* Package: sci-biology/t-coffee-11.00-r3:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking T-COFFEE_distribution_Version_11.00.4466924.tar.gz to /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work >>> Source unpacked in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work >>> Preparing source in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/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 ] * Applying t-coffee-11.00-makefile.patch ... [ ok ] >>> Source prepared. * Modern C testing: this build is using a /etc/portage/bashrc hook (2023-11-30T22:24)! * Modern C testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info. >>> Configuring source in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924 ... make -j4 -C t_coffee_source t_coffee make: Entering directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source' clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from util_lib/util_job_handling.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ In file included from util_lib/util_dps.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ In file included from util_lib/util_domain_constraints_list.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ util_lib/util_domain_constraints_list.c:52:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 52 | while (e=extract_entry (CL)) | ~^~~~~~~~~~~~~~~~~~~ util_lib/util_domain_constraints_list.c:52:11: note: place parentheses around the assignment to silence this warning 52 | while (e=extract_entry (CL)) | ^ | ( ) util_lib/util_domain_constraints_list.c:52:11: note: use '==' to turn this assignment into an equality comparison 52 | while (e=extract_entry (CL)) | ^ | == In file included from util_lib/util_constraints_list.c:38: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ 1 warning generated. clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] util_lib/util_constraints_list.c:855:119: warning: address of array 'method->executable2' will always evaluate to 'true' [-Wpointer-bool-conversion] 855 | ...vs %s], proba_pair will be used instead",(method->executable2)?method->e... | ~~~~~~~~^~~~~~~~~~~ ~ util_lib/util_constraints_list.c:1249:31: warning: address of array 'm->executable2' will always evaluate to 'true' [-Wpointer-bool-conversion] 1249 | if ( !m-> executable && ! m->executable2)return NULL; | ~ ~~~^~~~~~~~~~~ util_lib/util_constraints_list.c:1249:12: warning: address of array 'm->executable' will always evaluate to 'true' [-Wpointer-bool-conversion] 1249 | if ( !m-> executable && ! m->executable2)return NULL; | ~~~~~^~~~~~~~~~ util_lib/util_constraints_list.c:1263:9: warning: address of array 'm->seq_type' will always evaluate to 'true' [-Wpointer-bool-conversion] 1263 | if (m->seq_type)fprintf (fp, "SEQ_TYPE %s\n", m->seq_type); | ~~ ~~~^~~~~~~~ util_lib/util_constraints_list.c:1312:1: warning: non-void function does not return a value [-Wreturn-type] 1312 | } | ^ 2 warnings generated. 1 warning generated. util_lib/util_constraints_list.c:2225:79: warning: data argument not used by format string [-Wformat-extra-args] 2225 | ...( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c util_lib/util_constraints_list.c:2852:71: warning: data argument not used by format string [-Wformat-extra-args] 2852 | ...x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ~~~~~~~~~~~~~~~~~~~ ^ clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] util_lib/util_constraints_list.c:5107:175: warning: address of array 'NCL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] 5107 | ...%s][Similarity Measure: %s] \n", (NCL->dp_mode)?NCL->dp_mode:"NO_DP",mod... | ~~~~~^~~~~~~ ~ In file included from util_lib/util_analyse_constraints_list.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ In file included from util_lib/util_declare.c:38: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ 1 warning generated. clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c In file included from util_lib/util_aln_analyze.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] util_lib/util_aln_analyze.c:713:1: warning: non-void function does not return a value [-Wreturn-type] 713 | } | ^ util_lib/util_aln_analyze.c:4480:1: warning: non-void function does not return a value [-Wreturn-type] 4480 | } | ^ util_lib/util_aln_analyze.c:4914:36: warning: operator '?:' has lower precedence than '-'; '-' will be evaluated first [-Wparentheses] 4914 | valP=matP[p][res]-(sar=='I')?1:0; | ~~~~~~~~~~~~~~~~~~~~~~~^ util_lib/util_aln_analyze.c:4914:36: note: place parentheses around the '-' expression to silence this warning 4914 | valP=matP[p][res]-(sar=='I')?1:0; | ^ | ( ) util_lib/util_aln_analyze.c:4914:36: note: place parentheses around the '?:' expression to evaluate it first 4914 | valP=matP[p][res]-(sar=='I')?1:0; | ^ | ( ) util_lib/util_aln_analyze.c:4917:36: warning: operator '?:' has lower precedence than '-'; '-' will be evaluated first [-Wparentheses] 4917 | valN=matN[p][res]-(sar=='O')?1:0; | ~~~~~~~~~~~~~~~~~~~~~~~^ util_lib/util_aln_analyze.c:4917:36: note: place parentheses around the '-' expression to silence this warning 4917 | valN=matN[p][res]-(sar=='O')?1:0; | ^ | ( ) util_lib/util_aln_analyze.c:4917:36: note: place parentheses around the '?:' expression to evaluate it first 4917 | valN=matN[p][res]-(sar=='O')?1:0; | ^ | ( ) In file included from util_lib/hsearch.c:36: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ util_lib/hsearch.c:276:1: warning: '/*' within block comment [-Wcomment] 276 | /* */ | ^ 2 warnings generated. clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c 1 warning generated. clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang++ -O2 -pipe -march=native -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c clang++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from util_lib/util_make_tree.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ util_lib/util_make_tree.c:66:1: warning: non-void function does not return a value [-Wreturn-type] 66 | } | ^ util_lib/util_make_tree.c:852:2: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 852 | register int i; | ^~~~~~~~ In file included from util_lib/reformat_struc.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] 54 | /* */ | ^ 2 warnings and 1 error generated. util_lib/reformat_struc.c:125:28: warning: data argument not used by format string [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ~~~~~~~~ ^ make: *** [makefile:9: util_lib/util_make_tree.o] Error 1 make: *** Waiting for unfinished jobs.... util_lib/reformat_struc.c:755:17: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 755 | if (dUNDEFINED){bd=d;ba=a;bb=b;} | ~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:778:19: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 778 | if (dUNDEFINED){bd=d; ba=a; bb=b;} | ~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:808:17: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 808 | if (dUNDEFINED){bd=d;ba=a;bb=b;} | ~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:831:19: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 831 | if (dUNDEFINED){bd=d; ba=a; bb=b;} | ~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:907:11: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 907 | if (d>=UNDEFINED && d<=MaxD) | ~~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:920:25: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 920 | if (d=UNDEFINED){dist[a][b]=cd; A=CB=NULL;} | ~~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:951:11: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 951 | if (d>=UNDEFINED && d<=MaxD) | ~~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:964:25: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 964 | if (d=UNDEFINED){dist[a][b]=dist[b][a]=c... | ~~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:989:18: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 989 | dist[a][b]=UNDEFINED; | ~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:1013:31: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 1013 | dist[a][b]=dist[b][a]=UNDEFINED; | ~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:1033:11: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 1033 | if ( d<=UNDEFINED || d>30)return 0; | ~~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:1058:21: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 1058 | if (dUNDEFINED && dUNDEFINED && d=UNDEFINED){best_d=d;} | ~~^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:1110:25: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 1110 | if (best_d==99)return UNDEFINED; | ~~~~~~ ^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ util_lib/reformat_struc.c:1120:12: warning: implicit conversion from 'int' to 'float' changes value from -99999999 to -1.0E+8 [-Wimplicit-const-int-float-conversion] 1120 | return UNDEFINED; | ~~~~~~ ^~~~~~~~~ ./coffee_defines.h:265:26: note: expanded from macro 'UNDEFINED' 265 | #define UNDEFINED FORBIDEN | ^~~~~~~~ ./coffee_defines.h:239:26: note: expanded from macro 'FORBIDEN' 239 | #define FORBIDEN -99999999 | ^~~~~~~~~ 9 warnings generated. 19 warnings generated. 5 warnings generated. make: Leaving directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source' * ERROR: sci-biology/t-coffee-11.00-r3::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/t-coffee-11.00-r3::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/t-coffee-11.00-r3::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:t-coffee-11.00-r3:20231230-203538.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924' * S: '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924'