* 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'