* CPV: sci-biology/tree-puzzle-5.2 * REPO: gentoo * USE: elibc_glibc kernel_linux test userland_GNU x86 >>> Unpacking source... >>> Unpacking tree-puzzle-5.2.tar.gz to /var/tmp/portage/sci-biology/tree-puzzle-5.2/work >>> Source unpacked in /var/tmp/portage/sci-biology/tree-puzzle-5.2/work >>> Compiling source in /var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2 ... * econf: updating tree-puzzle-5.2/config.sub with /usr/share/gnuconfig/config.sub * econf: updating tree-puzzle-5.2/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets ${MAKE}... yes checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether i686-pc-linux-gnu-gcc accepts -g... yes checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking whether i686-pc-linux-gnu-gcc and cc understand -c and -o together... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets ${MAKE}... (cached) yes checking for mpcc... no checking for hcc... no checking for mpicc... /usr/bin/mpicc checking for mpicc_lam... no checking for mpicc_mpich... no checking for cc... /usr/bin/cc checking whether /usr/bin/mpicc works as MPI compiler... yes checking whether /usr/bin/mpicc handles quotes correctly... yes checking whether i686-pc-linux-gnu-gcc handles quotes correctly... yes checking for main in -lm... yes checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for i686-pc-linux-gnu-gcc option to accept ANSI C... none needed checking for an ANSI C-conforming const... yes checking for size_t... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/sprng/Makefile config.status: creating doc/Makefile config.status: creating data/Makefile config.status: creating tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands make -j14 Making all in src make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' make all-recursive make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' Making all in sprng make[3]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' i686-pc-linux-gnu-gcc -O2 -pipe -c makeseed.c i686-pc-linux-gnu-gcc -O2 -pipe -c store.c i686-pc-linux-gnu-gcc -O2 -pipe -c memory.c i686-pc-linux-gnu-gcc -O2 -pipe -c checkid.c i686-pc-linux-gnu-gcc -O2 -pipe -c lcg64.c i686-pc-linux-gnu-gcc -O2 -pipe -c primes-lcg64.c primes-lcg64.c: In function ‘getprime’: primes-lcg64.c:75: warning: incompatible implicit declaration of built-in function ‘memcpy’ make[3]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' make[3]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./gamma.c && mv gamma.o sgamma.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./ml1.c && mv ml1.o sml1.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./ml2.c && mv ml2.o sml2.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./mlparam.c && mv mlparam.o smlparam.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./model1.c && mv model1.o smodel1.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./model2.c && mv model2.o smodel2.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./puzzle1.c && mv puzzle1.o spuzzle1.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./puzzle2.c && mv puzzle2.o spuzzle2.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./pstep.c && mv pstep.o spstep.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./util.c && mv util.o sutil.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./consensus.c && mv consensus.o sconsensus.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./treesort.c && mv treesort.o streesort.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -O2 -pipe -c ./treetest.c && mv treetest.o streetest.o cd sprng && make makeseed.o store.o memory.o checkid.o lcg64.o primes-lcg64.o make[4]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' make[4]: `makeseed.o' is up to date. make[4]: `store.o' is up to date. make[4]: `memory.o' is up to date. make[4]: `checkid.o' is up to date. make[4]: `lcg64.o' is up to date. make[4]: `primes-lcg64.o' is up to date. make[4]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' ./puzzle2.c: In function ‘computeallquartets’: ./puzzle2.c:1463: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result ./puzzle1.c: In function ‘writeallquarts’: ./puzzle1.c:261: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result ./puzzle1.c: In function ‘readallquarts’: ./puzzle1.c:294: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result ./puzzle1.c:295: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result ./puzzle1.c:297: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result ./puzzle1.c:298: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result ./puzzle1.c:299: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result ./puzzle1.c:322: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result ./puzzle1.c:335: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result ./puzzle1.c: In function ‘setoptions’: ./puzzle1.c:718: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:776: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:795: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:813: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:915: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1115: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1149: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1164: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1181: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1449: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1478: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1502: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1515: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1524: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1533: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1542: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1551: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result ./puzzle1.c:1560: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o sprng/makeseed.o sprng/store.o sprng/memory.o sprng/checkid.o sprng/lcg64.o sprng/primes-lcg64.o -lm -o puzzle make[3]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' Making all in doc make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' Making all in data make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data' Making all in tests make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests' make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2' >>> Source compiled. >>> Test phase [check]: sci-biology/tree-puzzle-5.2 make -j14 -j1 check Making check in src make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' Making check in sprng make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' cd sprng && make makeseed.o store.o memory.o checkid.o lcg64.o primes-lcg64.o make[3]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' make[3]: `makeseed.o' is up to date. make[3]: `store.o' is up to date. make[3]: `memory.o' is up to date. make[3]: `checkid.o' is up to date. make[3]: `lcg64.o' is up to date. make[3]: `primes-lcg64.o' is up to date. make[3]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng' i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o sprng/makeseed.o sprng/store.o sprng/memory.o sprng/checkid.o sprng/lcg64.o sprng/primes-lcg64.o -lm -o puzzle make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src' Making check in doc make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc' Making check in data make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data' Making check in tests make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests' make check-TESTS make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests' Testing: binary data, quartet puzzling (qp-pure-bin) PASS: qp-pure-bin.test Testing: nucleotide data, default model, quartet puzzling (qp-pure-nucl) 101c101 < Thylacinus 0.00000 0.25 0.22032 0.24509 0.26007 0.24938 0.22246 --- > Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 103c103 < Sarcophilu 0.25 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 --- > Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 109c109 < Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28 --- > Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 113c113 < Philander 0.22246 0.26008 0.17801 0.23041 0.28 0.29036 0.00000 --- > Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 278c278 < Dasyurus 3 0.00 0.01273 11 0.04220 0.02513 --- > Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 290c290 < ((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995, --- > ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, FAIL: qp-pure-nucl.test Testing: nucleotide data, TN, quartet puzzling (qp-tn-nucl) 24,25c24,25 < Transition/transversion parameter (estimated from data set): 1.24 (S.E. 0.40) < Y/R transition parameter (estimated from data set): 2.27 (S.E. 0.68) --- > Transition/transversion parameter (estimated from data set): 1.24 (S.E. 0.61) > Y/R transition parameter (estimated from data set): 2.27 (S.E. 0.65) 102c102 < Thylacinus 0.00000 0.25968 0.22378 0.26 0.26619 0.25302 0.22610 --- > Thylacinus 0.00000 0.25968 0.22378 0.25026 0.26619 0.25302 0.22610 108c108 < Echymipera 0.26 0.27376 0.20328 0.00000 0.30289 0.34430 0.23479 --- > Echymipera 0.25026 0.27376 0.20328 0.00000 0.30289 0.34430 0.23479 113c113 < 0.33 --- > 0.33582 116c116 < Bos 0.24162 0.30169 0.24235 0.27773 0.27782 0.33 0.22749 --- > Bos 0.24162 0.30169 0.24235 0.27773 0.27782 0.33582 0.22749 277c277 < Thylacinus 1 0.11472 0.03957 9 0.04 0.03453 --- > Thylacinus 1 0.11472 0.03957 9 0.05924 0.03453 280c280 < Echymipera 4 0.14312 0.04216 12 0.09 0.03071 --- > Echymipera 4 0.14312 0.04216 12 0.05429 0.03071 290c290 < (Thylacinus:0.11472,(Trichosuru:0.10849,Phalanger:0.12332)94:0.04, --- > (Thylacinus:0.11472,(Trichosuru:0.10849,Phalanger:0.12332)94:0.05924, 292c292 < Bos:0.13724)67:0.04411,Echymipera:0.14312)63:0.09); --- > Bos:0.13724)67:0.04411,Echymipera:0.14312)63:0.05429); FAIL: qp-tn-nucl.test Testing: nucleotide data, HKY, clock, quartet puzzling (qp-hky-clock-nucl) 101c101 < Thylacinus 0.00000 0.25 0.22032 0.24509 0.26007 0.24938 0.22246 --- > Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 103c103 < Sarcophilu 0.25 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 --- > Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 109c109 < Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28 --- > Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 113c113 < Philander 0.22246 0.26008 0.17801 0.23041 0.28 0.29036 0.00000 --- > Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 278c278 < Dasyurus 3 0.00 0.01273 11 0.04220 0.02513 --- > Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 290c290 < ((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995, --- > ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, FAIL: qp-hky-clock-nucl.test Testing: nucleotide data, HKY, rate heterogeneity, quartet puzzling (qp-hky-rhet-nucl) 24c24 < Transition/transversion parameter (estimated from data set): 2.96 (S.E. 0.79) --- > Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) 29c29 < A-G rate: 5.85999 --- > A-G rate: 5.85063 32c32 < C-T rate: 5.85999 --- > C-T rate: 5.85063 42c42 < Expected transition/transversion ratio: 3.15 --- > Expected transition/transversion ratio: 3.14 101,115c101,115 < Thylacinus 0.00000 0.52969 0.37917 0.68 0.58959 0.56187 0.43958 < 0.55330 < Sarcophilu 0.52969 0.00000 0.17842 0.62570 0.69939 0.93662 0.62369 < 0.78648 < Dasyurus 0.37917 0.17842 0.00000 0.39056 0.53463 0.60411 0.31937 < 0.60 < Echymipera 0.68 0.62570 0.39056 0.00000 0.70269 0.94339 0.42036 < 0.66107 < Trichosuru 0.58959 0.69939 0.53463 0.70269 0.00000 0.39438 0.70062 < 0.62735 < Phalanger 0.56187 0.93662 0.60411 0.94339 0.39438 0.00000 0.78715 < 0.98990 < Philander 0.43958 0.62369 0.31937 0.42036 0.70062 0.78715 0.00000 < 0.49297 < Bos 0.55330 0.78648 0.60 0.66107 0.62735 0.98990 0.49297 --- > Thylacinus 0.00000 0.52940 0.37900 0.52236 0.58922 0.56150 0.43932 > 0.55291 > Sarcophilu 0.52940 0.00000 0.17837 0.62532 0.69892 0.93602 0.62327 > 0.78596 > Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 > 0.56220 > Echymipera 0.52236 0.62532 0.39032 0.00000 0.70229 0.94283 0.42016 > 0.66063 > Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 > 0.62697 > Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 > 0.98921 > Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 > 0.49264 > Bos 0.55291 0.78596 0.56220 0.66063 0.62697 0.98921 0.49264 118,120c118,120 < Average distance (over all possible pairs of sequences): 0.59133 < minimum : 0.17842, maximum : 0.98990 < variance : 0.03587, std.dev. : 0.18939 --- > Average distance (over all possible pairs of sequences): 0.59096 > minimum : 0.17837, maximum : 0.98921 > variance : 0.03581, std.dev. : 0.18924 300,307c300,307 < Thylacinus 1 0.23379 0.10258 9 0.19946 0.09586 < Sarcophilu 2 0.18915 0.06717 10 0.22314 0.13107 < Dasyurus 3 0.00001 0.00689 < Echymipera 4 0.27862 0.11701 < Trichosuru 5 0.17838 0.10170 < Phalanger 6 0.27546 0.12626 < Philander 7 0.22555 0.10280 10 iterations until convergence < Bos 8 0.38549 0.14583 log L: -570.33 --- > Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 > Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 > Dasyurus 3 0.00001 0.00200 > Echymipera 4 0.27841 0.11691 > Trichosuru 5 0.17822 0.10160 > Phalanger 6 0.27519 0.12613 > Philander 7 0.22533 0.10269 10 iterations until convergence > Bos 8 0.38507 0.14566 log L: -570.33 315,317c315,317 < (Thylacinus:0.23379,(Sarcophilu:0.18915,Dasyurus:0.00001)90:0.19946, < (Trichosuru:0.17838,Phalanger:0.27546)87:0.22314,Echymipera:0.27862, < Philander:0.22555,Bos:0.38549); --- > (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, > (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, > Philander:0.22533,Bos:0.38507); FAIL: qp-hky-rhet-nucl.test Testing: nucleotide data, HKY, clock, rate heterogeneity, quartet puzzling (qp-hky-rhet-clock-nucl) 24c24 < Transition/transversion parameter (estimated from data set): 2.96 (S.E. 0.79) --- > Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) 29c29 < A-G rate: 5.85999 --- > A-G rate: 5.85063 32c32 < C-T rate: 5.85999 --- > C-T rate: 5.85063 42c42 < Expected transition/transversion ratio: 3.15 --- > Expected transition/transversion ratio: 3.14 101,115c101,115 < Thylacinus 0.00000 0.52969 0.37917 0.68 0.58959 0.56187 0.43958 < 0.55330 < Sarcophilu 0.52969 0.00000 0.17842 0.62570 0.69939 0.93662 0.62369 < 0.78648 < Dasyurus 0.37917 0.17842 0.00000 0.39056 0.53463 0.60411 0.31937 < 0.60 < Echymipera 0.68 0.62570 0.39056 0.00000 0.70269 0.94339 0.42036 < 0.66107 < Trichosuru 0.58959 0.69939 0.53463 0.70269 0.00000 0.39438 0.70062 < 0.62735 < Phalanger 0.56187 0.93662 0.60411 0.94339 0.39438 0.00000 0.78715 < 0.98990 < Philander 0.43958 0.62369 0.31937 0.42036 0.70062 0.78715 0.00000 < 0.49297 < Bos 0.55330 0.78648 0.60 0.66107 0.62735 0.98990 0.49297 --- > Thylacinus 0.00000 0.52940 0.37900 0.52236 0.58922 0.56150 0.43932 > 0.55291 > Sarcophilu 0.52940 0.00000 0.17837 0.62532 0.69892 0.93602 0.62327 > 0.78596 > Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 > 0.56220 > Echymipera 0.52236 0.62532 0.39032 0.00000 0.70229 0.94283 0.42016 > 0.66063 > Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 > 0.62697 > Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 > 0.98921 > Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 > 0.49264 > Bos 0.55291 0.78596 0.56220 0.66063 0.62697 0.98921 0.49264 118,120c118,120 < Average distance (over all possible pairs of sequences): 0.59133 < minimum : 0.17842, maximum : 0.98990 < variance : 0.03587, std.dev. : 0.18939 --- > Average distance (over all possible pairs of sequences): 0.59096 > minimum : 0.17837, maximum : 0.98921 > variance : 0.03581, std.dev. : 0.18924 300,307c300,307 < Thylacinus 1 0.23379 0.10258 9 0.19946 0.09586 < Sarcophilu 2 0.18915 0.06717 10 0.22314 0.13107 < Dasyurus 3 0.00001 0.00689 < Echymipera 4 0.27862 0.11701 < Trichosuru 5 0.17838 0.10170 < Phalanger 6 0.27546 0.12626 < Philander 7 0.22555 0.10280 10 iterations until convergence < Bos 8 0.38549 0.14583 log L: -570.33 --- > Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 > Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 > Dasyurus 3 0.00001 0.00200 > Echymipera 4 0.27841 0.11691 > Trichosuru 5 0.17822 0.10160 > Phalanger 6 0.27519 0.12613 > Philander 7 0.22533 0.10269 10 iterations until convergence > Bos 8 0.38507 0.14566 log L: -570.33 315,317c315,317 < (Thylacinus:0.23379,(Sarcophilu:0.18915,Dasyurus:0.00001)90:0.19946, < (Trichosuru:0.17838,Phalanger:0.27546)87:0.22314,Echymipera:0.27862, < Philander:0.22555,Bos:0.38549); --- > (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, > (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, > Philander:0.22533,Bos:0.38507); 351,358c351,358 < Thylacinus 1 0.29802 0.784 9 0.20377 0.979 < Sarcophilu 2 0.09425 2.007 10 0.22869 0.976 < Dasyurus 3 0.09425 0.000 < Echymipera 4 0.29802 0.935 < Trichosuru 5 0.23493 0.759 < Phalanger 6 0.23493 1.173 < Philander 7 0.29802 0.757 16 iterations until convergence < Bos 8 0.29802 1.294 log L: -573.89 --- > Thylacinus 1 0.29776 0.785 9 0.20356 0.979 > Sarcophilu 2 0.09420 2.007 10 0.22846 0.976 > Dasyurus 3 0.09420 0.000 > Echymipera 4 0.29776 0.935 > Trichosuru 5 0.23472 0.759 > Phalanger 6 0.23472 1.172 > Philander 7 0.29776 0.757 16 iterations until convergence > Bos 8 0.29776 1.293 log L: -573.89 361,364c361,364 < 0.23493 0.07639 10 5 6 < 0.09425 0.03155 9 2 3 < 0.29802 0.05406 10 4 7 8 1 9 < 0.38082 0.07038 of root at branch 10 --- > 0.23472 0.07631 10 5 6 > 0.09420 0.03153 9 2 3 > 0.29776 0.05401 10 4 7 8 1 9 > 0.38047 0.07031 of root at branch 10 370,372c370,372 < ((Trichosuru:0.23493,Phalanger:0.23493)87:0.14589,(Echymipera:0.29802, < Philander:0.29802,Bos:0.29802,Thylacinus:0.29802,(Sarcophilu:0.09425, < Dasyurus:0.09425)90:0.20377):0.08280); --- > ((Trichosuru:0.23472,Phalanger:0.23472)87:0.14575,(Echymipera:0.29776, > Philander:0.29776,Bos:0.29776,Thylacinus:0.29776,(Sarcophilu:0.09420, > Dasyurus:0.09420)90:0.20356):0.08271); FAIL: qp-hky-rhet-clock-nucl.test Testing: protein data, default model, quartet puzzling (qp-pure-prot) 247,248c247,248 < HBA_HUMAN 3 0.02555 0.02185 10 0.34694 0.12 < HBA_HORSE 4 0.09 0.03153 11 0.60239 0.11261 --- > HBA_HUMAN 3 0.02555 0.02185 10 0.34694 0.12552 > HBA_HORSE 4 0.09542 0.03153 11 0.60239 0.11261 257c257 < (HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09)100:0.28345, --- > (HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09542)100:0.28345, FAIL: qp-pure-prot.test Testing: protein data, mtREV, quartet puzzling (qp-mtrev-prot) 107c107 < HBA_HORSE 1.16856 1.20524 0.13144 0.00000 2.44163 1.55 3.05140 --- > HBA_HORSE 1.16856 1.20524 0.13144 0.00000 2.44163 1.55582 3.05140 109c109 < GLB5_PETMA 2.15305 2.18071 1.43785 1.55 2.62256 0.00000 2.97722 --- > GLB5_PETMA 2.15305 2.18071 1.43785 1.55582 2.62256 0.00000 2.97722 FAIL: qp-mtrev-prot.test Testing: protein data, VT, quartet puzzling (qp-vt-prot) 244c244 < HBB_HUMAN 1 0.04599 0.03062 8 0.42025 0.11482 --- > HBB_HUMAN 1 0.04599 0.03062 8 0.42025 0.11481 246c246 < HBA_HUMAN 3 0.03150 0.02213 10 0.96 0.10035 --- > HBA_HUMAN 3 0.03150 0.02213 10 0.54296 0.10035 257c257 < 100:0.42025,(HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241)100:0.96, --- > 100:0.42025,(HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241)100:0.54296, FAIL: qp-vt-prot.test Testing: protein data, WAG, quartet puzzling (qp-wag-prot) 244c244 < HBB_HUMAN 1 0.08 0.03102 8 0.44299 0.11946 --- > HBB_HUMAN 1 0.05028 0.03102 8 0.44299 0.11946 246c246 < HBA_HUMAN 3 0.02934 0.02190 10 0.57110 0.10504 --- > HBA_HUMAN 3 0.02934 0.02189 10 0.57110 0.10504 256c256 < (HBB_HUMAN:0.08,((MYG_PHYCA:1.11230,GLB5_PETMA:0.59340,LGB2_LUPLU:1.46501) --- > (HBB_HUMAN:0.05028,((MYG_PHYCA:1.11230,GLB5_PETMA:0.59340,LGB2_LUPLU:1.46501) FAIL: qp-wag-prot.test Testing: default data, default model, clock, quartet puzzling (qp-clock) 101c101 < Thylacinus 0.00000 0.25 0.22032 0.24509 0.26007 0.24938 0.22246 --- > Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 103c103 < Sarcophilu 0.25 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 --- > Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 109c109 < Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28 --- > Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 113c113 < Philander 0.22246 0.26008 0.17801 0.23041 0.28 0.29036 0.00000 --- > Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 278c278 < Dasyurus 3 0.00 0.01273 11 0.04220 0.02513 --- > Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 290c290 < ((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995, --- > ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, FAIL: qp-clock.test Testing: protein data, JTT, quartet puzzling (qp-jtt-prot) 106,107c106,107 < HBA_HUMAN 0.93732 0.97297 0.00000 0.12200 1.93956 1.26 2.51688 < HBA_HORSE 0.96340 0.97742 0.12200 0.00000 1.99570 1.34817 2.47 --- > HBA_HUMAN 0.93732 0.97297 0.00000 0.12200 1.93956 1.25126 2.51688 > HBA_HORSE 0.96340 0.97742 0.12200 0.00000 1.99570 1.34817 2.47562 109,110c109,110 < GLB5_PETMA 1.74159 1.75271 1.26 1.34817 2.04426 0.00000 2.23399 < LGB2_LUPLU 2.60857 2.65715 2.51688 2.47 2.69086 2.23399 0.00000 --- > GLB5_PETMA 1.74159 1.75271 1.25126 1.34817 2.04426 0.00000 2.23399 > LGB2_LUPLU 2.60857 2.65715 2.51688 2.47562 2.69086 2.23399 0.00000 245c245 < HBB_HORSE 2 0.12734 0.03889 9 0.25371 0.08 --- > HBB_HORSE 2 0.12734 0.03889 9 0.25371 0.08572 FAIL: qp-jtt-prot.test Testing: protein data, JTT, rate heterogeneity, quartet puzzling (qp-jtt-rhet-prot) 270c270 < HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17282 --- > HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 FAIL: qp-jtt-rhet-prot.test Testing: protein data, JTT, clock, rate heterogeneity, quartet puzzling (qp-jtt-rhet-clock-prot) 270c270 < HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17282 --- > HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 316c316 < HBB_HUMAN 1 0.08775 0. 8 0.58020 0.874 --- > HBB_HUMAN 1 0.08775 0.562 8 0.58020 0.874 FAIL: qp-jtt-rhet-clock-prot.test Testing: protein data, default model, likelihood mapping (lm-pure-prot) PASS: lm-pure-prot.test Testing: protein data, default model, user tree evaluation (ut-pure-prot) 151c151 < HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00265 --- > HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00141 192,193c192,193 < HBB_HORSE 2 0.12604 0.03871 9 0.18149 0.13086 < HBA_HUMAN 3 0.02555 0.02185 10 0.34695 0.12 --- > HBB_HORSE 2 0.12604 0.03871 9 0.18149 0.13088 > HBA_HUMAN 3 0.02555 0.02185 10 0.34695 0.12552 196c196 < GLB5_PETMA 6 0.57473 0.13844 9 iterations until convergence --- > GLB5_PETMA 6 0.57473 0.13845 9 iterations until convergence 271c271 < HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11282 --- > HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 FAIL: ut-pure-prot.test Testing: protein data, default model, consensus construction (cons-pure-prot) PASS: cons-pure-prot.test *** *** !!! Important remark !!! *** *** Please note that only the output file *.puzzle is checked *** for identity. The overall precision reached in the program *** is heavily dependent on the compiler as well as the optimization *** level (-O) used to compile the executable. *** Hence, even if tests are marked as failed this might just be *** due to differences in less significant digits caused by rounding *** errors from less acurate computations for the sake of faster *** running times. (If you want to be sure about this please refer *** to your compiler's manual!) *** *** Please check the output file differences which are printed during the tests. *** The template files which the results are checked against have been *** generated with TREE-PUZZLE 5.2 compiled with GCC version 3.3-20030226 *** and default compiler flags '-g -O2' and using the SPRNG random number *** generator. *** ===================== 14 of 17 tests failed ===================== make[2]: *** [check-TESTS] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests' make[1]: *** [check-am] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests' make: *** [check-recursive] Error 1 * ERROR: sci-biology/tree-puzzle-5.2 failed: * Make check failed. See above for details. * * Call stack: * ebuild.sh, line 61: Called src_test * environment, line 1069: Called _eapi0_src_test * ebuild.sh, line 626: Called die * The specific snippet of code: * hasq test $FEATURES && die "Make check failed. See above for details." * * If you need support, post the output of 'emerge --info =sci-biology/tree-puzzle-5.2', * the complete build log and the output of 'emerge -pqv =sci-biology/tree-puzzle-5.2'. * The complete build log is located at '/var/log/portage/build/sci-biology/tree-puzzle-5.2:20091220-044809.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/tree-puzzle-5.2/temp/environment'. * S: '/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2' >>> Install tree-puzzle-5.2 into /var/tmp/portage/sci-biology/tree-puzzle-5.2/image/ category sci-biology >>> Completed installing tree-puzzle-5.2 into /var/tmp/portage/sci-biology/tree-puzzle-5.2/image/ strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment usr/bin/puzzle  * QA Notice: Package has poor programming practices which may compile * fine but exhibit random runtime failures. * primes-lcg64.c:75: warning: incompatible implicit declaration of built-in function ‘memcpy’  * Please do not file a Gentoo bug and instead report the above QA * issues directly to the upstream developers of this software. * Homepage: http://www.tree-puzzle.de * Removing /usr/share/doc * Removing /usr/share/info