sci-biology:trnascan-se-1.31-r2:20221003-005245.log

sci-biology:trnascan-se-1.31-r2:20221003-005245.log (text/plain), 3.73 KB, created by Toralf Förster on 2022-10-03 08:01:28 UTC

 * Package:    sci-biology/trnascan-se-1.31-r2:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking trnascan-se-1.31.tar.gz to /var/tmp/portage/sci-biology/trnascan-se-1.31-r2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/trnascan-se-1.31-r2/work
>>> Preparing source in /var/tmp/portage/sci-biology/trnascan-se-1.31-r2/work/tRNAscan-SE-1.3.1 ...
 * Applying trnascan-se-1.31-makefile.patch ...
 [ ok ]
 * Applying trnascan-se-1.31-portable-perl-shebangs.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/trnascan-se-1.31-r2/work/tRNAscan-SE-1.3.1 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/trnascan-se-1.31-r2/work/tRNAscan-SE-1.3.1 ...
make -j4 
clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int  -DTSCANDIR=\"/usr/share/trnascan-se\" -o trnascan-1.4 trnascan.c
clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int   -c align.c		
clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int   -c dbviterbi.c		
clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int   -c debug.c		
trnascan.c:335:1: error: type specifier missing, defaults to 'int'; ISO C99 and
      later do not support implicit int [-Werror,-Wimplicit-int]
main(int argc, char **argv)
^
int
trnascan.c:433:16: error: call to undeclared function 'getopt'; ISO C99 and
      later do not support implicit function declarations
      [-Werror,-Wimplicit-function-declaration]
while ((optc = getopt(argc, argv, "csraho:v:i:")) != -1)
               ^
trnascan.c:1180:7: warning: array index 2 is past the end of the array (which
      contains 2 elements) [-Warray-bounds]
      table_inv[k][2]=j;
      ^            ~
trnascan.c:1141:2: note: array 'table_inv' declared here
        int (*table_inv)[2],  /* table containing the position and the nature of
        ^
trnascan.c:1421:1: error: type specifier missing, defaults to 'int'; ISO C99 and
      later do not support implicit int [-Werror,-Wimplicit-int]
myindex (char *s, char *t)
^
int
trnascan.c:1496:12: warning: array index 2 is past the end of the array (which
      contains 2 elements) [-Warray-bounds]
        if ((j == table_inv[k][2]) || (j == -1))                 
                  ^            ~
trnascan.c:1441:9: note: array 'table_inv' declared here
               int (*table_inv)[2],  /* table containing the position an...
               ^
2 warnings and 3 errors generated.
make: *** [Makefile:120: trnascan-1.4] Error 1
make: *** Waiting for unfinished jobs....
 * ERROR: sci-biology/trnascan-se-1.31-r2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/trnascan-se-1.31-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/trnascan-se-1.31-r2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:trnascan-se-1.31-r2:20221003-005245.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/trnascan-se-1.31-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/trnascan-se-1.31-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/trnascan-se-1.31-r2/work/tRNAscan-SE-1.3.1'
 * S: '/var/tmp/portage/sci-biology/trnascan-se-1.31-r2/work/tRNAscan-SE-1.3.1/'