>>> Unpacking source... >>> Unpacking trnascan-se-1.23.tar.bz2 to /var/tmp/portage/sci-biology/trnascan-se-1.23-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/trnascan-se-1.23-r1/work >>> Compiling source in /var/tmp/portage/sci-biology/trnascan-se-1.23-r1/work/trnascan-se-1.23 ... make -j14 i686-pc-linux-gnu-gcc -O2 -pipe -c trnascan.c i686-pc-linux-gnu-gcc -O2 -pipe -c align.c i686-pc-linux-gnu-gcc -O2 -pipe -c dbviterbi.c i686-pc-linux-gnu-gcc -O2 -pipe -c debug.c i686-pc-linux-gnu-gcc -O2 -pipe -c emit.c i686-pc-linux-gnu-gcc -O2 -pipe -c fast-dbviterbi.c i686-pc-linux-gnu-gcc -O2 -pipe -c fastmodelmaker.c i686-pc-linux-gnu-gcc -O2 -pipe -c konings.c i686-pc-linux-gnu-gcc -O2 -pipe -c lengthdist.c i686-pc-linux-gnu-gcc -O2 -pipe -c maxmodelmaker.c i686-pc-linux-gnu-gcc -O2 -pipe -c misc.c i686-pc-linux-gnu-gcc -O2 -pipe -c model.c i686-pc-linux-gnu-gcc -O2 -pipe -c modelmaking.c i686-pc-linux-gnu-gcc -O2 -pipe -c prior.c debug.c: In function 'PrintTrace': debug.c:139: warning: format '%#12x' expects type 'unsigned int', but argument 3 has type 'struct trace_s *' debug.c:139: warning: format '%#10x' expects type 'unsigned int', but argument 8 has type 'struct trace_s *' debug.c:139: warning: format '%#10x' expects type 'unsigned int', but argument 9 has type 'struct trace_s *' debug.c:139: warning: format '%#10x' expects type 'unsigned int', but argument 10 has type 'struct trace_s *' i686-pc-linux-gnu-gcc -O2 -pipe -c probify.c i686-pc-linux-gnu-gcc -O2 -pipe -c save.c i686-pc-linux-gnu-gcc -O2 -pipe -c smallviterbi.c i686-pc-linux-gnu-gcc -O2 -pipe -c scorestack.c i686-pc-linux-gnu-gcc -O2 -pipe -c structs.c i686-pc-linux-gnu-gcc -O2 -pipe -c trace.c i686-pc-linux-gnu-gcc -O2 -pipe -c viterbi.c scorestack.c: In function 'free_hitstack': scorestack.c:247: warning: comparison between pointer and integer i686-pc-linux-gnu-gcc -O2 -pipe -c alignio.c i686-pc-linux-gnu-gcc -O2 -pipe -c sqerror.c i686-pc-linux-gnu-gcc -O2 -pipe -c sqio.c i686-pc-linux-gnu-gcc -O2 -pipe -c iupac.c i686-pc-linux-gnu-gcc -O2 -pipe -c msf.c i686-pc-linux-gnu-gcc -O2 -pipe -c revcomp.c i686-pc-linux-gnu-gcc -O2 -pipe -c selex.c i686-pc-linux-gnu-gcc -O2 -pipe -c sre_ctype.c i686-pc-linux-gnu-gcc -O2 -pipe -c sre_math.c save.c: In function 'WriteBinaryCM': save.c:105: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:108: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:114: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:117: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:118: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:121: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:124: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:125: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:128: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:129: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c:130: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result save.c: In function 'read_cm20': save.c:216: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:226: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:227: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:228: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:234: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:235: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:240: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:241: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:244: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:245: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:251: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:252: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:256: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:257: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:260: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result save.c:261: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result trnascan.c: In function 'main': trnascan.c:822: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:824: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c: In function 'lectval': trnascan.c:1165: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result trnascan.c: In function 'fgetseq': trnascan.c:1228: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1248: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1250: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1309: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1316: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c: In function 'getseqsize': trnascan.c:1352: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1366: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1368: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1396: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c:1402: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result trnascan.c: In function 'printresult': trnascan.c:1898: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1898: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1901: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1901: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1901: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1901: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1903: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1903: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1903: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1903: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1905: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1905: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1905: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1905: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1910: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1910: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1910: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1910: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1915: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1915: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1915: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1915: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1918: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1918: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1918: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1918: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1934: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1934: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1964: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1964: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1968: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1968: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1968: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1968: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1970: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1970: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1970: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1970: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1972: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1972: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1972: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1972: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1979: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1979: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1979: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1979: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1985: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1985: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1985: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1985: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:1989: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:1989: warning: format '%d' expects type 'int', but argument 4 has type 'long int' trnascan.c:1989: warning: format '%d' expects type 'int', but argument 5 has type 'long int' trnascan.c:1989: warning: format '%d' expects type 'int', but argument 6 has type 'long int' trnascan.c:2006: warning: format '%d' expects type 'int', but argument 3 has type 'long int' trnascan.c:2006: warning: format '%d' expects type 'int', but argument 4 has type 'long int' i686-pc-linux-gnu-gcc -O2 -pipe -c sre_string.c sqio.c:238: error: conflicting types for 'getline' /usr/include/stdio.h:651: note: previous declaration of 'getline' was here make: *** [sqio.o] Error 1 make: *** Waiting for unfinished jobs.... * * ERROR: sci-biology/trnascan-se-1.23-r1 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 987: Called die * The specific snippet of code: * emake || die; * The die message: * (no error message) * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sci-biology/trnascan-se-1.23-r1:20090728-230314.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/trnascan-se-1.23-r1/temp/environment'. *