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Gentoo's Bugzilla – Attachment 199545 Details for
Bug 279574
sci-biology/trnascan-se: fails to build with glibc-2.10
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Build log
trnascan-se-1.23-r1:20090728-230314.log (text/plain), 12.71 KB, created by
Diego Elio Pettenò (RETIRED)
on 2009-07-29 11:48:10 UTC
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Description:
Build log
Filename:
MIME Type:
Creator:
Diego Elio Pettenò (RETIRED)
Created:
2009-07-29 11:48:10 UTC
Size:
12.71 KB
patch
obsolete
>>>> 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.... > [31;01m*[0m > [31;01m*[0m ERROR: sci-biology/trnascan-se-1.23-r1 failed. > [31;01m*[0m Call stack: > [31;01m*[0m ebuild.sh, line 49: Called src_compile > [31;01m*[0m environment, line 987: Called die > [31;01m*[0m The specific snippet of code: > [31;01m*[0m emake || die; > [31;01m*[0m The die message: > [31;01m*[0m (no error message) > [31;01m*[0m > [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant. > [31;01m*[0m A complete build log is located at '/var/log/portage/sci-biology/trnascan-se-1.23-r1:20090728-230314.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/trnascan-se-1.23-r1/temp/environment'. > [31;01m*[0m
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bug 279574
: 199545