sci-biology:dialign-tx-1.0.2-r1:20151230-134842.log

sci-biology:dialign-tx-1.0.2-r1:20151230-134842.log (text/plain), 6.36 KB, created by Toralf Förster on 2015-12-30 14:17:20 UTC

 * Package:    sci-biology/dialign-tx-1.0.2-r1
 * Repository: gentoo
 * Maintainer: sci-biology
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking DIALIGN-TX_1.0.2.tar.gz to /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work
>>> Preparing source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2 ...
 * Applying dialign-tx-1.0.2-implicits.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2 ...
make -j1 -C source clean 
make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2/source'
rm -rf *.o *rtl *jump *addre* *cfg *life *reg *reload *flow* *stack  museq dialign-tx
make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2/source'
make -j1 -C source CC=x86_64-pc-linux-gnu-gcc CPPFLAGS= 
make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2/source'
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o museq.o museq.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o parameters.o parameters.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o io.o io.c
io.c: In function ‘read_anchors’:
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=]
   while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) 
                    ^
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 4 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=]
io.c: In function ‘read_scr_matrix’:
io.c:270:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf( fp, "%i", &is);
   ^
io.c:282:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp, "%s\n", rline);
     ^
io.c: In function ‘read_diag_prob_dist’:
io.c:371:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
       fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
       ^
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o diag.o diag.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o alig.o alig.c
alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined
 extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struc
                    ^
alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined
 extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
                    ^
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o assemble.o assemble.c
assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined
 extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatri
                    ^
assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined
 extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int p
                                ^
assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined
 extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smat
                                       ^
assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined
 extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struc
                    ^
assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined
 extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
                    ^
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o prob.o prob.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o orf.o orf.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -c -o translate.o translate.c
rm -f ./museq
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o ./museq \
./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o  \
-pipe -Wall -lm 
./diag.o: In function `find_all_diags':
diag.c:(.text+0x1940): undefined reference to `real_calc_weight'
diag.c:(.text+0x2864): undefined reference to `real_calc_weight'
./diag.o: In function `old_find_all_diags':
diag.c:(.text+0x449b): undefined reference to `real_calc_weight'
diag.c:(.text+0x5cc8): undefined reference to `real_calc_weight'
./assemble.o: In function `simple_aligner':
assemble.c:(.text+0x50e): undefined reference to `align_diag'
assemble.c:(.text+0x60c): undefined reference to `calc_weight'
assemble.c:(.text+0x690): undefined reference to `calc_weight'
collect2: error: ld returned 1 exit status
Makefile:35: recipe for target 'museq' failed
make: *** [museq] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2/source'
 * ERROR: sci-biology/dialign-tx-1.0.2-r1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/dialign-tx-1.0.2-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/dialign-tx-1.0.2-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:dialign-tx-1.0.2-r1:20151230-134842.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2'
 * S: '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r1/work/DIALIGN-TX_1.0.2'