* Package: sci-biology/t-coffee-11.00-r2 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; This ebuild was merged at the following commit: https://github.com/gentoo-mirror/gentoo/commit/0afe8006b19e05f59e53463eaadc1ed26dafd2be @@@@@ END @@@@@ >>> Unpacking source... >>> Unpacking T-COFFEE_distribution_Version_11.00.4466924.tar.gz to /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ... * Applying t-coffee-11.00-mayhem.patch ... [ ok ] * Applying t-coffee-11.00-set_proper_dir_permissions.patch ... [ ok ] * Applying t-coffee-11.00-cxx11.patch ... [ ok ] * Applying t-coffee-11.00-gcc7.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ... make -j2 V=1 V=1 CC=x86_64-pc-linux-gnu-clang++ 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result' -C t_coffee_source t_coffee make: Entering directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source' x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c clang-10clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] : warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/util_domain_dp_drivers.c:34: In file included from ./util_lib_header.hIn file included from dp_lib/util_dp_sim.c:33: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ :30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/util_dp_sim.c:173:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; ^~~~~~~~~ dp_lib/util_dp_sim.c:248:20: warning: empty parentheses interpreted as a function declaration [-Wvexing-parse] vertexptr findmax(); /* return the largest score node */ ^~ dp_lib/util_dp_sim.c:248:20: note: replace parentheses with an initializer to declare a variable vertexptr findmax(); /* return the largest score node */ ^~ = nullptr dp_lib/util_dp_sim.c:481:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:481:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:482:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c; /* best score at current point */ ^~~~~~~~~ dp_lib/util_dp_sim.c:483:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int f; /* best score ending with insertion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:484:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; /* best score ending with deletion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:485:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; /* best score at (i-1, j-1) */ ^~~~~~~~~ dp_lib/util_dp_sim.c:486:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:486:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:487:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:487:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:488:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:488:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:489:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:489:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:562:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:562:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:563:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c; /* best score at current point */ ^~~~~~~~~ dp_lib/util_dp_sim.c:564:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int f; /* best score ending with insertion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:565:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; /* best score ending with deletion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:566:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; /* best score at (i-1, j-1) */ ^~~~~~~~~ dp_lib/util_dp_sim.c:567:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:567:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:568:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di=0, dj=0; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:568:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di=0, dj=0; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:569:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:569:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:570:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:570:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:572:16: warning: empty parentheses interpreted as a function declaration [-Wvexing-parse] int addnode(); /* function for inserting a node */ ^~ dp_lib/util_dp_sim.c:572:16: note: replace parentheses with an initializer to declare a variable int addnode(); /* function for inserting a node */ ^~ = 0 dp_lib/util_dp_sim.c:786:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:786:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:787:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c; /* best score at current point */ ^~~~~~~~~ dp_lib/util_dp_sim.c:788:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int f; /* best score ending with insertion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:789:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; /* best score ending with deletion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:790:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; /* best score at (i-1, j-1) */ ^~~~~~~~~ dp_lib/util_dp_sim.c:791:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:791:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:792:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:792:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:793:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:793:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:794:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:794:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_domain_dp_drivers.c:590:16: warning: using thedp_lib/util_dp_sim.c:864:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dp_lib/util_dp_sim.c:864:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ result of an assignment as a condition without parentheses [-Wparentheses] while (entry=extract_entry (CL)) ~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_sim.cdp_lib/util_domain_dp_drivers.c:590:16: note: place parentheses around the assignment to silence this warning :883:3: warning while (entry=extract_entry (CL)) ^ ( ) : 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; dp_lib/util_domain_dp_drivers.c:590:16: note: use '==' to turn this assignment into an equality comparison ^~~~~~~~~ while (entry=extract_entry (CL)) ^ == dp_lib/util_dp_sim.c:911:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dp_lib/util_dp_sim.c:911:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ 2 warnings generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/util_domain_dp.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/fsa_dp.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 55 warnings generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/util_dp_generic_fasta_nw.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/pavie_dp.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/pavie_dp.c:1144:58: warning: operator '?:' has lower precedence than '*'; '*' will be evaluated first [-Wparentheses] gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ dp_lib/pavie_dp.c:1144:58: note: place parentheses around the '*' expression to silence this warning gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ^ ( ) dp_lib/pavie_dp.c:1144:58: note: place parentheses around the '?:' expression to evaluate it first gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ^ ( ) dp_lib/pavie_dp.c:1145:58: warning: operator '?:' has lower precedence than '*'; '*' will be evaluated first [-Wparentheses] gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ dp_lib/pavie_dp.c:1145:58: note: place parentheses around the '*' expression to silence this warning gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ^ ( ) dp_lib/pavie_dp.c:1145:58: note: place parentheses around the '?:' expression to evaluate it first gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ^ ( ) 3 warnings generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/util_dp_cdna_fasta_nw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_dp_mm_nw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/util_dp_cdna_fasta_nw.c:288:132: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] ...0+(M->F_TG_MODE==0)?M->f_gop:0; ~~~~~~~~~~~~~~~~~~~^ dp_lib/util_dp_cdna_fasta_nw.c:288:132: note: place parentheses around the '+' expression to silence this warning ...0+(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) dp_lib/util_dp_cdna_fasta_nw.c:288:132: note: place parentheses around the '?:' expression to evaluate it first ...(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) dp_lib/util_dp_cdna_fasta_nw.c:290:132: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] ...0+(M->F_TG_MODE==0)?M->f_gop:0; ~~~~~~~~~~~~~~~~~~~^ dp_lib/util_dp_cdna_fasta_nw.c:290:132: note: place parentheses around the '+' expression to silence this warning ...0+(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) dp_lib/util_dp_cdna_fasta_nw.c:290:132: note: place parentheses around the '?:' expression to evaluate it first ...(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/util_dp_drivers.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/util_dp_drivers.c:178:14: warning: address of array 'M->prfmode' will always evaluate to 'true' [-Wpointer-bool-conversion] if (M->prfmode && M->prfmode[0])mode=M->prfmode; ~~~^~~~~~~ ~~ dp_lib/util_dp_drivers.c:1080:6: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1108:6: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1149:4: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1280:2: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1328:10: warning: address of array 'M->param' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( M->param) ~~ ~~~^~~~~ dp_lib/util_dp_drivers.c:1445:3: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1451:11: warning: address of array 'M->param' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( M->param) ~~ ~~~^~~~~ dp_lib/util_dp_drivers.c:1462:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (A[a]=seq2R_template_profile(CL->S,s[a])) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1462:15: note: place parentheses around the assignment to silence this warning if (A[a]=seq2R_template_profile(CL->S,s[a])) ^ ( ) dp_lib/util_dp_drivers.c:1462:15: note: use '==' to turn this assignment into an equality comparison if (A[a]=seq2R_template_profile(CL->S,s[a])) ^ == dp_lib/util_dp_drivers.c:1581:3: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1587:11: warning: address of array 'M->param' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( M->param) ~~ ~~~^~~~~ dp_lib/util_dp_drivers.c:1717:4: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1774:4: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1906:4: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1981:4: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2051:13: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int a; ^~~~~~~~~ dp_lib/util_dp_drivers.c:2073:6: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2256:2: warning: ignoring return value of function declared with pure attribute [-Wunused-value] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2950:19: warning: address of array 'CL->tree_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( !CL || !CL->tree_mode || !CL->tree_mode[0]) ~~~~~^~~~~~~~~ 3 warnings generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c dp_lib/util_dp_drivers.c:4295:22: warning: address of array 'CL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse"))dump_co... ~~ ~~~~^~~~~~~ dp_lib/util_dp_drivers.c:4298:22: warning: address of array 'CL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse")) ~~ ~~~~^~~~~~~ dp_lib/util_dp_drivers.c:4383:38: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ... ^ ~ dp_lib/util_dp_drivers.c:4383:38: note: add parentheses after the '!' to evaluate the comparison first if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ... ^ ( ) dp_lib/util_dp_drivers.c:4383:38: note: add parentheses around left hand side expression to silence this warning if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ... ^ ( ) dp_lib/util_dp_drivers.c:4383:66: warning: result of comparison of constant 1 with expression of type 'bool' is always false [-Wtautological-constant-compare] if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/util_dp_suboptimal_nw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/util_dp_gotoh_sw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 24 warnings generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/evaluate.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_graph_maln.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/evaluate.c:2909:134: warning: format specifies type 'double' but the argument has type 'int' [-Wformat] ...%3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1... ~~~~~ ^~~ %3.2d dp_lib/evaluate.c:2909:138: warning: format specifies type 'int' but the argument has type 'float' [-Wformat] ...%3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th... ~~~ ^~~~~~~ %3f dp_lib/evaluate.c:2909:147: warning: format specifies type 'double' but the argument has type 'int' [-Wformat] ...%.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min... ~~~~ ^~~~~~~~ %.3d dp_lib/evaluate.c:2909:157: warning: format specifies type 'int' but the argument has type 'float' [-Wformat] ...%3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, ... ~~~ ^~~~~~ %3f dp_lib/evaluate.c:3850:14: warning: self-comparison always evaluates to false [-Wtautological-compare] if (prf1[0]!=prf1[0]){fprintf ( stderr, "\nERROR: Inconsistent number ... ^ 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/evaluate_for_domain.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from dp_lib/evaluate_dirichlet.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/evaluate_dirichlet.c:543:8: error: 'lgamma_r' is missing exception specification 'throw()' double lgamma_r(double x, int *signgamp) ^ throw() ./dp_lib/evaluate_dirichlet.h:57:8: note: previous declaration is here double lgamma_r(double x, int *signgamp); ^ 1 warning and 1 error generated. make: *** [makefile:11: dp_lib/evaluate_dirichlet.o] Error 1 make: *** Waiting for unfinished jobs.... 6 warnings generated. make: Leaving directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source' * ERROR: sci-biology/t-coffee-11.00-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/t-coffee-11.00-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/t-coffee-11.00-r2::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-biology/t-coffee-11.00-r2:20200708-182332.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924' * S: '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924' emerge --info: Portage 2.3.103 (python 3.7.8-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r5, 5.4.0-1015-aws x86_64) ================================================================= System uname: Linux-5.4.0-1015-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 KiB Mem: 7895548 total, 2137588 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 09 Jul 2020 10:35:22 +0000 sh bash 5.0_p17 ld GNU ld (Gentoo 2.34 p4) 2.34.0 app-shells/bash: 5.0_p17::gentoo dev-lang/perl: 5.30.3-r2::gentoo dev-lang/python: 2.7.18::gentoo, 3.7.8-r1::gentoo, 3.8.3-r1::gentoo, 3.9.0_beta4::gentoo dev-util/cmake: 3.18.0_rc3::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.20::gentoo sys-devel/autoconf: 2.69-r5::gentoo sys-devel/automake: 1.16.2::gentoo sys-devel/binutils: 2.34-r1::gentoo sys-devel/gcc: 10.1.0-r2::gentoo sys-devel/gcc-config: 2.3.1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.31-r5::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXX="x86_64-pc-linux-gnu-clang++" CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -fuse-ld=lld -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j2 V=1" PKGDIR="/root/.packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS