYPE", I think that >> is wrong with the symbol "$" but they say so) >> Then I enter in lib directory and write the command "make" and it get >> ERROR >> Then I enter in blatSrc directory and write "make" and It get the >> same ERROR >> >> In all case, with "chainBlock.c" modified (without "bestLeaf" lines) >> and unmodified, the ERROR is the same >> >> ########################################################################################################## >> >> >> ########################################################################################################## >> >> >> dnl@DNL-LAPTOP:~/Genetics/Tools/BLAT/blatSrc$ make >> cd lib && make >> make[1]: Entering directory `/home/dnl/Genetics/Tools/BLAT/blatSrc/lib' >> gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE >> -DMACHTYPE_i686 -DJK_WARN -Wall -Werror -I../inc -I../../inc >> -I../../../inc -I../../../../inc -I../../../../../inc -o cheapcgi.o >> -c cheapcgi.c >> cheapcgi.c: In function ‘cgiParseMultipart’: >> cheapcgi.c:172:75: error: variable ‘ct’ set but not used >> [-Werror=unused-but-set-variable] >> cc1: all warnings being treated as errors >> >> make[1]: *** [cheapcgi.o] Error 1 >> make[1]: Leaving directory `/home/dnl/Genetics/Tools/BLAT/blatSrc/lib' >> make: *** [all] Error 2 >> ########################################################################################################## >> >> >> ########################################################################################################## >> >> >> >> Daniel >> >> On 10/25/2011 06:48 PM, Galt Barber wrote: >>> >>> Hi, Daniel! >>> >>> Try adding this flag >>> -Wno-unused >>> >>> http://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html >>> >>> Alternatively, just edit src/lib/chainBlock.c and remove the two lines >>> that refer to the variable "bestLeaf" which is not being used. >>> >>> -Galt >>> >>> 10/25/2011 7:21 AM, Daniel Fernández: >>>> Sorry, I try to understand you, but how compile with waning >>>> disables (-w)? >>>> >>>> On 10/20/2011 01:13 PM, Galt Barber wrote: >>>>> I looked in the source code and removed the unused variable. >>>>> >>>>> You may need to compile with warnings disabled (-w). >>>>> >>>>> This warning is harmless. >>>>> >>>>> -Galt >>>>> >>>>> ----- Original Message ----- >>>>> >>>>> Hi, >>>>> >>>>> I try to install the BLAT in my computer, but I have a Error. >>>>> I use Linux, Ubuntu 11.10, i686, 32-bit >>>>> >>>>> First I download the last version blatSrc34 and unzip this >>>>> then in the terminal I write: >>>>> ~$ echo $MACHTYPE >>>>> ~$ MACHTYPE=i686 >>>>> ~$ export MACHTYPE=i686 >>>>> ~$ echo $MACHTYPE >>>>> ~$ i686 >>>>> >>>>> Then I created the $MACHTYPE in /usr/local/bin >>>>> ( my "echo $PATH" is: >>>>> /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games) >>>>> >>>>> >>>>> >>>>> >>>>> And finally I enter on my blatSrc and type >>>>> ~$ make >>>>> >>>>> And the Error in the terminal: >>>>> >>>>> dnl@DNL-LAPTOP:~/Genetics/Tools/BLAT/blatSrc$ make >>>>> cd lib&& make >>>>> make[1]: Entering directory >>>>> `/home/dnl/Genetics/Tools/BLAT/blatSrc/lib' >>>>> gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE >>>>> -DMACHTYPE_i686 -DJK_WARN -Wall -Werror -I../inc -I../../inc >>>>> -I../../../inc -I../../../../inc -I../../../../../inc -o >>>>> chainBlock.o -c >>>>> chainBlock.c >>>>> chainBlock.c: In function ‘findBestPredecessors’: >>>>> chainBlock.c:290:16: error: variable ‘bestLeaf’ set but not used >>>>> [-Werror=unused-but-set-variable] >>>>> cc1: all warnings being treated as errors >>>>> >>>>> make[1]: *** [chainBlock.o] Error 1 >>>>> make[1]: Leaving directory >>>>> `/home/dnl/Genetics/Tools/BLAT/blatSrc/lib' >>>>> make: *** [all] Error 2 >>>>> >>>>> >>>>> Any help would be appreciated! >>>>> >>>>> Thanks >>>>> >>>>> Daniel Antonio Fernández Ugaz >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Genome maillist - [email protected] >>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >>> >> >> >> -- >> */ /* _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
