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Gentoo's Bugzilla – Attachment 486218 Details for
Bug 625808
sci-biology/wise-2.4.0_alpha will not build with USE doc
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build.log
build-wise.txt (text/plain), 189.64 KB, created by
deference
on 2017-07-21 02:25:03 UTC
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hide
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Description:
build.log
Filename:
MIME Type:
Creator:
deference
Created:
2017-07-21 02:25:03 UTC
Size:
189.64 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-biology/wise-2.4.0_alpha >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: sci-biology@gentoo.org >[32;01m * [39;49;00mUSE: abi_x86_64 amd64 doc elibc_glibc kernel_linux static-libs userland_GNU >[32;01m * [39;49;00mFEATURES: preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking wise2.4.0alpha.tar.gz to /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work >>>> Source unpacked in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work >>>> Preparing source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha ... > [32;01m*[0m Applying wise-2.4.0_alpha-glibc-2.10.patch ... >[A[162C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying wise-2.4.0_alpha-cflags.patch ... >[A[162C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying wise-api.tex.patch ... >[A[162C [34;01m[ [32;01mok[34;01m ][0m >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha ... >make -j1 -C src CC=x86_64-pc-linux-gnu-gcc all >make: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >(cd base ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" libwisebase.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/base' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseconfig.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestring.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseerror.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisememman.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisefile.c >[01m[Kwisefile.dy:[m[K In function '[01m[KWise2_myfclose[m[K': >[01m[Kwisefile.dy:72:3:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 3 has type '[01m[Kstruct FILE *[m[K' [-Wformat=] > fprintf(stderr,"Closing %d\n",ofp); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiserandom.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisetime.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseoverlay.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestreaminterface.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include commandline.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include linesubs.c >ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o >ar: creating libwisebase.a >if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/base' >(cd HMMer2 ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" libhmmer.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/HMMer2' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alphabet.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c core_algorithms.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c debug.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emit.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emulation.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c histogram.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hmmio.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c mathsupport.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c masks.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c misc.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c modelmakers.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan7.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan9.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c prior.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c tophits.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c trace.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c aligneval.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alignio.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c cluster.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c dayhoff.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c file.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c getopt.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c gnuregex.c >[01m[Kgnuregex.c:[m[K In function '[01m[Kre_match_2[m[K': >[01m[Kgnuregex.c:3752:31:[m[K [01;35m[Kwarning: [m[Kcast from pointer to integer of different size [-Wpointer-to-int-cast] > if ((int) old_regend[r] >= (int) regstart[r]) >[01;32m[K ^[m[K >[01m[Kgnuregex.c:3752:54:[m[K [01;35m[Kwarning: [m[Kcast from pointer to integer of different size [-Wpointer-to-int-cast] > if ((int) old_regend[r] >= (int) regstart[r]) >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2394:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (lowest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:3758:19:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (p1 + mcnt, d, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2397:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (highest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:3758:19:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (p1 + mcnt, d, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2394:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (lowest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:3905:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (p + mcnt, NULL, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2397:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (highest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:3905:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (p + mcnt, NULL, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2394:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (lowest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:3958:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (p + mcnt, d, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2397:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (highest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:3958:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (p + mcnt, d, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2482:14:[m[K [01;35m[Kwarning: [m[Kcast from pointer to integer of different size [-Wpointer-to-int-cast] > high_reg = (unsigned) POP_FAILURE_ITEM (); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4064:13:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPOP_FAILURE_POINT[m[K' > POP_FAILURE_POINT (sdummy, pdummy, >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2485:13:[m[K [01;35m[Kwarning: [m[Kcast from pointer to integer of different size [-Wpointer-to-int-cast] > low_reg = (unsigned) POP_FAILURE_ITEM (); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4064:13:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPOP_FAILURE_POINT[m[K' > POP_FAILURE_POINT (sdummy, pdummy, >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2394:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (lowest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4097:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (0, 0, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2397:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (highest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4097:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (0, 0, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2394:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (lowest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4110:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (0, 0, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2315:42:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2397:5:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_ITEM[m[K' > PUSH_FAILURE_ITEM (highest_active_reg); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4110:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPUSH_FAILURE_POINT[m[K' > PUSH_FAILURE_POINT (0, 0, -2); >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2482:14:[m[K [01;35m[Kwarning: [m[Kcast from pointer to integer of different size [-Wpointer-to-int-cast] > high_reg = (unsigned) POP_FAILURE_ITEM (); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4278:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPOP_FAILURE_POINT[m[K' > POP_FAILURE_POINT (d, p, >[01;32m[K ^[m[K >[01m[Kgnuregex.c:2485:13:[m[K [01;35m[Kwarning: [m[Kcast from pointer to integer of different size [-Wpointer-to-int-cast] > low_reg = (unsigned) POP_FAILURE_ITEM (); \ >[01;32m[K ^[m[K >[01m[Kgnuregex.c:4278:11:[m[K [01;36m[Knote: [m[Kin expansion of macro '[01m[KPOP_FAILURE_POINT[m[K' > POP_FAILURE_POINT (d, p, >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c interleaved.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c iupac.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c msf.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c revcomp.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c selex.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sqerror.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sqio.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_ctype.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_math.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_string.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c stack.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c translate.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c types.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c weight.c >ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o >a - alphabet.o >a - core_algorithms.o >a - debug.o >a - emit.o >a - emulation.o >a - histogram.o >a - hmmio.o >a - mathsupport.o >a - masks.o >a - misc.o >a - modelmakers.o >a - plan7.o >a - plan9.o >a - prior.o >a - tophits.o >a - trace.o >a - aligneval.o >a - alignio.o >a - cluster.o >a - dayhoff.o >a - file.o >a - getopt.o >a - gnuregex.o >a - interleaved.o >a - iupac.o >a - msf.o >a - revcomp.o >a - selex.o >a - sqerror.o >a - sqio.o >a - sre_ctype.o >a - sre_math.o >a - sre_string.o >a - stack.o >a - translate.o >a - types.o >a - weight.o >if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi >if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi >chmod 644 libhmmer.a >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/HMMer2' >(cd dynlibsrc ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" libdyna.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ packaln.c >[01m[Kpackaln.dy:[m[K In function '[01m[KWise2_read_simple_PackAln[m[K': >[01m[Kpackaln.dy:88:3:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kfgets[m[K', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,MAXLINE,ifp); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ aln.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dnamatrix.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ probability.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ alnrange.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ alnconvert.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ basematrix.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shattermatrix.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ matrixdebug.c >[01m[Kmatrixdebug.dy:[m[K In function '[01m[KWise2_user_DebugMatrix[m[K': >[01m[Kmatrixdebug.dy:208:5:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kfgets[m[K', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,MAXLINE,in); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dpenvelope.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dbsearchimpl.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dprunimpl.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexsequence.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexevalset.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexconsensi.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequence.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequencestream.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ seqalign.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hitlist.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsp.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hspstream.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codon.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ compmat.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codonmatrix.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codonmapper.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequencedb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hscore.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ seqlookup.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ arrayseqlookup.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genericindexresult.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ linkedlist_lookpos.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ singlenumberspace.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ histogram.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ searchstatinterface.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ searchstatlookup.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteindb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ protein.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ pairbase.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ pairbaseseq.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomicdb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ randommodel.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ randomdb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomic.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ cdna.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ cdnadb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dna.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ embl.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomicregion.c >[01m[Kgenomicregion.dy:[m[K In function '[01m[KWise2_read_EMBL_FT_into_GenomicRegion[m[K': >[01m[Kgenomicregion.dy:756:3:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kfgets[m[K', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,maxlen,ifp); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ gene.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ transcript.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ translation.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ btcanvas.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ asciibtcanvas.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dynlibcross.c >ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o >ar: creating libdyna.a >if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >(cd dynlibsrc ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" libdyna_glib.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ subseqhash.c >[01m[Ksubseqhash.dy:[m[K In function '[01m[KWise2_is_populated_subseqhash_ghash[m[K': >[01m[Ksubseqhash.dy:111:29:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { >[01;32m[K ^[m[K >[01m[Ksubseqhash.dy:[m[K In function '[01m[KWise2_lookup_subseqhash_ghash[m[K': >[01m[Ksubseqhash.dy:128:85:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); >[01;32m[K ^[m[K >[01m[Ksubseqhash.dy:[m[K In function '[01m[KWise2_add_seq_subseqhash_ghash[m[K': >[01m[Ksubseqhash.dy:160:54:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { >[01;32m[K ^[m[K >[01m[Ksubseqhash.dy:161:29:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > g_hash_table_insert(h,(gpointer)seq_number,p); >[01;32m[K ^[m[K >[01m[Ksubseqhash.dy:[m[K In function '[01m[KWise2_add_direct_number_subseqhash_ghash[m[K': >[01m[Ksubseqhash.dy:188:52:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { >[01;32m[K ^[m[K >[01m[Ksubseqhash.dy:189:27:[m[K [01;35m[Kwarning: [m[Kcast to pointer from integer of different size [-Wint-to-pointer-cast] > g_hash_table_insert(h,(gpointer)seq_number,p); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ intallocator.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteinstreamedindex.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shadowseq.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shadowseqindex.c >[01m[Kshadowseqindex.dy:[m[K In function '[01m[KWise2_dump_stats_ShadowSequenceIndex[m[K': >[01m[Kshadowseqindex.dy:285:3:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%f[m[K' expects argument of type '[01m[Kdouble[m[K', but argument 4 has type '[01m[Klong unsigned int[m[K' [-Wformat=] > fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsphandler.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hspscaninterface.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsp2hitscan.c >[01m[Khsp2hitscan.dy:[m[K In function '[01m[KWise2_one_off_two_hit_HSPscan_query_direct[m[K': >[01m[Khsp2hitscan.dy:214:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 3 has type '[01m[K__time_t[m[K' [-Wformat=] > ); >[01;32m[K ^[m[K >[01m[Khsp2hitscan.dy:214:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 4 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:214:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 5 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:214:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 6 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:278:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 3 has type '[01m[K__time_t[m[K' [-Wformat=] > ); >[01;32m[K ^[m[K >[01m[Khsp2hitscan.dy:278:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 4 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:278:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 5 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:278:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 6 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:291:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 3 has type '[01m[K__time_t[m[K' [-Wformat=] > ); >[01;32m[K ^[m[K >[01m[Khsp2hitscan.dy:291:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 4 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:291:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 5 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:291:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 6 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:307:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 3 has type '[01m[K__time_t[m[K' [-Wformat=] > ); >[01;32m[K ^[m[K >[01m[Khsp2hitscan.dy:307:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 4 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:307:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 5 has type '[01m[K__time_t[m[K' [-Wformat=] >[01m[Khsp2hitscan.dy:307:4:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 6 has type '[01m[K__time_t[m[K' [-Wformat=] >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsplookupscan.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsplookupthreaded.c >[01m[Khsplookupthreaded.dy:[m[K In function '[01m[KWise2_one_off_ordered_HSPscan_scan_query_direct[m[K': >[01m[Khsplookupthreaded.dy:211:3:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 3 has type '[01m[Klong int[m[K' [-Wformat=] > fprintf(stderr,"Got seq %d numbers\n",current); >[01;32m[K ^[m[K >[01m[Khsplookupthreaded.dy:259:3:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 3 has type '[01m[Klong int[m[K' [-Wformat=] > fprintf(stderr,"retrieved array with %d elements\n",current_oph); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteinindexcons.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dnaindexcons.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ staticseq.c >ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o proteinindexcons.o dnaindexcons.o staticseq.o >ar: creating libdyna_glib.a >if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >(cd external ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external' >(cd mott; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include " all) >make[2]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external/mott' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c -o mott_api.o mott_api.c >[01m[Kmott_api.c:[m[K In function '[01m[KInitPvaluesMott[m[K': >[01m[Kmott_api.c:64:3:[m[K [01;35m[Kwarning: [m[Kincompatible implicit declaration of built-in function '[01m[Kfree[m[K' > free(freq0); >[01;32m[K ^[m[K >[01m[Kmott_api.c:[m[K In function '[01m[KSW_PValueMott[m[K': >[01m[Kmott_api.c:104:7:[m[K [01;35m[Kwarning: [m[Kincompatible implicit declaration of built-in function '[01m[Kfree[m[K' > free(freqA); >[01;32m[K ^[m[K >[01m[Kmott_api.c:[m[K In function '[01m[KKarlinAltschulStatistics2[m[K': >[01m[Kmott_api.c:144:5:[m[K [01;35m[Kwarning: [m[Kincompatible implicit declaration of built-in function '[01m[Kfree[m[K' > free(h+hmin); >[01;32m[K ^[m[K >[01m[Kmott_api.c:155:5:[m[K [01;35m[Kwarning: [m[Kincompatible implicit declaration of built-in function '[01m[Kfree[m[K' > free(h+hmin); >[01;32m[K ^[m[K >[01m[Kmott_api.c:[m[K In function '[01m[KGetHistogram[m[K': >[01m[Kmott_api.c:179:16:[m[K [01;35m[Kwarning: [m[Kincompatible implicit declaration of built-in function '[01m[Kcalloc[m[K' > h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; >[01;32m[K ^[m[K >[01m[Kmott_api.c:[m[K In function '[01m[KRobinsonResidueFrequencies2[m[K': >[01m[Kmott_api.c:230:27:[m[K [01;35m[Kwarning: [m[Kincompatible implicit declaration of built-in function '[01m[Kcalloc[m[K' > double *freq = (double*)calloc(256, sizeof(double)); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c -o gaplib.o gaplib.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c >ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o >ar: creating libmott.a >if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi >make[2]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external/mott' >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external' >(cd socket ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" libwisesocket.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/socket' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ functionserver.c >[01m[Kfunctionserver.dy:[m[K In function '[01m[KWise2_main_loop_forking_FunctionServer[m[K': >[01m[Kfunctionserver.dy:128:4:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kwrite[m[K', declared with attribute warn_unused_result [-Wunused-result] > write(new_socket,buf,9); >[01;32m[K ^[m[K >[01m[Kfunctionserver.dy:140:2:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kwrite[m[K', declared with attribute warn_unused_result [-Wunused-result] > write(new_socket,buf,6); >[01;32m[K ^[m[K >[01m[Kfunctionserver.dy:184:2:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kwrite[m[K', declared with attribute warn_unused_result [-Wunused-result] > write(new_socket,buf,5); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ functionclient.c >[01m[Kfunctionclient.dy:[m[K In function '[01m[KWise2_new_FunctionProxyCoordinator[m[K': >[01m[Kfunctionclient.dy:193:24:[m[K [01;35m[Kwarning: [m[Kpassing argument 2 of '[01m[Kconnect[m[K' from incompatible pointer type > connect(out->socket, &server, sizeof(server)); >[01;32m[K ^[m[K >In file included from [01m[Kfunctionclient.c:7:0[m[K: >[01m[K/usr/include/sys/socket.h:137:12:[m[K [01;36m[Knote: [m[Kexpected '[01m[Kconst struct sockaddr *[m[K' but argument is of type '[01m[Kstruct sockaddr_in *[m[K' > extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ anonobj.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ transferinterface.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ directsocketwrite.c >ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o >ar: creating libwisesocket.a >if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/socket' >(cd dnaindex ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dnaindex' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c >[01m[Kkmer_assembly.dy:[m[K In function '[01m[KWise2_remove_sequence_label_KmerAssemblyLink[m[K': >[01m[Kkmer_assembly.dy:365:3:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%ld[m[K' expects argument of type '[01m[Klong int[m[K', but argument 4 has type '[01m[Kstruct KmerAssemblyLink *[m[K' [-Wformat=] > fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); >[01;32m[K ^[m[K >[01m[Kkmer_assembly.dy:367:5:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects a matching '[01m[Kint[m[K' argument [-Wformat=] > fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c >[01m[Kkmer_assembly_untangler.dy:[m[K In function '[01m[KWise2_show_KmerAssemblyPath[m[K': >[01m[Kkmer_assembly_untangler.dy:52:65:[m[K [01;35m[Kwarning: [m[Kcast from pointer to integer of different size [-Wpointer-to-int-cast] > fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); >[01;32m[K ^[m[K >[01m[Kkmer_assembly_untangler.dy:[m[K In function '[01m[KWise2_old_attempt_forward_untangle_KmerAssembly[m[K': >[01m[Kkmer_assembly_untangler.dy:568:75:[m[K [01;35m[Kwarning: [m[Kpassing argument 4 of '[01m[KWise2_lift_backward_tangled_tail[m[K' from incompatible pointer type > lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); >[01;32m[K ^[m[K >In file included from [01m[Kkmer_assembly_untangler.c:4:0[m[K: >[01m[Kkmer_assembly_untangler.h:174:6:[m[K [01;36m[Knote: [m[Kexpected '[01m[Kint *[m[K' but argument is of type '[01m[Klong int *[m[K' > void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_l >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c >[01m[Kkmer_assembly_error.dy:[m[K In function '[01m[KWise2_extend_indel_path_KmerAssembly[m[K': >[01m[Kkmer_assembly_error.dy:351:2:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 4 has type '[01m[Kint *[m[K' [-Wformat=] > fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_po >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c >[01m[Kcompressed_protein_index.dy:[m[K In function '[01m[KWise2_add_direct_number_CompressedProteinIndex[m[K': >[01m[Kcompressed_protein_index.dy:223:3:[m[K [01;35m[Kwarning: [m[Kreturn makes integer from pointer without a cast > return NULL; >[01;32m[K ^[m[K >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dnaindex' >(cd network ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/network' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c >x86_64-pc-linux-gnu-gcc -g -o wise_proteinindex_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` -lpthread >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/network' >(cd models ; make CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-pipe -O2 -c -pthread `pkg-config glib-2.0 --cflags`" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/models' >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c >x86_64-pc-linux-gnu-gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c >x86_64-pc-linux-gnu-gcc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c >x86_64-pc-linux-gnu-gcc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c >[01m[Kdbac.c:[m[K In function '[01m[Kmake_SeqAlign_from_align[m[K': >[01m[Kdbac.c:413:3:[m[K [01;35m[Kwarning: [m[Kformat '[01m[K%d[m[K' expects argument of type '[01m[Kint[m[K', but argument 4 has type '[01m[Ksize_t[m[K' [-Wformat=] > fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c >x86_64-pc-linux-gnu-gcc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c >[01m[Kphasemodel.dy:[m[K In function '[01m[KWise2_read_fasta_PhasedProtein[m[K': >[01m[Kphasemodel.dy:142:3:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kfgets[m[K', declared with attribute warn_unused_result [-Wunused-result] > fgets(name,10000,ifp); >[01;32m[K ^[m[K >In file included from [01m[K/usr/include/stdio.h:936:0[m[K, > from [01m[K../base/wisebase.h:6[m[K, > from [01m[K../dynlibsrc/probability.h:7[m[K, > from [01m[Kgeneparser21.h:6[m[K, > from [01m[Kgenewisemodel.h:6[m[K, > from [01m[Kphasemodel.h:6[m[K, > from [01m[Kphasemodel.c:4[m[K: >In function '[01m[Kfgets[m[K', > inlined from '[01m[KWise2_read_fasta_PhasedProtein[m[K' at [01m[Kphasemodel.dy:142:3[m[K: >[01m[K/usr/include/bits/stdio2.h:261:2:[m[K [01;35m[Kwarning: [m[Kcall to '[01m[K__fgets_chk_warn[m[K' declared with attribute warning: fgets called with bigger size than length of destination buffer > return __fgets_chk_warn (__s, __bos (__s), __n, __stream); >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c >[01m[Kest_evidence.dy:[m[K In function '[01m[KWise2_new_est_GenomeEvidenceUnit[m[K': >[01m[Kest_evidence.dy:142:16:[m[K [01;35m[Kwarning: [m[Kassignment from incompatible pointer type > in->geu_free = free_EstEvidence; >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` promoterwise.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` localcishit.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c >[01m[Kmotifmatrix.c:[m[K In function '[01m[KWise2_MotifConsMatrix_alloc_matrix[m[K': >[01m[Kmotifmatrix.c:408:24:[m[K [01;35m[Kwarning: [m[Kassignment makes integer from pointer without a cast > for(i=0;i<leni;i++) { >[01;32m[K ^[m[K >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` -lpthread >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../external/mott `pkg-config glib-2.0 --cflags` scanwisep.c >x86_64-pc-linux-gnu-gcc -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` hsp2aln_sw.c >x86_64-pc-linux-gnu-gcc -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` -lpthread >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -pipe -O2 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-gcc -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread `pkg-config glib-2.0 --libs` >ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o >ar: creating libmodel.a >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/models' >make bin >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >mkdir bin >cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise ./bin >csh welcome.csh > >Welcome to Wise2.4 > >The executable programs are in the ./bin directory > >You must set your WISECONFIGDIR to the config directory >before using the programs > >ie, type setenv WISECONFIGDIR /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/../wisecfg/ > >to try an example, try cd example and then >../bin/genewise road.pep human.genomic > >to build perl, type make perl and follow the instructions > >to test the package, type make test >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >make: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=latex) > restricted \write18 enabled. >entering extended mode >(./api.tex >LaTeX2e <2015/01/01> patch level 2 >Babel <3.9l> and hyphenation patterns for 16 languages loaded. >(/usr/share/texmf-dist/tex/latex/base/latex209.def > > Entering LaTeX 2.09 COMPATIBILITY MODE > ************************************************************* > !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! > > This mode attempts to provide an emulation of the LaTeX 2.09 > author environment so that OLD documents can be successfully > processed. It should NOT be used for NEW documents! > > New documents should use Standard LaTeX conventions and start > with the \documentclass command. > > Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style > files that change any internal macros, especially not with > those that change the FONT SELECTION or OUTPUT ROUTINES. > > Therefore such style files MUST BE UPDATED to use > Current Standard LaTeX: LaTeX2e. > If you suspect that you may be using such a style file, which > is probably very, very old by now, then you should attempt to > get it updated by sending a copy of this error message to the > author of that file. > ************************************************************* > >(/usr/share/texmf-dist/tex/latex/base/tracefnt.sty) >(/usr/share/texmf-dist/tex/latex/base/latexsym.sty)) >(/usr/share/texmf-dist/tex/latex/base/article.cls >Document Class: article 2014/09/29 v1.4h Standard LaTeX document class >(/usr/share/texmf-dist/tex/latex/base/size10.clo)) >No file api.aux. >(/usr/share/texmf-dist/tex/latex/base/ulasy.fd) [1] >No file api.toc. >[2] [3] >Overfull \hbox (1.49698pt too wide) in paragraph at lines 107--107 >[] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w >ork!";[] >[4] [5] (/usr/share/texmf-dist/tex/latex/base/omscmr.fd) > >LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line >196. > > >LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19 >7. > > >LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 203 >. > > >LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 20 >4. > > >LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 205 >. > > >LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 206 >. > > >LaTeX Warning: Reference `module_sw_wrap' on page 6 undefined on input line 207 >. > > >LaTeX Warning: Reference `module_seqaligndisplay' on page 6 undefined on input >line 208. > > >LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 213 >. > > >LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 21 >3. > >[6] > >LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 >14. > > >LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 >15. > > >LaTeX Warning: Reference `module_sw_wrap' on page 7 undefined on input line 216 >. > > >LaTeX Warning: Reference `object_Hscore' on page 7 undefined on input line 217. > > > >LaTeX Warning: Reference `object_DataEntry' on page 7 undefined on input line 2 >19. > > >LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 >19. > > >LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 >6. > > >LaTeX Warning: Reference `object_Protein' on page 7 undefined on input line 227 >. > > >LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 >8. > > >LaTeX Warning: Reference `object_Genomic' on page 7 undefined on input line 229 >. > > >LaTeX Warning: Reference `object_GeneFrequency' on page 7 undefined on input li >ne 231. > > >LaTeX Warning: Reference `object_CodonTable' on page 7 undefined on input line >232. > > >LaTeX Warning: Reference `object_RandomModelDNA' on page 7 undefined on input l >ine 233. > > >LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 234. > > >LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 235. > > >Overfull \hbox (21.30891pt too wide) in paragraph at lines 235--236 >[]\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: >:GeneParameter21[]wrap > >LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 236. > > >LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 237. > >[7] [8] [9] > >LaTeX Warning: Reference `module_gwrap' on page 10 undefined on input line 387. > > >[10] > >LaTeX Warning: Reference `module_estwrap' on page 11 undefined on input line 38 >9. > > >LaTeX Warning: Reference `module_sw_wrap' on page 11 undefined on input line 39 >1. > > >LaTeX Warning: Reference `module_genedisplay' on page 11 undefined on input lin >e 393. > > >LaTeX Warning: Reference `module_seqaligndisplay' on page 11 undefined on input > line 395. > > >LaTeX Warning: Reference `module_threestatemodel' on page 11 undefined on input > line 397. > > >LaTeX Warning: Reference `module_threestatedb' on page 11 undefined on input li >ne 398. > > >LaTeX Warning: Reference `module_genefrequency' on page 11 undefined on input l >ine 399. > > >LaTeX Warning: Reference `module_geneparameter' on page 11 undefined on input l >ine 400. > > >LaTeX Warning: Reference `module_cdparser' on page 11 undefined on input line 4 >01. > > >LaTeX Warning: Reference `module_sequence' on page 11 undefined on input line 4 >08. > > >LaTeX Warning: Reference `module_sequencedb' on page 11 undefined on input line > 409. > > >LaTeX Warning: Reference `module_protein' on page 11 undefined on input line 41 >0. > > >LaTeX Warning: Reference `module_proteindb' on page 11 undefined on input line >411. > > >LaTeX Warning: Reference `module_genomic' on page 11 undefined on input line 41 >2. > > >LaTeX Warning: Reference `module_genomicdb' on page 11 undefined on input line >413. > > >LaTeX Warning: Reference `module_cdna' on page 11 undefined on input line 414. > > >LaTeX Warning: Reference `module_cdnadb' on page 11 undefined on input line 415 >. > > >LaTeX Warning: Reference `module_probability' on page 11 undefined on input lin >e 421. > > >LaTeX Warning: Reference `module_codon' on page 11 undefined on input line 422. > > > >LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42 >3. > > >LaTeX Warning: Reference `module_codonmat' on page 11 undefined on input line 4 >24. > > >LaTeX Warning: Reference `module_codonmapper' on page 11 undefined on input lin >e 425. > >[11] > >LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 431 >. > > >LaTeX Warning: Reference `module_histogram' on page 12 undefined on input line >432. > > >LaTeX Warning: Reference `module_dbimpl' on page 12 undefined on input line 433 >. > > >LaTeX Warning: Reference `module_aln' on page 12 undefined on input line 439. > > >LaTeX Warning: Reference `module_packaln' on page 12 undefined on input line 44 >0. > > >LaTeX Warning: Reference `module_basematrix' on page 12 undefined on input line > 441. > > >LaTeX Warning: Reference `object_cDNAParser' on page 12 undefined on input line > 449. > > >LaTeX Warning: Reference `accessing_fields' on page 12 undefined on input line >479. > >[12] > >LaTeX Warning: Reference `object_DnaStartEnd' on page 13 undefined on input lin >e 502. > > >Overfull \hbox (62.7533pt too wide) in paragraph at lines 509--510 >[]\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, >text,dpri) > >Overfull \hbox (40.0498pt too wide) in paragraph at lines 510--511 >[]\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap >,text,dpri) >[13] > >LaTeX Warning: Reference `accessing_fields' on page 14 undefined on input line >555. > > >Overfull \hbox (335.96082pt too wide) in paragraph at lines 571--572 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy >n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) > >Overfull \hbox (313.25732pt too wide) in paragraph at lines 572--573 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s >yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) >[14] >Overfull \hbox (329.87091pt too wide) in paragraph at lines 598--599 >[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c >m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) > >Overfull \hbox (270.41774pt too wide) in paragraph at lines 599--600 >[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, >cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) >[15] >Overfull \hbox (265.40146pt too wide) in paragraph at lines 632--633 >[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct >,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) > >Overfull \hbox (205.94829pt too wide) in paragraph at lines 633--634 >[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c >t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) >[16] >Overfull \hbox (47.00343pt too wide) in paragraph at lines 680--681 >[]\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma >in,ofp) > >Overfull \hbox (24.29994pt too wide) in paragraph at lines 681--682 >[]\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m >ain,ofp) > >Overfull \hbox (188.7522pt too wide) in paragraph at lines 701--702 >[]\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p >rotoff,cdna,ct,name,main,mult,ofp) > >Overfull \hbox (166.0487pt too wide) in paragraph at lines 702--703 >[]\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, >protoff,cdna,ct,name,main,mult,ofp) >[17] > >LaTeX Warning: Reference `object_GeneFrequency21' on page 18 undefined on input > line 730. > > >LaTeX Warning: Reference `object_GeneConsensus' on page 18 undefined on input l >ine 732. > > >LaTeX Warning: Reference `object_GeneSingleCons' on page 18 undefined on input >line 734. > >[18] > >LaTeX Warning: Reference `accessing_fields' on page 19 undefined on input line >779. > > >Overfull \hbox (1.40793pt too wide) in paragraph at lines 793--794 >[]\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : >Scalar] > >LaTeX Warning: Reference `accessing_fields' on page 19 undefined on input line >806. > >[19] > >LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line >821. > > >LaTeX Warning: Reference `object_GeneParameter21' on page 20 undefined on input > line 837. > > >LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line >844. > >[20] > >LaTeX Warning: Reference `object_MatchSummarySet' on page 21 undefined on input > line 890. > > >LaTeX Warning: Reference `object_MatchSummary' on page 21 undefined on input li >ne 892. > > >LaTeX Warning: Reference `accessing_fields' on page 21 undefined on input line >899. > > >Overfull \hbox (71.7832pt too wide) in paragraph at lines 914--915 >[]\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o >ffset,target) > >Overfull \hbox (1.83012pt too wide) in paragraph at lines 915--916 >[]\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es >twise > >Overfull \hbox (62.22557pt too wide) in paragraph at lines 917--918 >[]\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]estwise(qname,offset, >target) >[21] >Overfull \hbox (82.28311pt too wide) in paragraph at lines 940--941 >[]\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, >protoff,target) > >Overfull \hbox (7.08008pt too wide) in paragraph at lines 941--942 >[]\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge >newise > >Overfull \hbox (72.72548pt too wide) in paragraph at lines 943--944 >[]\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]genewise(qname,protof >f,target) > >LaTeX Warning: Reference `accessing_fields' on page 22 undefined on input line >965. > >[22] > >LaTeX Warning: Reference `object_PfamHmmer1DB' on page 23 undefined on input li >ne 1007. > > >LaTeX Warning: Reference `object_PfamHmmer1Entry' on page 23 undefined on input > line 1009. > > >LaTeX Warning: Reference `accessing_fields' on page 23 undefined on input line >1016. > > >LaTeX Warning: Reference `accessing_fields' on page 23 undefined on input line >1052. > >[23] >Overfull \hbox (92.78302pt too wide) in paragraph at lines 1074--1075 >[]\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ >et,name,main,ofp) > >Overfull \hbox (70.07953pt too wide) in paragraph at lines 1075--1076 >[]\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar >get,name,main,ofp) >[24] >Overfull \hbox (3.5338pt too wide) in paragraph at lines 1117--1118 >[]\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) > > >LaTeX Warning: Reference `object_DnaSequenceHitList' on page 25 undefined on in >put line 1143. > > >LaTeX Warning: Reference `object_SegmentHitList' on page 25 undefined on input >line 1145. > > >LaTeX Warning: Reference `object_SegmentHit' on page 25 undefined on input line > 1147. > >[25] > >LaTeX Warning: Reference `accessing_fields' on page 26 undefined on input line >1154. > > >Overfull \hbox (29.5499pt too wide) in paragraph at lines 1190--1191 >[]\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL >ist (ifp) >[26] > >LaTeX Warning: Reference `accessing_fields' on page 27 undefined on input line >1207. > > >LaTeX Warning: Reference `accessing_fields' on page 27 undefined on input line >1220. > > >Overfull \hbox (99.50298pt too wide) in paragraph at lines 1248--1249 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga >p,ext,dpenv,dpri) > >Overfull \hbox (76.79948pt too wide) in paragraph at lines 1249--1250 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g >ap,ext,dpenv,dpri) >[27] >Overfull \hbox (110.00288pt too wide) in paragraph at lines 1273--1274 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, >gap,ext,dpenv,dpri) > >Overfull \hbox (87.2994pt too wide) in paragraph at lines 1274--1275 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp >,gap,ext,dpenv,dpri) > >Overfull \hbox (7.58401pt too wide) in paragraph at lines 1286--1287 >[]\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men >t [AlnBlock >[28] >Overfull \hbox (68.00325pt too wide) in paragraph at lines 1307--1308 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, >dpenv,dpri) > >Overfull \hbox (45.29976pt too wide) in paragraph at lines 1308--1309 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext >,dpenv,dpri) > >Overfull \hbox (5.0038pt too wide) in paragraph at lines 1334--1335 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) > >[29] >Overfull \hbox (47.00343pt too wide) in paragraph at lines 1355--1356 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen >v,dpri) > >Overfull \hbox (24.29994pt too wide) in paragraph at lines 1356--1357 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe >nv,dpri) > >Overfull \hbox (86.01088pt too wide) in paragraph at lines 1371--1374 >\OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A >lign[]Sequences[]ProteinSmithWaterman > >Overfull \hbox (240.62169pt too wide) in paragraph at lines 1378--1379 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex >t,bits[]cutoff,report[]level,die[]on[]error,dbsi) > >Overfull \hbox (217.9182pt too wide) in paragraph at lines 1379--1380 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e >xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) >[30] >Overfull \hbox (235.37173pt too wide) in paragraph at lines 1400--1401 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c >,bits[]cutoff,report[]level,die[]on[]error,dbsi) > >Overfull \hbox (212.66824pt too wide) in paragraph at lines 1401--1402 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, >c,bits[]cutoff,report[]level,die[]on[]error,dbsi) >[31] >Overfull \hbox (359.90063pt too wide) in paragraph at lines 1423--1424 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry >,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) > >Overfull \hbox (337.19714pt too wide) in paragraph at lines 1424--1425 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr >y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) > >LaTeX Warning: Reference `object_ThreeStateDB' on page 32 undefined on input li >ne 1452. > > >LaTeX Warning: Reference `accessing_fields' on page 32 undefined on input line >1459. > >[32] >Overfull \hbox (15.42177pt too wide) in paragraph at lines 1487--1488 >[]\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( >ThreeStateDB * tdb,int > >Overfull \hbox (3.42192pt too wide) in paragraph at lines 1494--1495 >[]\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB >* tdb,DataEntry > >Overfull \hbox (41.78299pt too wide) in paragraph at lines 1498--1499 >[]\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T >hreeStateDB *tdb,DataEntry >[33] >Overfull \hbox (29.5499pt too wide) in paragraph at lines 1569--1570 >[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp >,gap,ext) >[34] [35] > >LaTeX Warning: Reference `object_ThreeStateModel' on page 36 undefined on input > line 1632. > > >LaTeX Warning: Reference `object_ThreeStateUnit' on page 36 undefined on input >line 1634. > > >LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line >1675. > >[36] >Overfull \hbox (16.10999pt too wide) in paragraph at lines 1702--1703 >[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int >o[]model) > >Overfull \hbox (102.65288pt too wide) in paragraph at lines 1722--1723 >[]\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, >ratio[]start,ratio[]end) > >Overfull \hbox (169.19861pt too wide) in paragraph at lines 1723--1724 >[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, >prob[]into[]model,ratio[]start,ratio[]end) > >Overfull \hbox (93.09525pt too wide) in paragraph at lines 1725--1726 >[]\OT1/cmtt/m/n/10 $obj->force[]weighted[]local[]model(prob[]into[]model,ratio[ >]start,ratio[]end) > >Overfull \hbox (49.31339pt too wide) in paragraph at lines 1745--1746 >[]\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r >m,gap,ext) >[37] >Overfull \hbox (5.61008pt too wide) in paragraph at lines 1746--1747 >[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S >equence > >Overfull \hbox (39.75575pt too wide) in paragraph at lines 1748--1749 >[]\OT1/cmtt/m/n/10 $obj->ThreeStateModel[]from[]half[]bit[]Sequence(mat,rm,gap, >ext) > >Overfull \hbox (51.38966pt too wide) in paragraph at lines 1772--1773 >[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta >teModel (tsm,ofp) > >LaTeX Warning: Reference `accessing_fields' on page 38 undefined on input line >1790. > >[38] > >LaTeX Warning: Reference `object_AlnRange' on page 39 undefined on input line 1 >815. > > >LaTeX Warning: Reference `object_AlnRangeSet' on page 39 undefined on input lin >e 1817. > > >LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line >1824. > > >LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line >1851. > >[39] > >LaTeX Warning: Reference `object_AlnBlock' on page 40 undefined on input line 1 >867. > > >LaTeX Warning: Reference `object_AlnColumn' on page 40 undefined on input line >1869. > > >LaTeX Warning: Reference `object_AlnUnit' on page 40 undefined on input line 18 >71. > > >LaTeX Warning: Reference `object_AlnSequence' on page 40 undefined on input lin >e 1873. > > >LaTeX Warning: Reference `accessing_fields' on page 40 undefined on input line >1880. > > >Overfull \hbox (6.8248pt too wide) in paragraph at lines 1891--1898 >\OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- >na-mite. Each AlnBlock >[40] > >LaTeX Warning: Reference `accessing_fields' on page 41 undefined on input line >1929. > > >LaTeX Warning: Reference `accessing_fields' on page 41 undefined on input line >1971. > >[41] [42] > >LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line >2039. > >[43] > >LaTeX Warning: Reference `object_cDNADB' on page 44 undefined on input line 210 >5. > > >LaTeX Warning: Reference `accessing_fields' on page 44 undefined on input line >2145. > >[44] [45] > >LaTeX Warning: Reference `object_cDNA' on page 46 undefined on input line 2226. > > > >LaTeX Warning: Reference `accessing_fields' on page 46 undefined on input line >2233. > >[46] [47] > >LaTeX Warning: Reference `object_CodonMapper' on page 48 undefined on input lin >e 2369. > >[48] > >LaTeX Warning: Reference `accessing_fields' on page 49 undefined on input line >2397. > > >Overfull \hbox (12.33003pt too wide) in paragraph at lines 2424--2425 >[]\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm >,error) >[49] > >LaTeX Warning: Reference `object_CodonTable' on page 50 undefined on input line > 2448. > >[50] [51] [52] > >LaTeX Warning: Reference `accessing_fields' on page 53 undefined on input line >2656. > >[53] [54] [55] > >LaTeX Warning: Reference `object_ComplexSequence' on page 56 undefined on input > line 2806. > > >LaTeX Warning: Reference `object_ComplexSequenceEvalSet' on page 56 undefined o >n input line 2808. > > >LaTeX Warning: Reference `accessing_fields' on page 56 undefined on input line >2815. > > >LaTeX Warning: Reference `accessing_fields' on page 56 undefined on input line >2846. > >[56] > >LaTeX Warning: Reference `object_CompMat' on page 57 undefined on input line 28 >81. > > >LaTeX Warning: Reference `accessing_fields' on page 57 undefined on input line >2888. > >[57] [58] > >LaTeX Warning: Reference `object_DBSearchImpl' on page 59 undefined on input li >ne 2988. > > >LaTeX Warning: Reference `accessing_fields' on page 59 undefined on input line >3035. > >[59] > >LaTeX Warning: Reference `object_DnaMatrix' on page 60 undefined on input line >3100. > > >LaTeX Warning: Reference `object_DnaProbMatrix' on page 60 undefined on input l >ine 3102. > >[60] [61] > >LaTeX Warning: Reference `accessing_fields' on page 62 undefined on input line >3163. > > >LaTeX Warning: Reference `accessing_fields' on page 62 undefined on input line >3176. > > >LaTeX Warning: Reference `object_Gene' on page 62 undefined on input line 3208. > > >[62] > >LaTeX Warning: Reference `accessing_fields' on page 63 undefined on input line >3215. > >[63] > >LaTeX Warning: Reference `object_GenomicDB' on page 64 undefined on input line >3312. > > >Overfull \hbox (65.9032pt too wide) in paragraph at lines 3319--3320 >[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in >[]repeat[]coding) > >Overfull \hbox (43.1997pt too wide) in paragraph at lines 3320--3321 >[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i >n[]repeat[]coding) >[64] >Overfull \hbox (41.12343pt too wide) in paragraph at lines 3336--3337 >[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] >cds[]score) > >Overfull \hbox (18.41994pt too wide) in paragraph at lines 3337--3338 >[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ >]cds[]score) > >LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line >3357. > >[65] [66] > >LaTeX Warning: Reference `object_GenomicRegion' on page 67 undefined on input l >ine 3442. > > >LaTeX Warning: Reference `accessing_fields' on page 67 undefined on input line >3449. > > >Overfull \hbox (1.83012pt too wide) in paragraph at lines 3492--3493 >[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file >name) >[67] >Overfull \hbox (7.08008pt too wide) in paragraph at lines 3545--3546 >[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam >e,ofp) >[68] >Overfull \hbox (3.5338pt too wide) in paragraph at lines 3570--3571 >[]\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) > > >Overfull \hbox (59.57962pt too wide) in paragraph at lines 3571--3572 >[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ >]supporting,ofp) >[69] > >LaTeX Warning: Reference `object_Genomic' on page 70 undefined on input line 36 >49. > > >LaTeX Warning: Reference `object_GenomicRepeat' on page 70 undefined on input l >ine 3651. > >[70] >Overfull \hbox (0.5938pt too wide) in paragraph at lines 3690--3691 >[]\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] >N) > >LaTeX Warning: Reference `accessing_fields' on page 71 undefined on input line >3739. > >[71] [72] > >LaTeX Warning: Reference `accessing_fields' on page 73 undefined on input line >3851. > >[73] > >LaTeX Warning: Reference `object_Histogram' on page 74 undefined on input line >3869. > > >LaTeX Warning: Reference `accessing_fields' on page 74 undefined on input line >3917. > >[74] >Overfull \hbox (32.9967pt too wide) in paragraph at lines 3956--3956 >[] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would >be possible.[] >[75] [76] [77] >Overfull \hbox (123.4428pt too wide) in paragraph at lines 4158--4159 >[]\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo >und,wonka,ndegrees) > >Overfull \hbox (67.76958pt too wide) in paragraph at lines 4159--4160 >[]\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, >wonka,ndegrees) > >Overfull \hbox (33.66585pt too wide) in paragraph at lines 4161--4162 >[]\OT1/cmtt/m/n/10 $obj->set[]EVD(mu,lambda,lowbound,highbound,wonka,ndegrees) > >[78] [79] > >LaTeX Warning: Reference `object_Hscore' on page 80 undefined on input line 429 >4. > > >LaTeX Warning: Reference `object_DataScore' on page 80 undefined on input line >4296. > > >LaTeX Warning: Reference `object_DataEntry' on page 80 undefined on input line >4298. > >[80] > >LaTeX Warning: Reference `accessing_fields' on page 81 undefined on input line >4325. > > >Overfull \hbox (30.97293pt too wide) in paragraph at lines 4335--4336 >[]\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score >,double in-ter-nal[]score[]level) >[81] [82] [83] > >LaTeX Warning: Reference `accessing_fields' on page 84 undefined on input line >4526. > > >LaTeX Warning: Reference `accessing_fields' on page 84 undefined on input line >4552. > >[84] > >LaTeX Warning: Reference `object_PackAln' on page 85 undefined on input line 45 >93. > > >LaTeX Warning: Reference `object_PackAlnUnit' on page 85 undefined on input lin >e 4595. > > >LaTeX Warning: Reference `accessing_fields' on page 85 undefined on input line >4602. > >[85] > >LaTeX Warning: Reference `accessing_fields' on page 86 undefined on input line >4672. > >[86] [87] [88] > >LaTeX Warning: Reference `object_ProteinDB' on page 89 undefined on input line >4795. > > >LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line >4852. > >[89] > >LaTeX Warning: Reference `object_Protein' on page 90 undefined on input line 48 >97. > > >LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line >4904. > >[90] > >LaTeX Warning: Reference `object_RandomProteinDB' on page 91 undefined on input > line 4954. > > >LaTeX Warning: Reference `object_RandomDNADB' on page 91 undefined on input lin >e 4956. > > >LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line >4963. > > >LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line >4984. > >[91] > >LaTeX Warning: Reference `object_RandomModelDNA' on page 92 undefined on input >line 5006. > > >LaTeX Warning: Reference `object_RandomModel' on page 92 undefined on input lin >e 5008. > > >LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line >5046. > >[92] > >LaTeX Warning: Reference `accessing_fields' on page 93 undefined on input line >5061. > >[93] > >LaTeX Warning: Reference `object_SequenceDB' on page 94 undefined on input line > 5148. > > >LaTeX Warning: Reference `object_FileSource' on page 94 undefined on input line > 5150. > >[94] > >LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line >5177. > >[95] > >LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line >5238. > > >LaTeX Warning: Reference `object_Sequence' on page 96 undefined on input line 5 >264. > > >LaTeX Warning: Reference `object_SequenceSet' on page 96 undefined on input lin >e 5266. > >[96] > >LaTeX Warning: Reference `accessing_fields' on page 97 undefined on input line >5330. > >[97] >Overfull \hbox (16.34366pt too wide) in paragraph at lines 5390--5391 >[]\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co >nver) >[98] [99] [100] [101] [102] [103] > >LaTeX Warning: Reference `accessing_fields' on page 104 undefined on input line > 5727. > >[104] > >LaTeX Warning: Reference `object_Exon' on page 105 undefined on input line 5745 >. > > >LaTeX Warning: Reference `object_Transcript' on page 105 undefined on input lin >e 5747. > > >LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line > 5754. > > >LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line > 5777. > >[105] > >LaTeX Warning: Reference `object_Translation' on page 106 undefined on input li >ne 5846. > > >LaTeX Warning: Reference `accessing_fields' on page 106 undefined on input line > 5853. > >[106] >Overfull \hbox (24.01358pt too wide) in paragraph at lines 5872--5879 >\OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P >rotein[]from[]Translation() >[107] (./api.aux) > >LaTeX Warning: There were undefined references. > > >LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. > > ) >(see the transcript file for additional information) >Output written on api.dvi (107 pages, 230604 bytes). >Transcript written on api.log. >This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=latex) > restricted \write18 enabled. >entering extended mode >(./api.tex >LaTeX2e <2015/01/01> patch level 2 >Babel <3.9l> and hyphenation patterns for 16 languages loaded. >(/usr/share/texmf-dist/tex/latex/base/latex209.def > > Entering LaTeX 2.09 COMPATIBILITY MODE > ************************************************************* > !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! > > This mode attempts to provide an emulation of the LaTeX 2.09 > author environment so that OLD documents can be successfully > processed. It should NOT be used for NEW documents! > > New documents should use Standard LaTeX conventions and start > with the \documentclass command. > > Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style > files that change any internal macros, especially not with > those that change the FONT SELECTION or OUTPUT ROUTINES. > > Therefore such style files MUST BE UPDATED to use > Current Standard LaTeX: LaTeX2e. > If you suspect that you may be using such a style file, which > is probably very, very old by now, then you should attempt to > get it updated by sending a copy of this error message to the > author of that file. > ************************************************************* > >(/usr/share/texmf-dist/tex/latex/base/tracefnt.sty) >(/usr/share/texmf-dist/tex/latex/base/latexsym.sty)) >(/usr/share/texmf-dist/tex/latex/base/article.cls >Document Class: article 2014/09/29 v1.4h Standard LaTeX document class >(/usr/share/texmf-dist/tex/latex/base/size10.clo)) (./api.aux) >(/usr/share/texmf-dist/tex/latex/base/ulasy.fd) [1] (./api.toc [2] [3] [4] >[5] [6] [7] [8] [9]) [10] [11] >Overfull \hbox (1.49698pt too wide) in paragraph at lines 107--107 >[] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w >ork!";[] >[12] [13] (/usr/share/texmf-dist/tex/latex/base/omscmr.fd) [14] > >LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l >ine 231. > > >LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 234. > > > >LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 235. > > > >Overfull \hbox (21.30891pt too wide) in paragraph at lines 235--236 >[]\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: >:GeneParameter21[]wrap > >LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 236. > > > >LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 237. > > >[15] [16] [17] > >LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 387. > > >[18] > >LaTeX Warning: Reference `module_codonmat' on page 19 undefined on input line 4 >24. > >[19] > >LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 433 >. > >[20] >Overfull \hbox (62.7533pt too wide) in paragraph at lines 509--510 >[]\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, >text,dpri) > >Overfull \hbox (40.0498pt too wide) in paragraph at lines 510--511 >[]\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap >,text,dpri) >[21] >Overfull \hbox (335.96082pt too wide) in paragraph at lines 571--572 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy >n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) > >Overfull \hbox (313.25732pt too wide) in paragraph at lines 572--573 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s >yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) >[22] >Overfull \hbox (329.87091pt too wide) in paragraph at lines 598--599 >[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c >m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) > >Overfull \hbox (270.41774pt too wide) in paragraph at lines 599--600 >[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, >cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) >[23] >Overfull \hbox (265.40146pt too wide) in paragraph at lines 632--633 >[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct >,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) > >Overfull \hbox (205.94829pt too wide) in paragraph at lines 633--634 >[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c >t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) >[24] >Overfull \hbox (47.00343pt too wide) in paragraph at lines 680--681 >[]\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma >in,ofp) > >Overfull \hbox (24.29994pt too wide) in paragraph at lines 681--682 >[]\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m >ain,ofp) > >Overfull \hbox (188.7522pt too wide) in paragraph at lines 701--702 >[]\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p >rotoff,cdna,ct,name,main,mult,ofp) > >Overfull \hbox (166.0487pt too wide) in paragraph at lines 702--703 >[]\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, >protoff,cdna,ct,name,main,mult,ofp) >[25] [26] >Overfull \hbox (1.40793pt too wide) in paragraph at lines 793--794 >[]\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : >Scalar] >[27] [28] >Overfull \hbox (71.7832pt too wide) in paragraph at lines 914--915 >[]\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o >ffset,target) > >Overfull \hbox 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(70.07953pt too wide) in paragraph at lines 1075--1076 >[]\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar >get,name,main,ofp) >[32] >Overfull \hbox (3.5338pt too wide) in paragraph at lines 1117--1118 >[]\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) > >[33] >Overfull \hbox (29.5499pt too wide) in paragraph at lines 1190--1191 >[]\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL >ist (ifp) >[34] >Overfull \hbox (99.50298pt too wide) in paragraph at lines 1248--1249 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga >p,ext,dpenv,dpri) > >Overfull \hbox (76.79948pt too wide) in paragraph at lines 1249--1250 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g >ap,ext,dpenv,dpri) >[35] >Overfull \hbox (110.00288pt too wide) in paragraph at lines 1273--1274 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, >gap,ext,dpenv,dpri) > >Overfull \hbox (87.2994pt too wide) in paragraph at lines 1274--1275 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp >,gap,ext,dpenv,dpri) > >Overfull \hbox (7.58401pt too wide) in paragraph at lines 1286--1287 >[]\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men >t [AlnBlock >[36] >Overfull \hbox (68.00325pt too wide) in paragraph at lines 1307--1308 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, >dpenv,dpri) > >Overfull \hbox (45.29976pt too wide) in paragraph at lines 1308--1309 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext >,dpenv,dpri) > >Overfull \hbox (5.0038pt too wide) in paragraph at lines 1334--1335 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) > >[37] >Overfull \hbox (47.00343pt too wide) in paragraph at lines 1355--1356 >[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen >v,dpri) > >Overfull \hbox (24.29994pt too wide) in paragraph at lines 1356--1357 >[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe >nv,dpri) > >Overfull \hbox (86.01088pt too wide) in paragraph at lines 1371--1374 >\OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A >lign[]Sequences[]ProteinSmithWaterman > >Overfull \hbox (240.62169pt too wide) in paragraph at lines 1378--1379 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex >t,bits[]cutoff,report[]level,die[]on[]error,dbsi) > >Overfull \hbox (217.9182pt too wide) in paragraph at lines 1379--1380 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e >xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) >[38] >Overfull \hbox (235.37173pt too wide) in paragraph at lines 1400--1401 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c >,bits[]cutoff,report[]level,die[]on[]error,dbsi) > >Overfull \hbox (212.66824pt too wide) in paragraph at lines 1401--1402 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, >c,bits[]cutoff,report[]level,die[]on[]error,dbsi) >[39] >Overfull \hbox (359.90063pt too wide) in paragraph at lines 1423--1424 >[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry >,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) > >Overfull \hbox (337.19714pt too wide) in paragraph at lines 1424--1425 >[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr >y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) >[40] >Overfull \hbox (15.42177pt too wide) in paragraph at lines 1487--1488 >[]\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( >ThreeStateDB * tdb,int > >Overfull \hbox (3.42192pt too wide) in paragraph at lines 1494--1495 >[]\OT1/cmr/m/n/10 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Each AlnBlock >[48] [49] [50] [51] [52] [53] [54] [55] [56] >Overfull \hbox (12.33003pt too wide) in paragraph at lines 2424--2425 >[]\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm >,error) >[57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] >Overfull \hbox (65.9032pt too wide) in paragraph at lines 3319--3320 >[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in >[]repeat[]coding) > >Overfull \hbox (43.1997pt too wide) in paragraph at lines 3320--3321 >[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i >n[]repeat[]coding) >[72] >Overfull \hbox (41.12343pt too wide) in paragraph at lines 3336--3337 >[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] >cds[]score) > >Overfull \hbox (18.41994pt too wide) in paragraph at lines 3337--3338 >[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ >]cds[]score) >[73] [74] >Overfull \hbox (1.83012pt too wide) in paragraph at lines 3492--3493 >[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file >name) >[75] >Overfull \hbox (7.08008pt too wide) in paragraph at lines 3545--3546 >[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam >e,ofp) >[76] >Overfull \hbox (3.5338pt too wide) in paragraph at lines 3570--3571 >[]\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) > > >Overfull \hbox (59.57962pt too wide) in paragraph at lines 3571--3572 >[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ >]supporting,ofp) >[77] [78] >Overfull \hbox (0.5938pt too wide) in paragraph at lines 3690--3691 >[]\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] >N) >[79] [80] [81] [82] >Overfull \hbox (32.9967pt too wide) in paragraph at lines 3956--3956 >[] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would >be possible.[] >[83] [84] [85] >Overfull \hbox (123.4428pt too wide) in paragraph at lines 4158--4159 >[]\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo >und,wonka,ndegrees) > >Overfull \hbox (67.76958pt too wide) in paragraph at lines 4159--4160 >[]\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, >wonka,ndegrees) > >Overfull \hbox (33.66585pt too wide) in paragraph at lines 4161--4162 >[]\OT1/cmtt/m/n/10 $obj->set[]EVD(mu,lambda,lowbound,highbound,wonka,ndegrees) > >[86] [87] [88] >Overfull \hbox (30.97293pt too wide) in paragraph at lines 4335--4336 >[]\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score >,double in-ter-nal[]score[]level) >[89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] >[103] [104] [105] >Overfull \hbox (16.34366pt too wide) in paragraph at lines 5390--5391 >[]\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co >nver) >[106] [107] [108] [109] [110] [111] [112] [113] [114] >Overfull \hbox (24.01358pt too wide) in paragraph at lines 5872--5879 >\OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P >rotein[]from[]Translation() >[115] (./api.aux) > >LaTeX Warning: There were undefined references. > > >LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. > > ) >(see the transcript file for additional information) >Output written on api.dvi (115 pages, 306360 bytes). >Transcript written on api.log. >This is dvips(k) 5.995 Copyright 2015 Radical Eye Software (www.radicaleye.com) >' TeX output 2017.05.04:0148' -> api.ps ></usr/share/texmf-dist/dvips/base/tex.pro> ></usr/share/texmf-dist/dvips/base/texps.pro>. ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb>[1] [2] [3] >[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] >[20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] >[35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] >[50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] >[65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] >[80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] >[95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] >[108] [109] [110] [111] [112] [113] [114] [115] >This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=latex) > restricted \write18 enabled. >entering extended mode >(./appendix.tex >LaTeX2e <2015/01/01> patch level 2 >Babel <3.9l> and hyphenation patterns for 16 languages loaded. >(/usr/share/texmf-dist/tex/latex/base/latex209.def > > Entering LaTeX 2.09 COMPATIBILITY MODE > ************************************************************* > !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! > > This mode attempts to provide an emulation of the LaTeX 2.09 > author environment so that OLD documents can be successfully > processed. 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line 475 >. > > >LaTeX Warning: Reference `central_emission' on page 8 undefined on input line 4 >75. > > >LaTeX Warning: Reference `py_length' on page 8 undefined on input line 476. > > >LaTeX Warning: Reference `py_emission' on page 8 undefined on input line 476. > > >LaTeX Warning: Reference `spacer_length' on page 8 undefined on input line 476. > > > >LaTeX Warning: Reference `spacer_emission' on page 8 undefined on input line 47 >7. > >[8] > >LaTeX Warning: Reference `intron_correction_term' on page 9 undefined on input >line 492. > > >LaTeX Warning: Reference `5'SS_term' on page 9 undefined on input line 499. > > >LaTeX Warning: Reference `5'SS_term' on page 9 undefined on input line 508. > > >LaTeX Warning: Reference `central_emission' on page 9 undefined on input line 5 >09. > >[9] > >LaTeX Warning: Reference `central_emission' on page 10 undefined on input line >517. > > >LaTeX Warning: Reference `py_emission' on page 10 undefined on input line 523. > > >LaTeX Warning: Reference `py_emission' on page 10 undefined on input line 530. > > >LaTeX Warning: Reference `spacer_emission' on page 10 undefined on input line 5 >36. > > >LaTeX Warning: Reference `spacer_emission' on page 10 undefined on input line 5 >44. > > >LaTeX Warning: Reference `intron_correction_term' on page 10 undefined on input > line 551. > > >LaTeX Warning: Reference `3'SS_term' on page 10 undefined on input line 552. > >[10] >Overfull \hbox (72.28273pt too wide) detected at line 585 >\OML/cmm/m/it/10.95 Prob\OT1/cmr/m/n/10.95 ([] \OMS/cmsy/m/n/10.95 ! []\OT1/cmr >/m/n/10.95 )(1 \OMS/cmsy/m/n/10.95 ^^@ \OML/cmm/m/it/10.95 P\OT1/cmr/m/n/10.95 >([] \OMS/cmsy/m/n/10.95 j \OML/cmm/m/it/10.95 S\OT1/cmr/m/n/10.95 ) \OMS/cmsy/m >/n/10.95 ^^@ \OML/cmm/m/it/10.95 P\OT1/cmr/m/n/10.95 ([] \OMS/cmsy/m/n/10.95 j >\OML/cmm/m/it/10.95 S\OT1/cmr/m/n/10.95 ) \OMS/cmsy/m/n/10.95 ^^@ \OML/cmm/m/it >/10.95 P\OT1/cmr/m/n/10.95 ([] \OMS/cmsy/m/n/10.95 j \OML/cmm/m/it/10.95 S\OT1/ >cmr/m/n/10.95 )) >[11] (./appendix.aux) > >LaTeX Warning: There were undefined references. > > >LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. > > ) >(see the transcript file for additional information) >Output written on appendix.dvi (11 pages, 28944 bytes). >Transcript written on appendix.log. >This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=latex) > restricted \write18 enabled. >entering extended mode >(./appendix.tex >LaTeX2e <2015/01/01> patch level 2 >Babel <3.9l> and hyphenation patterns for 16 languages loaded. >(/usr/share/texmf-dist/tex/latex/base/latex209.def > > Entering LaTeX 2.09 COMPATIBILITY MODE > ************************************************************* > !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! > > This mode attempts to provide an emulation of the LaTeX 2.09 > author environment so that OLD documents can be successfully > processed. It should NOT be used for NEW documents! > > New documents should use Standard LaTeX conventions and start > with the \documentclass command. > > Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style > files that change any internal macros, especially not with > those that change the FONT SELECTION or OUTPUT ROUTINES. > > Therefore such style files MUST BE UPDATED to use > Current Standard LaTeX: LaTeX2e. > If you suspect that you may be using such a style file, which > is probably very, very old by now, then you should attempt to > get it updated by sending a copy of this error message to the > author of that file. > ************************************************************* > >(/usr/share/texmf-dist/tex/latex/base/tracefnt.sty) >(/usr/share/texmf-dist/tex/latex/base/latexsym.sty)) >(/usr/share/texmf-dist/tex/latex/base/article.cls >Document Class: article 2014/09/29 v1.4h Standard LaTeX document class >(/usr/share/texmf-dist/tex/latex/base/fleqn.clo) >(/usr/share/texmf-dist/tex/latex/base/size11.clo)) (./appendix.aux) >(/usr/share/texmf-dist/tex/latex/base/ulasy.fd) [1] [2] [3] [4] [5] [6] >[7] [8] [9] [10] >Overfull \hbox (72.28273pt too wide) detected at line 585 >\OML/cmm/m/it/10.95 Prob\OT1/cmr/m/n/10.95 ([] \OMS/cmsy/m/n/10.95 ! []\OT1/cmr >/m/n/10.95 )(1 \OMS/cmsy/m/n/10.95 ^^@ \OML/cmm/m/it/10.95 P\OT1/cmr/m/n/10.95 >([] \OMS/cmsy/m/n/10.95 j \OML/cmm/m/it/10.95 S\OT1/cmr/m/n/10.95 ) \OMS/cmsy/m >/n/10.95 ^^@ \OML/cmm/m/it/10.95 P\OT1/cmr/m/n/10.95 ([] \OMS/cmsy/m/n/10.95 j >\OML/cmm/m/it/10.95 S\OT1/cmr/m/n/10.95 ) \OMS/cmsy/m/n/10.95 ^^@ \OML/cmm/m/it >/10.95 P\OT1/cmr/m/n/10.95 ([] \OMS/cmsy/m/n/10.95 j \OML/cmm/m/it/10.95 S\OT1/ >cmr/m/n/10.95 )) >[11] (./appendix.aux) ) >(see the transcript file for additional information) >Output written on appendix.dvi (11 pages, 28568 bytes). >Transcript written on appendix.log. >This is dvips(k) 5.995 Copyright 2015 Radical Eye Software (www.radicaleye.com) >' TeX output 2017.05.04:0148' -> appendix.ps ></usr/share/texmf-dist/dvips/base/tex.pro> ></usr/share/texmf-dist/dvips/base/texps.pro>. ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr6.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb>[1] [2] [3] >[4] [5] [6] [7] [8] [9] [10] [11] >This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=latex) > restricted \write18 enabled. >entering extended mode >(./dynamite.tex >LaTeX2e <2015/01/01> patch level 2 >Babel <3.9l> and hyphenation patterns for 16 languages loaded. >(/usr/share/texmf-dist/tex/latex/base/latex209.def > > Entering LaTeX 2.09 COMPATIBILITY MODE > ************************************************************* > !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! > > This mode attempts to provide an emulation of the LaTeX 2.09 > author environment so that OLD documents can be successfully > processed. It should NOT be used for NEW documents! > > New documents should use Standard LaTeX conventions and start > with the \documentclass command. > > Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style > files that change any internal macros, especially not with > those that change the FONT SELECTION or OUTPUT ROUTINES. > > Therefore such style files MUST BE UPDATED to use > Current Standard LaTeX: LaTeX2e. > If you suspect that you may be using such a style file, which > is probably very, very old by now, then you should attempt to > get it updated by sending a copy of this error message to the > author of that file. > ************************************************************* > >(/usr/share/texmf-dist/tex/latex/base/tracefnt.sty) >(/usr/share/texmf-dist/tex/latex/base/latexsym.sty)) >(/usr/share/texmf-dist/tex/latex/base/article.cls >Document Class: article 2014/09/29 v1.4h Standard LaTeX document class >(/usr/share/texmf-dist/tex/latex/base/size10.clo)) >No file dynamite.aux. >(/usr/share/texmf-dist/tex/latex/base/ulasy.fd) [1] >No file dynamite.toc. >[2] (/usr/share/texmf-dist/tex/latex/base/omscmr.fd) [3] > >LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 75. > >[4] [5] [6] >Overfull \hbox (4.11092pt too wide) in paragraph at lines 251--255 >\OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy >n.x.tar.Z' (where >[7] [8] [9] [10] >Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw <options> seq1 seq2\nBoth sequences in >fasta format\n"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p >rocessing[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p >rocessing[] >[11] >Overfull \hbox (269.24464pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || >strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc >e 2 %d",argc);[] >[12] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current >directory.[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex >plicit memory.[] >[13] >Overfull \hbox (59.24648pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp >,-gap,-ext,NULL);[] > >Overfull \hbox (80.24629pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query >->name,target->name);[] >[14] >Overfull \hbox (48.74657pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex >plicit memory.[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp >,-gap,-ext,NULL);[] >[15] >Overfull \hbox (80.24629pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query >->name,target->name);[] > >Overfull \hbox (32.9967pt too wide) in paragraph at lines 637--637 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp >,-gap,-ext);[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 652--652 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] >[16] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR >DPTTKRSRGF[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR >DP TKRSRGF[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR >DPNTKRSRGF[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN >RSESNVSTKR[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D >R ++++ K+[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ >RPGAHLTVKK[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP >RGFGFVTFDD[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K >RGF FVTFDD[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK >RGFAFVTFDD[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD >RETRGGRSRD[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A > ++ GRS[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- >-SSQRGRSGS[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG >GYGGDYGG--[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G >G G Y G[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG >GSGDGYNGFG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG >PQQQQQGGWG[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G > GG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS >YDSYNNGGGR[] >[17] [18] >Overfull \hbox (48.88945pt too wide) in paragraph at lines 791--793 >[]\OT1/cmr/m/n/10 The align-ment is the set of (i,j,<state>) triples, where sta >te is one of (Match,Insert,Delete) >[19] [20] >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] >[21] >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] >[22] >Overfull \hbox (32.64503pt too wide) in paragraph at lines 1013--1017 >\OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from >GE-NOMIC[]INSERT > >Overfull \hbox (38.24666pt too wide) in paragraph at lines 1114--1114 >[]\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b >ase1][base2])[] >[23] >Overfull \hbox (11.99689pt too wide) in paragraph at lines 1114--1114 >[] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar >get,j))"[] >[24] [25] >Overfull \hbox (122.24593pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen <options> est-seq genomic-seq\nBoth > sequences in fasta format\n"[] >[26] >Overfull \hbox (269.24464pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || >strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] >[27] >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc >e 2 %d",argc);[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a >genomic one[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T >he 'default' one[] > >Overfull \hbox (38.24666pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI >(= -infinity)[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc >onsensi and[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi >se code if you[] >[28] >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet >ers to this[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea >ch side of the[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between >the gap/extension[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro >ns. Here we have[] > >Overfull \hbox (64.49643pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can >be set, to prevent[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have >a probabilistic[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m >ap them to ints[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil >ity2Score).[] > >Overfull \hbox (101.24611pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga >p,-ext,-gap,-ext,0,NULL);[] > >Overfull \hbox (80.24629pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query >->name,target->name);[] >[29] >Overfull \hbox (74.99634pt too wide) in paragraph at lines 1340--1340 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga >p,-ext,-gap,-ext,0);[] >[30] >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a >genomic one[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T >he 'default' one[] > >Overfull \hbox (38.24666pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI >(= -infinity)[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc >onsensi and[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi >se code if you[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA >GATGGT-TAT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA >GAT T T T[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA >GAT--TAT-T[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA >CTGACCGAGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA >CTGACCGAGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA >CTGACCGAGG[] >[31] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG >ACGACCATGA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG >ACGACCATGA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG >ACGACCATGA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA >AATACCATAC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA >AATACCATAC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA >AATACCATAC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC >AAAGCAAGAG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC >AAAGCAAGAG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC >AAAGCAAGAG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG > GTCGAAGT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG > GTCGAAGT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 >->GTCGAAGT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC >GGTGGGAATG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC >GGTGGGAATG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC >GGTGGGAATG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 >660:2793->[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT >GGCAGTGGGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT >GGCAGTGGGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT >GGCAGTGGGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG > GAAGCAATT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG > GAAGCAATT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >>GAAGCAATT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat >gcA-CAATCA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + > +A CAATCA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- >-CAACAATCA[] >[32] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG >AGGCAGAAGC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG >AGGCAGAAGC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG >AGGCAGAAGC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA >CCACGAAACC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA >CCACGAAACC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA >CCACGAAACC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC >AGCAGTAGCT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC >AGCAGTAGCT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC >AGCAGTAGCT[] >[33] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1570--1570 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1570--1570 >[]\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o >f_sequence"[] >[34] [35] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1598--1598 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 1632--1632 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, >-2,NULL);[] > >Overfull \hbox (127.49588pt too wide) in paragraph at lines 1632--1632 >[] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni >t->i+1,unit->j+1,unit->score);[] >[36] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1725--1725 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1725--1725 >[]\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o >f_sequence"[] >[37] [38] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1847--1847 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1847--1847 >[]\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o >f_sequence"[] >[39] >Overfull \hbox (258.74474pt too wide) in paragraph at lines 1847--1847 >[] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) > + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] >[40] [41] >Overfull \hbox (20.54509pt too wide) in paragraph at lines 1909--1910 >[]\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of >the cdna2genomic.dy > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 1926--1926 >[] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta >rget,j))"[] >[42] >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1942--1942 >[] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b >ase] got [codon][] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 1953--1953 >[] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar >get,j))"[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 1965--1965 >[] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu >ery, which do not[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 1965--1965 >[]\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn >ing that[] >[43] >Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 >[] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr >ix",one);[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 >[] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr >ix",two);[] >[44] [45] >Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] <protein-seq> <protein- >fasta-database>\n");[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap > penalty*/[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im >plementations are[] > >Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, >there is the problem[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl >options, but that[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future >proof wrt to new[] >[46] >Overfull \hbox (43.49661pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k >now either (!)[] >[47] >Overfull \hbox (106.49606pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on > stderr search progress */[] > >Overfull \hbox (32.9967pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != > SEARCH_OK )[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing > ungracefully");[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (174.74547pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> >ds[i]->target->name,out->ds[i]->score);[] > >Overfull \hbox (1.49698pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta >rget);[] >[48] >Overfull \hbox (69.74638pt too wide) in paragraph at lines 2253--2253 >[]\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te >mp->baseseq->name);[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, >mat,-12,-2,NULL);[] > >Overfull \hbox (95.99615pt too wide) in paragraph at lines 2253--2253 >[]\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na >me,temp->baseseq->name);[] > >Overfull \hbox (6.74693pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s >tdout);[] > >Overfull \hbox (32.9967pt too wide) in paragraph at lines 2261--2261 >[] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != > SEARCH_OK )[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 2261--2261 >[] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing > ungracefully");[] >[49] >Overfull \hbox (1.49698pt too wide) in paragraph at lines 2290--2290 >[] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta >rget);[] >[50] [51] [52] [53] [54] >Overfull \hbox (1.32472pt too wide) in paragraph at lines 2526--2532 >\OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac >h "state...endstate" >[55] [56] [57] [58] [59] >Overfull \hbox (1.75064pt too wide) in paragraph at lines 2770--2774 >\OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made >by mistyp-ing ``MATCH'' > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2790--2790 >[] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA >TCH2 but there is[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 2790--2790 >[] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li >ne parsing[] >[60] [61] [62] (./dynamite.aux) > >LaTeX Warning: There were undefined references. > > >LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. > > ) >(see the transcript file for additional information) >Output written on dynamite.dvi (62 pages, 118388 bytes). >Transcript written on dynamite.log. >This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=latex) > restricted \write18 enabled. >entering extended mode >(./dynamite.tex >LaTeX2e <2015/01/01> patch level 2 >Babel <3.9l> and hyphenation patterns for 16 languages loaded. >(/usr/share/texmf-dist/tex/latex/base/latex209.def > > Entering LaTeX 2.09 COMPATIBILITY MODE > ************************************************************* > !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! > > This mode attempts to provide an emulation of the LaTeX 2.09 > author environment so that OLD documents can be successfully > processed. It should NOT be used for NEW documents! > > New documents should use Standard LaTeX conventions and start > with the \documentclass command. > > Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style > files that change any internal macros, especially not with > those that change the FONT SELECTION or OUTPUT ROUTINES. > > Therefore such style files MUST BE UPDATED to use > Current Standard LaTeX: LaTeX2e. > If you suspect that you may be using such a style file, which > is probably very, very old by now, then you should attempt to > get it updated by sending a copy of this error message to the > author of that file. > ************************************************************* > >(/usr/share/texmf-dist/tex/latex/base/tracefnt.sty) >(/usr/share/texmf-dist/tex/latex/base/latexsym.sty)) >(/usr/share/texmf-dist/tex/latex/base/article.cls >Document Class: article 2014/09/29 v1.4h Standard LaTeX document class >(/usr/share/texmf-dist/tex/latex/base/size10.clo)) (./dynamite.aux) >(/usr/share/texmf-dist/tex/latex/base/ulasy.fd) [1] (./dynamite.toc [2] >Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50 > [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT >CH]. >) [3] [4] (/usr/share/texmf-dist/tex/latex/base/omscmr.fd) [5] [6] [7] [8] >Overfull \hbox (4.11092pt too wide) in paragraph at lines 251--255 >\OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy >n.x.tar.Z' (where >[9] [10] [11] [12] >Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw <options> seq1 seq2\nBoth sequences in >fasta format\n"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p >rocessing[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p >rocessing[] >[13] >Overfull \hbox (269.24464pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || >strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc >e 2 %d",argc);[] >[14] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current >directory.[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex >plicit memory.[] >[15] >Overfull \hbox (59.24648pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp >,-gap,-ext,NULL);[] > >Overfull \hbox (80.24629pt too wide) in paragraph at lines 586--586 >[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query >->name,target->name);[] >[16] >Overfull \hbox (48.74657pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex >plicit memory.[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp >,-gap,-ext,NULL);[] >[17] >Overfull \hbox (80.24629pt too wide) in paragraph at lines 630--630 >[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query >->name,target->name);[] > >Overfull \hbox (32.9967pt too wide) in paragraph at lines 637--637 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp >,-gap,-ext);[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 652--652 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] >[18] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR >DPTTKRSRGF[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR >DP TKRSRGF[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR >DPNTKRSRGF[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN >RSESNVSTKR[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D >R ++++ K+[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ >RPGAHLTVKK[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP >RGFGFVTFDD[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K >RGF FVTFDD[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK >RGFAFVTFDD[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD >RETRGGRSRD[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A > ++ GRS[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- >-SSQRGRSGS[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG >GYGGDYGG--[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G >G G Y G[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG >GSGDGYNGFG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG >PQQQQQGGWG[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 >[] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G > GG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 >[]\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS >YDSYNNGGGR[] >[19] [20] >Overfull \hbox (48.88945pt too wide) in paragraph at lines 791--793 >[]\OT1/cmr/m/n/10 The align-ment is the set of (i,j,<state>) triples, where sta >te is one of (Match,Insert,Delete) >[21] [22] >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] >[23] >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 >[] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta >rget,j))"[] >[24] >Overfull \hbox (32.64503pt too wide) in paragraph at lines 1013--1017 >\OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from >GE-NOMIC[]INSERT > >Overfull \hbox (38.24666pt too wide) in paragraph at lines 1114--1114 >[]\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b >ase1][base2])[] >[25] >Overfull \hbox (11.99689pt too wide) in paragraph at lines 1114--1114 >[] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar >get,j))"[] >[26] [27] >Overfull \hbox (122.24593pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen <options> est-seq genomic-seq\nBoth > sequences in fasta format\n"[] >[28] >Overfull \hbox (269.24464pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || >strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] >[29] >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc >e 2 %d",argc);[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a >genomic one[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T >he 'default' one[] > >Overfull \hbox (38.24666pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI >(= -infinity)[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc >onsensi and[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi >se code if you[] >[30] >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet >ers to this[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea >ch side of the[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between >the gap/extension[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro >ns. Here we have[] > >Overfull \hbox (64.49643pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can >be set, to prevent[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have >a probabilistic[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m >ap them to ints[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil >ity2Score).[] > >Overfull \hbox (101.24611pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga >p,-ext,-gap,-ext,0,NULL);[] > >Overfull \hbox (80.24629pt too wide) in paragraph at lines 1333--1333 >[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query >->name,target->name);[] >[31] >Overfull \hbox (74.99634pt too wide) in paragraph at lines 1340--1340 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga >p,-ext,-gap,-ext,0);[] >[32] >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a >genomic one[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T >he 'default' one[] > >Overfull \hbox (38.24666pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI >(= -infinity)[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc >onsensi and[] > >Overfull \hbox (43.49661pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi >se code if you[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",target->name);[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA >GATGGT-TAT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA >GAT T T T[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA >GAT--TAT-T[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA >CTGACCGAGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA >CTGACCGAGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA >CTGACCGAGG[] >[33] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG >ACGACCATGA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG >ACGACCATGA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG >ACGACCATGA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA >AATACCATAC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA >AATACCATAC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA >AATACCATAC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC >AAAGCAAGAG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC >AAAGCAAGAG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC >AAAGCAAGAG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG > GTCGAAGT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG > GTCGAAGT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 >->GTCGAAGT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC >GGTGGGAATG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC >GGTGGGAATG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC >GGTGGGAATG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 >660:2793->[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT >GGCAGTGGGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT >GGCAGTGGGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT >GGCAGTGGGG[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG > GAAGCAATT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG > GAAGCAATT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >>GAAGCAATT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat >gcA-CAATCA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + > +A CAATCA[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- >-CAACAATCA[] >[34] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG >AGGCAGAAGC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG >AGGCAGAAGC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG >AGGCAGAAGC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA >CCACGAAACC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA >CCACGAAACC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA >CCACGAAACC[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC >AGCAGTAGCT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC >AGCAGTAGCT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 >[]\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC >AGCAGTAGCT[] >[35] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1570--1570 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1570--1570 >[]\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o >f_sequence"[] >[36] [37] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1598--1598 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 1632--1632 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, >-2,NULL);[] > >Overfull \hbox (127.49588pt too wide) in paragraph at lines 1632--1632 >[] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni >t->i+1,unit->j+1,unit->score);[] >[38] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1725--1725 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1725--1725 >[]\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o >f_sequence"[] >[39] [40] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 1847--1847 >[]\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of >_sequence"[] > >Overfull \hbox (27.74675pt too wide) in paragraph at lines 1847--1847 >[]\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o >f_sequence"[] >[41] >Overfull \hbox (258.74474pt too wide) in paragraph at lines 1847--1847 >[] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) > + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] >[42] [43] >Overfull \hbox (20.54509pt too wide) in paragraph at lines 1909--1910 >[]\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of >the cdna2genomic.dy > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 1926--1926 >[] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta >rget,j))"[] >[44] >Overfull \hbox (53.99652pt too wide) in paragraph at lines 1942--1942 >[] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b >ase] got [codon][] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 1953--1953 >[] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar >get,j))"[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 1965--1965 >[] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu >ery, which do not[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 1965--1965 >[]\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn >ing that[] >[45] >Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 >[] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr >ix",one);[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 >[] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr >ix",two);[] >[46] [47] >Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] <protein-seq> <protein- >fasta-database>\n");[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap > penalty*/[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im >plementations are[] > >Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, >there is the problem[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl >options, but that[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future >proof wrt to new[] >[48] >Overfull \hbox (43.49661pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k >now either (!)[] >[49] >Overfull \hbox (106.49606pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on > stderr search progress */[] > >Overfull \hbox (32.9967pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != > SEARCH_OK )[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing > ungracefully");[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s >",query->name);[] > >Overfull \hbox (174.74547pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> >ds[i]->target->name,out->ds[i]->score);[] > >Overfull \hbox (1.49698pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta >rget);[] >[50] >Overfull \hbox (69.74638pt too wide) in paragraph at lines 2253--2253 >[]\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te >mp->baseseq->name);[] > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, >mat,-12,-2,NULL);[] > >Overfull \hbox (95.99615pt too wide) in paragraph at lines 2253--2253 >[]\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na >me,temp->baseseq->name);[] > >Overfull \hbox (6.74693pt too wide) in paragraph at lines 2253--2253 >[] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s >tdout);[] > >Overfull \hbox (32.9967pt too wide) in paragraph at lines 2261--2261 >[] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != > SEARCH_OK )[] > >Overfull \hbox (53.99652pt too wide) in paragraph at lines 2261--2261 >[] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing > ungracefully");[] >[51] >Overfull \hbox (1.49698pt too wide) in paragraph at lines 2290--2290 >[] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta >rget);[] >[52] [53] [54] [55] [56] >Overfull \hbox (1.32472pt too wide) in paragraph at lines 2526--2532 >\OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac >h "state...endstate" >[57] [58] [59] [60] [61] >Overfull \hbox (1.75064pt too wide) in paragraph at lines 2770--2774 >\OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made >by mistyp-ing ``MATCH'' > >Overfull \hbox (59.24648pt too wide) in paragraph at lines 2790--2790 >[] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA >TCH2 but there is[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 2790--2790 >[] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li >ne parsing[] >[62] [63] [64] (./dynamite.aux) > >LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. > > ) >(see the transcript file for additional information) >Output written on dynamite.dvi (64 pages, 133472 bytes). >Transcript written on dynamite.log. >This is dvips(k) 5.995 Copyright 2015 Radical Eye Software (www.radicaleye.com) >' TeX output 2017.05.04:0148' -> dynamite.ps ></usr/share/texmf-dist/dvips/base/tex.pro> ></usr/share/texmf-dist/dvips/base/texps.pro>. ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb> ></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb>[1] [2] [3] >[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] >[20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] >[35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] >[50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] >This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=latex) > restricted \write18 enabled. >entering extended mode >(./wise2.tex >LaTeX2e <2015/01/01> patch level 2 >Babel <3.9l> and hyphenation patterns for 16 languages loaded. >(/usr/share/texmf-dist/tex/latex/base/article.cls >Document Class: article 2014/09/29 v1.4h Standard LaTeX document class >(/usr/share/texmf-dist/tex/latex/base/size10.clo)) >(/usr/share/texmf-dist/tex/latex/graphics/epsfig.sty >(/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty >(/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) >(/usr/share/texmf-dist/tex/latex/graphics/graphics.sty >(/usr/share/texmf-dist/tex/latex/graphics/trig.sty) >(/usr/share/texmf-dist/tex/latex/latexconfig/graphics.cfg) >(/usr/share/texmf-dist/tex/latex/graphics/dvips.def)))) >No file wise2.aux. >[1] >No file wise2.toc. >[2] [3] [4] > >LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 107 >. > > >LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 110. > > > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d >irectory[] > >Overfull \hbox (48.74657pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep >arate copyright[] >[5] >Overfull \hbox (32.9967pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for > single seqs[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ > DID[] > >Overfull \hbox (11.99689pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ > D[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE > DSQ[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron >2 TAGgtc[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 >083]-0>aca[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa > tta[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN >IVIDKETGKK[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I >I+ D+ +GKK[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE >IMTDRGSGKK[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag >aaagcgagaa[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta >ttcaggggaa[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta >cgtcactcga[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV > QKQHQ[] > >Overfull \hbox (17.24684pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V > QK H[] >[6] >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] > QKYHT[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[]\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 >TAGTTcatca[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] >-1> aaaac[] > >Overfull \hbox (22.4968pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 gctctactcctccgtgtc > gactt[] > >Overfull \hbox (6.74693pt too wide) in paragraph at lines 203--203 >[] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 >: 2793][] >(/usr/share/texmf-dist/tex/latex/base/omscmr.fd) [7] [8] > >LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 294. > > >[9] > >LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34 >3. > >[10] [11] > >LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45 >2. > > >LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 452 >. > > >LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4 >63. > > >LaTeX Warning: Reference `half_and_blast' on page 12 undefined on input line 47 >0. > >[12] > >LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51 >0. > >[13] [14] > >LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6 >10. > >[15] [16] [17] > >LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line > 705. > ><genewise21.eps> [18] [19] [20] [21] > >LaTeX Warning: Reference `Figure:genewise623' on page 22 undefined on input lin >e 896. > ><genewise6.eps> [22] [23] >Overfull \hbox (2.03789pt too wide) in paragraph at lines 960--963 >[]\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti >ve-word state-number:transition- >[24] [25] [26] >Overfull \hbox (68.08423pt too wide) in paragraph at lines 1103--1104 >[]\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac >.uk/pub/birney/wise2/halfwise >[27] > >LaTeX Warning: Reference `sec:commonmode' on page 28 undefined on input line 11 >76. > >[28] > >LaTeX Warning: Reference `sec:start_end' on page 29 undefined on input line 120 >5. > >[29] >Overfull \hbox (42.24687pt too wide) in paragraph at lines 1263--1263 > []\OT1/cmtt/m/n/10 pexon <start-in-dna> <end-in-dna> <start-in-protein> <end-i >n-protein>[] > >Overfull \hbox (42.24687pt too wide) in paragraph at lines 1263--1263 > []\OT1/cmtt/m/n/10 pexon <start-in-dna> <end-in-dna> <start-in-protein> <end-i >n-protein>[] >[30] > >LaTeX Warning: Reference `sec:alg' on page 31 undefined on input line 1271. > > >Overfull \hbox (36.99692pt too wide) in paragraph at lines 1307--1307 > []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel >s introns[] > >Overfull \hbox (5.4972pt too wide) in paragraph at lines 1307--1307 > []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 > 6[] >[31] [32] > >LaTeX Warning: Reference `sec:start_end' on page 33 undefined on input line 137 >2. > >[33] [34] [35] > >LaTeX Warning: Reference `sec:start_end' on page 36 undefined on input line 146 >4. > >[36] [37] > >LaTeX Warning: Reference `compile_pthread' on page 38 undefined on input line 1 >556. > >[38] [39] [40] > >! LaTeX Error: Bad math environment delimiter. > >See the LaTeX manual or LaTeX Companion for explanation. >Type H <return> for immediate help. > ... > >l.1620 \item[-\[no\]dycache] > implicitly cache dy matrix usage (default yes) >? >! Emergency stop. > ... > >l.1620 \item[-\[no\]dycache] > implicitly cache dy matrix usage (default yes) >Output written on wise2.dvi (40 pages, 99176 bytes). >Transcript written on wise2.log. > [31;01m*[0m ERROR: sci-biology/wise-2.4.0_alpha::gentoo failed (compile phase): > [31;01m*[0m (no error message) > [31;01m*[0m > [31;01m*[0m Call stack: > [31;01m*[0m ebuild.sh, line 115: Called src_compile > [31;01m*[0m environment, line 2251: Called die > [31;01m*[0m The specific snippet of code: > [31;01m*[0m latex ${i} || die; > [31;01m*[0m > [31;01m*[0m If you need support, post the output of `emerge --info '=sci-biology/wise-2.4.0_alpha::gentoo'`, > [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-biology/wise-2.4.0_alpha::gentoo'`. > [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/temp/environment'. > [31;01m*[0m Working directory: '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/docs' > [31;01m*[0m S: '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha'
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