printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild infernal 2>&1 The package 'infernal' will be built without being installed. Reading build dependency for infernal-1.0.2-1... Reading dependency for infernal-1.0.2-1... Reading build conflict for infernal-1.0.2-1... The following package will be rebuilt: infernal curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/infernal-1.0.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 0 14.5M 0 93874 0 0 41784 0 0:06:03 0:00:02 0:06:01 41777 0 14.5M 0 100k 0 0 29300 0 0:08:38 0:00:03 0:08:35 29295 4 14.5M 4 672k 0 0 160k 0 0:01:32 0:00:04 0:01:28 160k 5 14.5M 5 815k 0 0 137k 0 0:01:48 0:00:05 0:01:43 141k 5 14.5M 5 817k 0 0 125k 0 0:01:57 0:00:06 0:01:51 154k 7 14.5M 7 1130k 0 0 150k 0 0:01:38 0:00:07 0:01:31 196k 8 14.5M 8 1330k 0 0 149k 0 0:01:39 0:00:08 0:01:31 228k 8 14.5M 8 1333k 0 0 135k 0 0:01:49 0:00:09 0:01:40 117k 10 14.5M 10 1576k 0 0 153k 0 0:01:36 0:00:10 0:01:26 176k 14 14.5M 14 2224k 0 0 198k 0 0:01:14 0:00:11 0:01:03 299k 20 14.5M 20 2994k 0 0 245k 0 0:01:00 0:00:12 0:00:48 399k 21 14.5M 21 3131k 0 0 224k 0 0:01:06 0:00:13 0:00:53 357k 22 14.5M 22 3321k 0 0 233k 0 0:01:03 0:00:14 0:00:49 450k 26 14.5M 26 3963k 0 0 260k 0 0:00:56 0:00:15 0:00:41 482k 31 14.5M 31 4718k 0 0 291k 0 0:00:50 0:00:16 0:00:34 499k 35 14.5M 35 5262k 0 0 294k 0 0:00:50 0:00:17 0:00:33 398k 36 14.5M 36 5465k 0 0 299k 0 0:00:49 0:00:18 0:00:31 542k 39 14.5M 39 5889k 0 0 306k 0 0:00:48 0:00:19 0:00:29 517k 43 14.5M 43 6437k 0 0 318k 0 0:00:46 0:00:20 0:00:26 494k 46 14.5M 46 6882k 0 0 314k 0 0:00:47 0:00:21 0:00:26 378k 47 14.5M 47 7068k 0 0 317k 0 0:00:46 0:00:22 0:00:24 415k 49 14.5M 49 7359k 0 0 316k 0 0:00:46 0:00:23 0:00:23 377k 53 14.5M 53 7956k 0 0 328k 0 0:00:45 0:00:24 0:00:21 411k 56 14.5M 56 8448k 0 0 326k 0 0:00:45 0:00:25 0:00:20 352k 58 14.5M 58 8659k 0 0 330k 0 0:00:44 0:00:26 0:00:18 412k 60 14.5M 60 9000k 0 0 330k 0 0:00:44 0:00:27 0:00:17 385k 64 14.5M 64 9585k 0 0 340k 0 0:00:43 0:00:28 0:00:15 450k 68 14.5M 68 9.9M 0 0 349k 0 0:00:42 0:00:29 0:00:13 452k 70 14.5M 70 10.1M 0 0 336k 0 0:00:44 0:00:30 0:00:14 387k 71 14.5M 71 10.3M 0 0 338k 0 0:00:43 0:00:31 0:00:12 379k 72 14.5M 72 10.5M 0 0 329k 0 0:00:45 0:00:32 0:00:13 324k 75 14.5M 75 10.9M 0 0 339k 0 0:00:43 0:00:33 0:00:10 335k 76 14.5M 76 11.1M 0 0 333k 0 0:00:44 0:00:34 0:00:10 237k 81 14.5M 81 11.7M 0 0 342k 0 0:00:43 0:00:35 0:00:08 386k 86 14.5M 86 12.5M 0 0 355k 0 0:00:41 0:00:36 0:00:05 463k 92 14.5M 92 13.4M 0 0 363k 0 0:00:40 0:00:37 0:00:03 580k 93 14.5M 93 13.5M 0 0 355k 0 0:00:41 0:00:38 0:00:03 448k 93 14.5M 93 13.5M 0 0 346k 0 0:00:42 0:00:39 0:00:03 423k 93 14.5M 93 13.5M 0 0 337k 0 0:00:43 0:00:40 0:00:03 311k 93 14.5M 93 13.5M 0 0 329k 0 0:00:45 0:00:41 0:00:04 168k 93 14.5M 93 13.5M 0 0 329k 0 0:00:45 0:00:42 0:00:03 37181 94 14.5M 94 13.7M 0 0 323k 0 0:00:45 0:00:43 0:00:02 59502 96 14.5M 96 13.9M 0 0 323k 0 0:00:45 0:00:44 0:00:01 108k 97 14.5M 97 14.1M 0 0 321k 0 0:00:46 0:00:45 0:00:01 164k 100 14.5M 100 14.5M 0 0 322k 0 0:00:46 0:00:46 --:--:-- 249k Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-infernal-1.0.2-1 /sw/build.build dpkg-deb: building package `fink-buildlock-infernal-1.0.2-1' in `/sw/build.build/fink-buildlock-infernal-1.0.2-1_2014.08.01-14.15.53_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-infernal-1.0.2-1_2014.08.01-14.15.53_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-infernal-1.0.2-1. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-buildlock-infernal-1.0.2-1 (from .../fink-buildlock-infernal-1.0.2-1_2014.08.01-14.15.53_darwin-x86_64.deb) ... Setting up fink-buildlock-infernal-1.0.2-1 (2014.08.01-14.15.53) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.yqeiL env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/infernal-1.0.2.tar.gz infernal-1.0.2/ infernal-1.0.2/00README-MPI infernal-1.0.2/scripts/ infernal-1.0.2/scripts/cm_multi2indi.pl infernal-1.0.2/scripts/stk2rf_cc_stk.pl infernal-1.0.2/scripts/cmsearch_pp.pl infernal-1.0.2/src/ infernal-1.0.2/src/dispatch.c infernal-1.0.2/src/stats.c infernal-1.0.2/src/histogram.h infernal-1.0.2/src/stats.h infernal-1.0.2/src/cm.c infernal-1.0.2/src/old_cm_dpsearch.c infernal-1.0.2/src/Makefile.in infernal-1.0.2/src/cm_dpsearch.c infernal-1.0.2/src/display.c infernal-1.0.2/src/rna.null infernal-1.0.2/src/cm_dpsmall.c infernal-1.0.2/src/seqstoaln.c infernal-1.0.2/src/cmsearch.c infernal-1.0.2/src/old_cp9_dp.c infernal-1.0.2/src/errors.c infernal-1.0.2/src/rnamat.c infernal-1.0.2/src/cmemit.c infernal-1.0.2/src/cmcalibrate-hybrid.c infernal-1.0.2/src/rnamat.h infernal-1.0.2/src/old_miscfuncs.c infernal-1.0.2/src/cp9.c infernal-1.0.2/src/default.pri infernal-1.0.2/src/cm_mx.c infernal-1.0.2/src/cm_submodel.c infernal-1.0.2/src/logsum.c infernal-1.0.2/src/cplan9.h infernal-1.0.2/src/cm_qdband.c infernal-1.0.2/src/config.h.in infernal-1.0.2/src/cmbuild.c infernal-1.0.2/src/sa-Makefile.in infernal-1.0.2/src/cm_modelmaker.c infernal-1.0.2/src/prior.h infernal-1.0.2/src/cmcalibrate.c infernal-1.0.2/src/partial-test.c infernal-1.0.2/src/old_funcs.h infernal-1.0.2/src/cmalign.c infernal-1.0.2/src/cm_modelconfig.c infernal-1.0.2/src/hybridsearch.c infernal-1.0.2/src/cp9_trace.c infernal-1.0.2/src/hmmband.h infernal-1.0.2/src/mpisupport.c infernal-1.0.2/src/structs.h infernal-1.0.2/src/cp9_modelconfig.c infernal-1.0.2/src/cm_dispatch.h infernal-1.0.2/src/cm_postprob.h infernal-1.0.2/src/cm_io.c infernal-1.0.2/src/prior.c infernal-1.0.2/src/trcyk.c infernal-1.0.2/src/truncyk_check.c infernal-1.0.2/src/cm_parsetree.c infernal-1.0.2/src/scancyk.c infernal-1.0.2/src/globals.c infernal-1.0.2/src/funcs.h infernal-1.0.2/src/cmstat.c infernal-1.0.2/src/cp9_modelmaker.c infernal-1.0.2/src/histogram.c infernal-1.0.2/src/cm_dpalign.c infernal-1.0.2/src/searchinfo.c infernal-1.0.2/src/alphabet.c infernal-1.0.2/src/mpifuncs.c infernal-1.0.2/src/CP9_hmmio.c infernal-1.0.2/src/mpifuncs.h infernal-1.0.2/src/old_cm_dpalign.c infernal-1.0.2/src/eweight.c infernal-1.0.2/src/cmscore.c infernal-1.0.2/src/hmmband.c infernal-1.0.2/src/nearzero.prior infernal-1.0.2/src/cp9_mx.c infernal-1.0.2/src/truncyk.c infernal-1.0.2/src/cp9_dp.c infernal-1.0.2/config.guess infernal-1.0.2/testsuite/ infernal-1.0.2/testsuite/cmstat.sqc infernal-1.0.2/testsuite/cmscore.sqc infernal-1.0.2/testsuite/at25.null infernal-1.0.2/testsuite/DicF.seed infernal-1.0.2/testsuite/ffs-frag.fa infernal-1.0.2/testsuite/vault.fa infernal-1.0.2/testsuite/Makefile.in infernal-1.0.2/testsuite/dev-exercises.sqc infernal-1.0.2/testsuite/mito-ascaris.gb infernal-1.0.2/testsuite/DicF-0.71.cm infernal-1.0.2/testsuite/trna.xmask infernal-1.0.2/testsuite/DicF-0.55.cm infernal-1.0.2/testsuite/trna.calibrated.cm infernal-1.0.2/testsuite/srp-euk.sto infernal-1.0.2/testsuite/trna1415G.sto infernal-1.0.2/testsuite/vault.sto infernal-1.0.2/testsuite/plus1.prior infernal-1.0.2/testsuite/1k.fa infernal-1.0.2/testsuite/bandcyk-truncation-test.c infernal-1.0.2/testsuite/00README infernal-1.0.2/testsuite/DicF-0.8.cm infernal-1.0.2/testsuite/RIBOSUM85-60.mat infernal-1.0.2/testsuite/at4.null infernal-1.0.2/testsuite/3trnas.gb infernal-1.0.2/testsuite/DicF-0.6.cm infernal-1.0.2/testsuite/trna-regression.fa infernal-1.0.2/testsuite/rnaseP-bsu.fa infernal-1.0.2/testsuite/se.1.stk infernal-1.0.2/testsuite/trna.list infernal-1.0.2/testsuite/cmsearch.sqc infernal-1.0.2/testsuite/3.4.12.stk infernal-1.0.2/testsuite/10wide.mask infernal-1.0.2/testsuite/test.sqc infernal-1.0.2/testsuite/bandcyk-montecarlo-test.c infernal-1.0.2/testsuite/exercises.sqc infernal-1.0.2/testsuite/mito-ascaris.fa infernal-1.0.2/testsuite/3trnas.embl infernal-1.0.2/testsuite/DicF-0.72.cm infernal-1.0.2/testsuite/cp9-test.c infernal-1.0.2/testsuite/hairpin.sto infernal-1.0.2/testsuite/cmbuild.sqc infernal-1.0.2/testsuite/se.stk infernal-1.0.2/testsuite/cmcalibrate.sqc infernal-1.0.2/testsuite/regressions.sqc infernal-1.0.2/testsuite/3.4.12.calibrated.cm infernal-1.0.2/testsuite/rnaseP-frag.fa infernal-1.0.2/testsuite/3.4.12.rf.stk infernal-1.0.2/testsuite/rnaseP-eubact.sto infernal-1.0.2/testsuite/ffs-ecoli.fa infernal-1.0.2/testsuite/DicF-1.0.1.cm infernal-1.0.2/testsuite/cmalign.sqc infernal-1.0.2/testsuite/DicF-1.0.cm infernal-1.0.2/testsuite/cmemit.sqc infernal-1.0.2/testsuite/3trnas.fa infernal-1.0.2/testsuite/esl-alimanip.sqc infernal-1.0.2/testsuite/benchmarks.sqc infernal-1.0.2/testsuite/2hairpins.sto infernal-1.0.2/testsuite/DicF-0.7.cm infernal-1.0.2/testsuite/sub_cm-test.c infernal-1.0.2/testsuite/se.rf.stk infernal-1.0.2/testsuite/sqc infernal-1.0.2/intro/ infernal-1.0.2/intro/5S_ecoli.fa infernal-1.0.2/intro/tutorial.fa infernal-1.0.2/intro/trna_yeast_phe.fa infernal-1.0.2/intro/RNaseP_ecoli.fa infernal-1.0.2/intro/5S.sto infernal-1.0.2/intro/RNaseP.sto infernal-1.0.2/intro/lsu_ecoli.fa infernal-1.0.2/intro/tutorial.sto infernal-1.0.2/intro/lsu.sto infernal-1.0.2/intro/trna.sto infernal-1.0.2/intro/ssu_ecoli.fa infernal-1.0.2/intro/SRP_euk.sto infernal-1.0.2/intro/ssu.sto infernal-1.0.2/intro/SRP_human.fa infernal-1.0.2/intro/tutorial.db infernal-1.0.2/intro/tutorial.big.db infernal-1.0.2/00README infernal-1.0.2/tutorial/ infernal-1.0.2/tutorial/orig_files/ infernal-1.0.2/tutorial/orig_files/toalign.5.fa infernal-1.0.2/tutorial/orig_files/toalign.1.fa infernal-1.0.2/tutorial/orig_files/toalign.1trunc.fa infernal-1.0.2/tutorial/orig_files/tosearch.300Kb.db infernal-1.0.2/tutorial/orig_files/trna.5.sto infernal-1.0.2/tutorial/toalign.1.fa infernal-1.0.2/tutorial/purine.2.c.cm infernal-1.0.2/tutorial/rfam10.c.cm infernal-1.0.2/tutorial/toalign.3.fa infernal-1.0.2/tutorial/toalign.1trunc.fa infernal-1.0.2/tutorial/purine.teng.fa infernal-1.0.2/tutorial/my.c.cm infernal-1.0.2/tutorial/C.psychrerythraea.genome.fa infernal-1.0.2/tutorial/purine.2.sto infernal-1.0.2/tutorial/purine.1.sto infernal-1.0.2/tutorial/purine.2.nofilter.cmsearch infernal-1.0.2/tutorial/T.tengcongensis.genome.fa infernal-1.0.2/tutorial/purine.3.sto infernal-1.0.2/tutorial/purine.psych.fa infernal-1.0.2/tutorial/purine.1.c.cm infernal-1.0.2/tutorial/tosearch.300Kb.db infernal-1.0.2/tutorial/trna.5.sto infernal-1.0.2/iinfernal-1/ infernal-1.0.2/iinfernal-1/cm_config.h.in infernal-1.0.2/iinfernal-1/Makefile.in infernal-1.0.2/iinfernal-1/infernal.h infernal-1.0.2/iinfernal-1/cm_core.c infernal-1.0.2/matrices/ infernal-1.0.2/matrices/RIBOSUM60-30.mat infernal-1.0.2/matrices/RIBOSUM70-30.mat infernal-1.0.2/matrices/RIBOSUM80-30.mat infernal-1.0.2/matrices/RIBOSUM90-30.mat infernal-1.0.2/matrices/RIBOSUM45-40.mat infernal-1.0.2/matrices/RIBOSUM55-40.mat infernal-1.0.2/matrices/RIBOSUM65-40.mat infernal-1.0.2/matrices/RIBOSUM75-40.mat infernal-1.0.2/matrices/RIBOSUM85-40.mat infernal-1.0.2/matrices/RIBOSUM60-75.mat infernal-1.0.2/matrices/RIBOSUM95-40.mat infernal-1.0.2/matrices/RIBOSUM70-75.mat infernal-1.0.2/matrices/RIBOSUM80-75.mat infernal-1.0.2/matrices/RIBOSUM100-85.mat infernal-1.0.2/matrices/RIBOSUM90-75.mat infernal-1.0.2/matrices/RIBOSUM75-85.mat infernal-1.0.2/matrices/RIBOSUM85-85.mat infernal-1.0.2/matrices/RIBOSUM95-85.mat infernal-1.0.2/matrices/RIBOSUM90.mat infernal-1.0.2/matrices/RIBOSUM55.mat infernal-1.0.2/matrices/RIBOSUM100-90.mat infernal-1.0.2/matrices/RIBOSUM60-80.mat infernal-1.0.2/matrices/RIBOSUM70-80.mat infernal-1.0.2/matrices/RIBOSUM60-45.mat infernal-1.0.2/matrices/RIBOSUM80-80.mat infernal-1.0.2/matrices/RIBOSUM70-45.mat infernal-1.0.2/matrices/RIBOSUM80-45.mat infernal-1.0.2/matrices/RIBOSUM90-80.mat infernal-1.0.2/matrices/RIBOSUM90-45.mat infernal-1.0.2/matrices/RIBOSUM45-55.mat infernal-1.0.2/matrices/RIBOSUM55-90.mat infernal-1.0.2/matrices/RIBOSUM65-90.mat infernal-1.0.2/matrices/RIBOSUM55-55.mat infernal-1.0.2/matrices/RIBOSUM75-90.mat infernal-1.0.2/matrices/RIBOSUM65-55.mat infernal-1.0.2/matrices/RIBOSUM75-55.mat infernal-1.0.2/matrices/RIBOSUM85-90.mat infernal-1.0.2/matrices/RIBOSUM85-55.mat infernal-1.0.2/matrices/RIBOSUM95-90.mat infernal-1.0.2/matrices/RIBOSUM95-55.mat infernal-1.0.2/matrices/RIBOSUM60.mat infernal-1.0.2/matrices/RIBOSUM65-60.mat infernal-1.0.2/matrices/RIBOSUM100-55.mat infernal-1.0.2/matrices/RIBOSUM60-50.mat infernal-1.0.2/matrices/RIBOSUM70-50.mat infernal-1.0.2/matrices/RIBOSUM80-50.mat infernal-1.0.2/matrices/RIBOSUM90-50.mat infernal-1.0.2/matrices/RIBOSUM45-60.mat infernal-1.0.2/matrices/RIBOSUM55-60.mat infernal-1.0.2/matrices/RIBOSUM100-60.mat infernal-1.0.2/matrices/RIBOSUM55-25.mat infernal-1.0.2/matrices/RIBOSUM75-60.mat infernal-1.0.2/matrices/RIBOSUM65-25.mat infernal-1.0.2/matrices/RIBOSUM75-25.mat infernal-1.0.2/matrices/RIBOSUM85-60.mat infernal-1.0.2/matrices/RIBOSUM85-25.mat infernal-1.0.2/matrices/RIBOSUM60-95.mat infernal-1.0.2/matrices/RIBOSUM95-60.mat infernal-1.0.2/matrices/RIBOSUM70-95.mat infernal-1.0.2/matrices/RIBOSUM80-95.mat infernal-1.0.2/matrices/RIBOSUM100-25.mat infernal-1.0.2/matrices/RIBOSUM90-95.mat infernal-1.0.2/matrices/RIBOSUM75-30.mat infernal-1.0.2/matrices/RIBOSUM75.mat infernal-1.0.2/matrices/RIBOSUM45-30.mat infernal-1.0.2/matrices/RIBOSUM55-30.mat infernal-1.0.2/matrices/RIBOSUM65-30.mat infernal-1.0.2/matrices/RIBOSUM100-30.mat infernal-1.0.2/matrices/RIBOSUM85-30.mat infernal-1.0.2/matrices/RIBOSUM60-65.mat infernal-1.0.2/matrices/RIBOSUM95-30.mat infernal-1.0.2/matrices/RIBOSUM70-65.mat infernal-1.0.2/matrices/RIBOSUM80-65.mat infernal-1.0.2/matrices/RIBOSUM100-75.mat infernal-1.0.2/matrices/RIBOSUM90-65.mat infernal-1.0.2/matrices/RIBOSUM45-75.mat infernal-1.0.2/matrices/RIBOSUM55-75.mat infernal-1.0.2/matrices/RIBOSUM65-75.mat infernal-1.0.2/matrices/RIBOSUM75-75.mat infernal-1.0.2/matrices/RIBOSUM85-75.mat infernal-1.0.2/matrices/RIBOSUM95-75.mat infernal-1.0.2/matrices/RIBOSUM80.mat infernal-1.0.2/matrices/RIBOSUM45.mat infernal-1.0.2/matrices/RIBOSUM60-70.mat infernal-1.0.2/matrices/RIBOSUM100.mat infernal-1.0.2/matrices/RIBOSUM100-80.mat infernal-1.0.2/matrices/RIBOSUM70-70.mat infernal-1.0.2/matrices/RIBOSUM60-35.mat infernal-1.0.2/matrices/RIBOSUM80-70.mat infernal-1.0.2/matrices/RIBOSUM70-35.mat infernal-1.0.2/matrices/RIBOSUM80-35.mat infernal-1.0.2/matrices/RIBOSUM90-70.mat infernal-1.0.2/matrices/RIBOSUM45-80.mat infernal-1.0.2/matrices/RIBOSUM90-35.mat infernal-1.0.2/matrices/RIBOSUM45-45.mat infernal-1.0.2/matrices/RIBOSUM55-80.mat infernal-1.0.2/matrices/RIBOSUM65-80.mat infernal-1.0.2/matrices/RIBOSUM55-45.mat infernal-1.0.2/matrices/RIBOSUM75-80.mat infernal-1.0.2/matrices/RIBOSUM65-45.mat infernal-1.0.2/matrices/RIBOSUM75-45.mat infernal-1.0.2/matrices/RIBOSUM85-80.mat infernal-1.0.2/matrices/RIBOSUM85-45.mat infernal-1.0.2/matrices/RIBOSUM95-80.mat infernal-1.0.2/matrices/RIBOSUM95-45.mat infernal-1.0.2/matrices/RIBOSUM100-95.mat infernal-1.0.2/matrices/RIBOSUM100-45.mat infernal-1.0.2/matrices/RIBOSUM95.mat infernal-1.0.2/matrices/RIBOSUM60-40.mat infernal-1.0.2/matrices/RIBOSUM70-40.mat infernal-1.0.2/matrices/RIBOSUM80-40.mat infernal-1.0.2/matrices/RIBOSUM90-40.mat infernal-1.0.2/matrices/RIBOSUM45-50.mat infernal-1.0.2/matrices/RIBOSUM55-50.mat infernal-1.0.2/matrices/RIBOSUM65-50.mat infernal-1.0.2/matrices/RIBOSUM75-50.mat infernal-1.0.2/matrices/RIBOSUM85-50.mat infernal-1.0.2/matrices/RIBOSUM60-85.mat infernal-1.0.2/matrices/RIBOSUM95-50.mat infernal-1.0.2/matrices/RIBOSUM70-85.mat infernal-1.0.2/matrices/RIBOSUM80-85.mat infernal-1.0.2/matrices/RIBOSUM100-50.mat infernal-1.0.2/matrices/RIBOSUM90-85.mat infernal-1.0.2/matrices/RIBOSUM55-95.mat infernal-1.0.2/matrices/RIBOSUM65-95.mat infernal-1.0.2/matrices/RIBOSUM75-95.mat infernal-1.0.2/matrices/RIBOSUM85-95.mat infernal-1.0.2/matrices/RIBOSUM95-95.mat infernal-1.0.2/matrices/RIBOSUM65.mat infernal-1.0.2/matrices/RIBOSUM100-65.mat infernal-1.0.2/matrices/RIBOSUM60-90.mat infernal-1.0.2/matrices/RIBOSUM70-90.mat infernal-1.0.2/matrices/RIBOSUM60-55.mat infernal-1.0.2/matrices/RIBOSUM80-90.mat infernal-1.0.2/matrices/RIBOSUM70-55.mat infernal-1.0.2/matrices/RIBOSUM80-55.mat infernal-1.0.2/matrices/RIBOSUM90-90.mat infernal-1.0.2/matrices/RIBOSUM90-55.mat infernal-1.0.2/matrices/RIBOSUM45-65.mat infernal-1.0.2/matrices/RIBOSUM55-65.mat infernal-1.0.2/matrices/RIBOSUM65-65.mat infernal-1.0.2/matrices/RIBOSUM75-65.mat infernal-1.0.2/matrices/RIBOSUM85-65.mat infernal-1.0.2/matrices/RIBOSUM95-65.mat infernal-1.0.2/matrices/RIBOSUM70.mat infernal-1.0.2/matrices/RIBOSUM100-70.mat infernal-1.0.2/matrices/RIBOSUM60-60.mat infernal-1.0.2/matrices/RIBOSUM70-60.mat infernal-1.0.2/matrices/RIBOSUM60-25.mat infernal-1.0.2/matrices/RIBOSUM80-60.mat infernal-1.0.2/matrices/RIBOSUM70-25.mat infernal-1.0.2/matrices/RIBOSUM80-25.mat infernal-1.0.2/matrices/RIBOSUM90-60.mat infernal-1.0.2/matrices/RIBOSUM45-70.mat infernal-1.0.2/matrices/RIBOSUM45-35.mat infernal-1.0.2/matrices/RIBOSUM55-70.mat infernal-1.0.2/matrices/RIBOSUM65-70.mat infernal-1.0.2/matrices/RIBOSUM55-35.mat infernal-1.0.2/matrices/RIBOSUM75-70.mat infernal-1.0.2/matrices/RIBOSUM65-35.mat infernal-1.0.2/matrices/RIBOSUM75-35.mat infernal-1.0.2/matrices/RIBOSUM85-70.mat infernal-1.0.2/matrices/RIBOSUM85-35.mat infernal-1.0.2/matrices/RIBOSUM95-70.mat infernal-1.0.2/matrices/RIBOSUM95-35.mat infernal-1.0.2/matrices/RIBOSUM100-40.mat infernal-1.0.2/matrices/RIBOSUM100-35.mat infernal-1.0.2/matrices/RIBOSUM85.mat infernal-1.0.2/matrices/RIBOSUM55-85.mat infernal-1.0.2/matrices/RIBOSUM65-85.mat infernal-1.0.2/documentation/ infernal-1.0.2/documentation/release-notes/ infernal-1.0.2/documentation/release-notes/RELEASE-0.7 infernal-1.0.2/documentation/release-notes/RELEASE-0.6 infernal-1.0.2/documentation/release-notes/RELEASE-0.71 infernal-1.0.2/documentation/release-notes/RELEASE-0.53 infernal-1.0.2/documentation/release-notes/RELEASE-0.81 infernal-1.0.2/documentation/release-notes/RELEASE-0.72 infernal-1.0.2/documentation/release-notes/RELEASE-0.54 infernal-1.0.2/documentation/release-notes/RELEASE-1.0.2 infernal-1.0.2/documentation/release-notes/RELEASE-0.8 infernal-1.0.2/documentation/release-notes/RELEASE-1.0.1 infernal-1.0.2/documentation/release-notes/RELEASE-0.55 infernal-1.0.2/documentation/release-notes/RELEASE-1.0 infernal-1.0.2/documentation/manpages/ infernal-1.0.2/documentation/manpages/truncyk_check.man infernal-1.0.2/documentation/manpages/cmcalibrate.man infernal-1.0.2/documentation/manpages/cmemit.man infernal-1.0.2/documentation/manpages/cmsearch.man infernal-1.0.2/documentation/manpages/cm2hmm.man infernal-1.0.2/documentation/manpages/cm2hmmsearch.man infernal-1.0.2/documentation/manpages/cmstat.man infernal-1.0.2/documentation/manpages/cmalign.man infernal-1.0.2/documentation/manpages/cmscore.man infernal-1.0.2/documentation/manpages/trcyk.man infernal-1.0.2/documentation/manpages/cmbuild.man infernal-1.0.2/documentation/userguide/ infernal-1.0.2/documentation/userguide/filter.tex infernal-1.0.2/documentation/userguide/local.bib infernal-1.0.2/documentation/userguide/apalike.sty infernal-1.0.2/documentation/userguide/intro.tex infernal-1.0.2/documentation/userguide/trna.5.c.cm infernal-1.0.2/documentation/userguide/tutorial.tex infernal-1.0.2/documentation/userguide/scores.tex infernal-1.0.2/documentation/userguide/Figures/ infernal-1.0.2/documentation/userguide/Figures/input_alignment.eps infernal-1.0.2/documentation/userguide/Figures/trna1-DF6280.eps infernal-1.0.2/documentation/userguide/Figures/rnaseP-bsu-alignment.ai infernal-1.0.2/documentation/userguide/Figures/purine1_small.pdf infernal-1.0.2/documentation/userguide/Figures/trna1-DF6280.ai infernal-1.0.2/documentation/userguide/Figures/purine2_small.pdf infernal-1.0.2/documentation/userguide/Figures/purine3_small.pdf infernal-1.0.2/documentation/userguide/Figures/rnaseP-ecoli.pdf infernal-1.0.2/documentation/userguide/Figures/rnaseP-bsu-alignment.pdf infernal-1.0.2/documentation/userguide/Figures/purineC_small.pdf infernal-1.0.2/documentation/userguide/Figures/parsetrees.ai infernal-1.0.2/documentation/userguide/Figures/rnaseP-ecoli.eps infernal-1.0.2/documentation/userguide/Figures/stl9-63.ai infernal-1.0.2/documentation/userguide/Figures/purine1_full.pdf infernal-1.0.2/documentation/userguide/Figures/purine3_full.pdf infernal-1.0.2/documentation/userguide/Figures/rnaseP-bsu-alignment.eps infernal-1.0.2/documentation/userguide/Figures/rna_elements.pdf infernal-1.0.2/documentation/userguide/Figures/input_alignment.ai infernal-1.0.2/documentation/userguide/Figures/parsetrees.pdf infernal-1.0.2/documentation/userguide/Figures/cm_graph.pdf infernal-1.0.2/documentation/userguide/Figures/cm_nodetree.pdf infernal-1.0.2/documentation/userguide/Figures/purineC_full.pdf infernal-1.0.2/documentation/userguide/Figures/rna_elements.eps infernal-1.0.2/documentation/userguide/Figures/parsetrees.eps infernal-1.0.2/documentation/userguide/Figures/rna_elements.ai infernal-1.0.2/documentation/userguide/Figures/trna1-DF6280.pdf infernal-1.0.2/documentation/userguide/Figures/input_alignment.pdf infernal-1.0.2/documentation/userguide/Figures/cm_graph.eps infernal-1.0.2/documentation/userguide/Figures/cm_graph.ai infernal-1.0.2/documentation/userguide/Figures/rnaseP-ecoli.ai infernal-1.0.2/documentation/userguide/Figures/cm_nodetree.eps infernal-1.0.2/documentation/userguide/Figures/cm_nodetree.ai infernal-1.0.2/documentation/userguide/Figures/purine2_full.pdf infernal-1.0.2/documentation/userguide/Figures/stl9-63.pdf infernal-1.0.2/documentation/userguide/Figures/purine.ai infernal-1.0.2/documentation/userguide/rigfilters_doc.html infernal-1.0.2/documentation/userguide/format_prior.tex infernal-1.0.2/documentation/userguide/titlepage.tex infernal-1.0.2/documentation/userguide/macros.tex infernal-1.0.2/documentation/userguide/install.tex infernal-1.0.2/documentation/userguide/main.tex infernal-1.0.2/documentation/userguide/copyright.tex infernal-1.0.2/documentation/userguide/Makefile infernal-1.0.2/documentation/userguide/formats.tex infernal-1.0.2/documentation/userguide/cmbuild.tex infernal-1.0.2/documentation/userguide/main.faq infernal-1.0.2/easel/ infernal-1.0.2/easel/easel.h infernal-1.0.2/easel/configure.ac infernal-1.0.2/easel/esl_regexp.h infernal-1.0.2/easel/esl_msacluster.c infernal-1.0.2/easel/esl_minimizer.c infernal-1.0.2/easel/esl_dirichlet.c infernal-1.0.2/easel/esl_minimizer.h infernal-1.0.2/easel/esl_dirichlet.h infernal-1.0.2/easel/esl_msa.c infernal-1.0.2/easel/esl_gev.c infernal-1.0.2/easel/esl_gev.h infernal-1.0.2/easel/esl_msa.h infernal-1.0.2/easel/easel.c infernal-1.0.2/easel/esl_rootfinder.tex infernal-1.0.2/easel/esl_msacluster.h infernal-1.0.2/easel/esl_randomseq.c infernal-1.0.2/easel/esl_keyhash.c infernal-1.0.2/easel/esl_sse.c infernal-1.0.2/easel/esl_msa.tex infernal-1.0.2/easel/miniapps/ infernal-1.0.2/easel/miniapps/esl-shuffle.man infernal-1.0.2/easel/miniapps/esl-seqstat.man infernal-1.0.2/easel/miniapps/esl-weight.man infernal-1.0.2/easel/miniapps/esl-reformat.c infernal-1.0.2/easel/miniapps/Makefile.in infernal-1.0.2/easel/miniapps/esl-alimanip.man infernal-1.0.2/easel/miniapps/esl-afetch.man infernal-1.0.2/easel/miniapps/esl-construct.c infernal-1.0.2/easel/miniapps/esl-seqstat.c infernal-1.0.2/easel/miniapps/esl-selectn.man infernal-1.0.2/easel/miniapps/esl-weight.c infernal-1.0.2/easel/miniapps/esl-alistat.man infernal-1.0.2/easel/miniapps/esl-selectn.c infernal-1.0.2/easel/miniapps/esl-alimanip.c infernal-1.0.2/easel/miniapps/esl-afetch.c infernal-1.0.2/easel/miniapps/esl-compstruct.c infernal-1.0.2/easel/miniapps/esl-shuffle.c infernal-1.0.2/easel/miniapps/esl-histplot.man infernal-1.0.2/easel/miniapps/esl-reformat.man infernal-1.0.2/easel/miniapps/esl-alistat.c infernal-1.0.2/easel/miniapps/esl-alimap.c infernal-1.0.2/easel/miniapps/esl-ssdraw.c infernal-1.0.2/easel/miniapps/esl-sfetch.man infernal-1.0.2/easel/miniapps/esl-compalign.c infernal-1.0.2/easel/miniapps/esl-compstruct.man infernal-1.0.2/easel/miniapps/esl-histplot.c infernal-1.0.2/easel/miniapps/esl-sfetch.c infernal-1.0.2/easel/esl_sse.h infernal-1.0.2/easel/esl_ssi.c infernal-1.0.2/easel/esl_randomseq.h infernal-1.0.2/easel/esl_stack.tex infernal-1.0.2/easel/testsuite/ infernal-1.0.2/easel/testsuite/dmatrix-t1.c infernal-1.0.2/easel/testsuite/parse-t1.dat infernal-1.0.2/easel/testsuite/driver_report.pl infernal-1.0.2/easel/testsuite/Makefile.in infernal-1.0.2/easel/testsuite/parse-t1.c infernal-1.0.2/easel/testsuite/coverage_report.pl infernal-1.0.2/easel/testsuite/testsuite.sqc infernal-1.0.2/easel/testsuite/dmatrix-t2.c infernal-1.0.2/easel/testsuite/valgrind_report.pl infernal-1.0.2/easel/esl_keyhash.h infernal-1.0.2/easel/esl_ssi.h infernal-1.0.2/easel/esl_keyhash.tex infernal-1.0.2/easel/esl_vmx.h infernal-1.0.2/easel/esl_vmx.c infernal-1.0.2/easel/esl_histogram.tex infernal-1.0.2/easel/esl_wuss.tex infernal-1.0.2/easel/esl_exponential.c infernal-1.0.2/easel/esl_gamma.c infernal-1.0.2/easel/esl_scorematrix.c infernal-1.0.2/easel/esl_gumbel.tex infernal-1.0.2/easel/INSTALL infernal-1.0.2/easel/esl_scorematrix.tex infernal-1.0.2/easel/00README infernal-1.0.2/easel/esl_gamma.h infernal-1.0.2/easel/esl_normal.c infernal-1.0.2/easel/esl_exponential.h infernal-1.0.2/easel/esl_distance.c infernal-1.0.2/easel/esl_cluster.tex infernal-1.0.2/easel/esl_normal.h infernal-1.0.2/easel/esl_distance.h infernal-1.0.2/easel/config.guess infernal-1.0.2/easel/esl_mpi.tex infernal-1.0.2/easel/esl_stopwatch.c infernal-1.0.2/easel/esl_normal.tex infernal-1.0.2/easel/esl_scorematrix.h infernal-1.0.2/easel/esl_rootfinder.c infernal-1.0.2/easel/esl_sqio.tex infernal-1.0.2/easel/esl_ratematrix.c infernal-1.0.2/easel/esl_rootfinder.h infernal-1.0.2/easel/esl_stopwatch.h infernal-1.0.2/easel/esl_randomseq.tex infernal-1.0.2/easel/esl_vectorops.c infernal-1.0.2/easel/esl_stopwatch.tex infernal-1.0.2/easel/esl_ratematrix.h infernal-1.0.2/easel/esl_swat.tex infernal-1.0.2/easel/esl_paml.c infernal-1.0.2/easel/esl_stats.h infernal-1.0.2/easel/esl_gev.tex infernal-1.0.2/easel/esl_stats.c infernal-1.0.2/easel/esl_ratematrix.tex infernal-1.0.2/easel/esl_paml.h infernal-1.0.2/easel/esl_tree.tex infernal-1.0.2/easel/esl_dmatrix.c infernal-1.0.2/easel/esl_gumbel.c infernal-1.0.2/easel/esl_dmatrix.h infernal-1.0.2/easel/LICENSE.csh.in infernal-1.0.2/easel/esl_dmatrix.tex infernal-1.0.2/easel/esl_gumbel.h infernal-1.0.2/easel/interface_lapack.h infernal-1.0.2/easel/esl_hyperexp.h infernal-1.0.2/easel/esl_dirichlet.tex infernal-1.0.2/easel/esl_sq.c infernal-1.0.2/easel/formats/ infernal-1.0.2/easel/formats/genbank infernal-1.0.2/easel/formats/fasta.odd.1 infernal-1.0.2/easel/formats/fasta.bad.1 infernal-1.0.2/easel/formats/fasta.bad.3 infernal-1.0.2/easel/formats/fasta.bad.2 infernal-1.0.2/easel/formats/genbank.bad.1 infernal-1.0.2/easel/formats/genbank.2 infernal-1.0.2/easel/formats/wag.dat infernal-1.0.2/easel/formats/BLOSUM62 infernal-1.0.2/easel/formats/fasta.2 infernal-1.0.2/easel/formats/fasta infernal-1.0.2/easel/formats/embl infernal-1.0.2/easel/esl_getopts.c infernal-1.0.2/easel/install-sh infernal-1.0.2/easel/esl_vectorops.h infernal-1.0.2/easel/esl_stretchexp.c infernal-1.0.2/easel/aclocal.m4 infernal-1.0.2/easel/esl_vectorops.tex infernal-1.0.2/easel/esl_getopts.h infernal-1.0.2/easel/esl_msacluster.tex infernal-1.0.2/easel/esl_stretchexp.h infernal-1.0.2/easel/Makefile.in infernal-1.0.2/easel/esl_regexp.tex infernal-1.0.2/easel/esl_sqio.h infernal-1.0.2/easel/esl_sqio.c infernal-1.0.2/easel/esl_config.h.in infernal-1.0.2/easel/esl_weibull.tex infernal-1.0.2/easel/COPYRIGHT infernal-1.0.2/easel/esl_sq.tex infernal-1.0.2/easel/esl_tree.c infernal-1.0.2/easel/esl_msaweight.c infernal-1.0.2/easel/LICENSE infernal-1.0.2/easel/esl_fileparser.c infernal-1.0.2/easel/esl_msaweight.h infernal-1.0.2/easel/esl_mixgev.c infernal-1.0.2/easel/easel.tex infernal-1.0.2/easel/devkit/ infernal-1.0.2/easel/devkit/rmanprocess.pl infernal-1.0.2/easel/devkit/sqc infernal-1.0.2/easel/devkit/cexcerpt.man infernal-1.0.2/easel/devkit/esl-dependencies infernal-1.0.2/easel/devkit/sedition-pp infernal-1.0.2/easel/devkit/cexcerpt infernal-1.0.2/easel/devkit/autodoc infernal-1.0.2/easel/devkit/sedition infernal-1.0.2/easel/esl_tree.h infernal-1.0.2/easel/esl_fileparser.h infernal-1.0.2/easel/esl_msaweight.tex infernal-1.0.2/easel/interface_gsl.c infernal-1.0.2/easel/esl_mixgev.h infernal-1.0.2/easel/esl_sse.tex infernal-1.0.2/easel/esl_paml.tex infernal-1.0.2/easel/esl_getopts.tex infernal-1.0.2/easel/esl_fileparser.tex infernal-1.0.2/easel/interface_gsl.h infernal-1.0.2/easel/esl_ssi.tex infernal-1.0.2/easel/esl_msashuffle.c infernal-1.0.2/easel/esl_random.c infernal-1.0.2/easel/esl_random.tex infernal-1.0.2/easel/config.sub infernal-1.0.2/easel/esl_alphabet.c infernal-1.0.2/easel/esl_random.h infernal-1.0.2/easel/esl_alphabet.h infernal-1.0.2/easel/esl_alphabet.tex infernal-1.0.2/easel/esl_gamma.tex infernal-1.0.2/easel/esl_minimizer.tex infernal-1.0.2/easel/esl_msashuffle.h infernal-1.0.2/easel/esl_exponential.tex infernal-1.0.2/easel/esl_weibull.c infernal-1.0.2/easel/esl_stretchexp.tex infernal-1.0.2/easel/esl_hyperexp.c infernal-1.0.2/easel/esl_distance.tex infernal-1.0.2/easel/interface_lapack.c infernal-1.0.2/easel/esl_weibull.h infernal-1.0.2/easel/esl_swat.c infernal-1.0.2/easel/esl_hyperexp.tex infernal-1.0.2/easel/esl_wuss.c infernal-1.0.2/easel/esl_sq.h infernal-1.0.2/easel/esl_stats.tex infernal-1.0.2/easel/esl_histogram.h infernal-1.0.2/easel/esl_histogram.c infernal-1.0.2/easel/esl_mpi.h infernal-1.0.2/easel/documentation/ infernal-1.0.2/easel/documentation/figures/ infernal-1.0.2/easel/documentation/figures/rnaseP-bsu-alignment.ai infernal-1.0.2/easel/documentation/figures/rnaseP-bsu-alignment.pdf infernal-1.0.2/easel/documentation/figures/rna_elements.ai infernal-1.0.2/easel/documentation/figures/rna_elements.pdf infernal-1.0.2/easel/documentation/figures/evd_basic.pdf infernal-1.0.2/easel/documentation/figures/rnaseP-ecoli.eps infernal-1.0.2/easel/documentation/figures/gev_density.pdf infernal-1.0.2/easel/documentation/figures/rnaseP-ecoli.ai infernal-1.0.2/easel/documentation/figures/rnaseP-ecoli.pdf infernal-1.0.2/easel/documentation/figures/gev_logdensity.pdf infernal-1.0.2/easel/documentation/figures/evd_scale.pdf infernal-1.0.2/easel/documentation/figures/evd_location.pdf infernal-1.0.2/easel/documentation/figures/rnaseP-bsu-alignment.eps infernal-1.0.2/easel/documentation/figures/rna_elements.eps infernal-1.0.2/easel/documentation/macros.tex infernal-1.0.2/easel/documentation/install.tex infernal-1.0.2/easel/documentation/format_stockholm.tex infernal-1.0.2/easel/documentation/typography.tex infernal-1.0.2/easel/documentation/copyright.tex infernal-1.0.2/easel/documentation/format_wuss.tex infernal-1.0.2/easel/documentation/statistics.tex infernal-1.0.2/easel/documentation/codestyle.tex infernal-1.0.2/easel/documentation/main.tex infernal-1.0.2/easel/documentation/Makefile infernal-1.0.2/easel/documentation/installation.tex infernal-1.0.2/easel/documentation/titlepage.tex infernal-1.0.2/easel/documentation/doctricks.tex infernal-1.0.2/easel/documentation/intro.tex infernal-1.0.2/easel/esl_stack.c infernal-1.0.2/easel/esl_wuss.h infernal-1.0.2/easel/esl_stack.h infernal-1.0.2/easel/configure infernal-1.0.2/easel/esl_cluster.c infernal-1.0.2/easel/esl_mpi.c infernal-1.0.2/easel/esl_cluster.h infernal-1.0.2/easel/esl_regexp.c infernal-1.0.2/COPYRIGHT infernal-1.0.2/rigfilters/ infernal-1.0.2/rigfilters/cm2hmm-1.0/ infernal-1.0.2/rigfilters/cm2hmm-1.0/CovarianceModel.h infernal-1.0.2/rigfilters/cm2hmm-1.0/MarkovModelStats.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/ScanHMM_NonTemplated.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/data/ infernal-1.0.2/rigfilters/cm2hmm-1.0/data/RF00095.cm infernal-1.0.2/rigfilters/cm2hmm-1.0/data/AL096836.fna infernal-1.0.2/rigfilters/cm2hmm-1.0/data/Bordetella_0mm.mm infernal-1.0.2/rigfilters/cm2hmm-1.0/data/Saureus_0mm.mm infernal-1.0.2/rigfilters/cm2hmm-1.0/data/hum_0mm.mm infernal-1.0.2/rigfilters/cm2hmm-1.0/data/Ecoli_0mm.mm infernal-1.0.2/rigfilters/cm2hmm-1.0/stdafx.h infernal-1.0.2/rigfilters/cm2hmm-1.0/Cm2HmmOptimize_cfsqp.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/InfernalHmm.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/Makefile.in infernal-1.0.2/rigfilters/cm2hmm-1.0/Cm2HmmOptimize.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/HmmType1.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/cmzashaUtils.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/stl_extra.h infernal-1.0.2/rigfilters/cm2hmm-1.0/NaryCounter.h infernal-1.0.2/rigfilters/cm2hmm-1.0/SequenceSet.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/CommaSepFileReader.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/Cm2HMM.h infernal-1.0.2/rigfilters/cm2hmm-1.0/vectorPlus.h infernal-1.0.2/rigfilters/cm2hmm-1.0/SymbolicMath.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/CovarianceModel.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/NoUnderflowDouble.h infernal-1.0.2/rigfilters/cm2hmm-1.0/MiscExceptions.h infernal-1.0.2/rigfilters/cm2hmm-1.0/MarkovModelStats.h infernal-1.0.2/rigfilters/cm2hmm-1.0/InfernalHmm.h infernal-1.0.2/rigfilters/cm2hmm-1.0/ForwardHMM.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/NaryCounter.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/Cm2HmmOptimize.h infernal-1.0.2/rigfilters/cm2hmm-1.0/HmmType1.h infernal-1.0.2/rigfilters/cm2hmm-1.0/Cm2HmmSearchMain.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/Makefile.test infernal-1.0.2/rigfilters/cm2hmm-1.0/multiDimVector.h infernal-1.0.2/rigfilters/cm2hmm-1.0/UseDebugNew.h infernal-1.0.2/rigfilters/cm2hmm-1.0/README.html infernal-1.0.2/rigfilters/cm2hmm-1.0/SequenceSet.h infernal-1.0.2/rigfilters/cm2hmm-1.0/Cm2HMM.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/Cm2HmmMain.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/SymbolicMath.h infernal-1.0.2/rigfilters/cm2hmm-1.0/cmzasha.h infernal-1.0.2/rigfilters/cm2hmm-1.0/MiscExceptions.cpp infernal-1.0.2/rigfilters/cm2hmm-1.0/CommaSepFileReader.h infernal-1.0.2/rigfilters/cfsqp/ infernal-1.0.2/rigfilters/cfsqp/Makefile.in infernal-1.0.2/rigfilters/Makefile.in infernal-1.0.2/benchmarks/ infernal-1.0.2/benchmarks/cmsearch-rmark/ infernal-1.0.2/benchmarks/cmsearch-rmark/rmark_clusterfy.pl infernal-1.0.2/benchmarks/cmsearch-rmark/duplicate_full_bm.sh infernal-1.0.2/benchmarks/cmsearch-rmark/do_rmark-test.sh infernal-1.0.2/benchmarks/cmsearch-rmark/infernal2glbf.pl infernal-1.0.2/benchmarks/cmsearch-rmark/infernal.rmm infernal-1.0.2/benchmarks/cmsearch-rmark/sre.pl infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/ infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00031.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00005.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00005.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/rmark-test.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00031.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00005.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00031.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00005.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/rmark-test.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/RF00031.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-test/rmark-test.fa infernal-1.0.2/benchmarks/cmsearch-rmark/infernal_55_W.rmm infernal-1.0.2/benchmarks/cmsearch-rmark/rmark_times.pl infernal-1.0.2/benchmarks/cmsearch-rmark/00README infernal-1.0.2/benchmarks/cmsearch-rmark/blast.rmm infernal-1.0.2/benchmarks/cmsearch-rmark/plus1.prior infernal-1.0.2/benchmarks/cmsearch-rmark/rmark_process_glbf.pl infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/ infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00104.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00023.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00029.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr11.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr5.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00030.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00504.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00029.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00066.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr11.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00030.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr15.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr13.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr17.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr19.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00002.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00080.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00008.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00030.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00054.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00030.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr19.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00163.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00066.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00002.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00004.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr8.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00080.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00008.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00163.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00165.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00002.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00167.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr20.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00004.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00169.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr14.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr20.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00170.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00054.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00163.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00011.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00165.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00167.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00023.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00104.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00169.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00213.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00002.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00004.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr3.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00019.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00011.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00080.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00008.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00059.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00163.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00168.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00015.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00165.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00017.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00379.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00015.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00167.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00019.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00169.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00174.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00373.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00011.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00015.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00379.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00017.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00170.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr17.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00054.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00019.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00101.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00020.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00174.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00373.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00004.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00011.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00206.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00234.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr9.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr1.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00028.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00101.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00020.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00165.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr6.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00017.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00170.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr3.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00054.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00096.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00019.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00177.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr5.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00024.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00448.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00174.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr7.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00373.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00379.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00028.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00025.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00380.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00067.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00101.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00020.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00379.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr12.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00024.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00028.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00380.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00067.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00101.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00025.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00020.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr1.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00009.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00037.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00024.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00380.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00174.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1.chrlist infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00031.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00028.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00230.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr9.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00033.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00114.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00380.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00067.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00234.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00037.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00031.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00230.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr10.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00033.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00114.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr15.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr12.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00234.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr14.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00037.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00010.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr16.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr18.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00018.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00230.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr4.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00033.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00114.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00003.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00373.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00040.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00167.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00234.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00037.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00005.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00206.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00009.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr10.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00003.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00168.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00040.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00448.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00005.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00206.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00009.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr18.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00003.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00031.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00168.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00015.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00448.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00003.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00040.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00504.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00055.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00005.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00010.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00067.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00012.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00206.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr7.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00009.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00213.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00018.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00055.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00168.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00448.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00010.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00059.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00096.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00012.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00177.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr13.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00213.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00018.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00055.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00012.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00059.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00040.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00096.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00177.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00230.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00010.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00024.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00080.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00008.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00012.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr2.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00213.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr2.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00018.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr4.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00055.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00023.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00104.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00169.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr6.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00025.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr8.ebd infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00059.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00504.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00096.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00177.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00029.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00066.raw infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00023.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00104.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00025.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/rmark-1_chr16.fa infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00504.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00029.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00066.ali infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00005.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00033.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00114.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00017.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00170.test infernal-1.0.2/benchmarks/cmsearch-rmark/rmark-1/RF00031.idx infernal-1.0.2/benchmarks/cmsearch-rmark/rmark_MPI_cmsearch.pl infernal-1.0.2/benchmarks/cmsearch-rmark/infernal.pm infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/ infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/inf_p1_noent-72.rmk infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/blast_w7.rmk infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/inf-72.rmk infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/inf_p1-72.rmk infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/inf-55.rmk infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/inf_noent-72.rmk infernal-1.0.2/benchmarks/cmsearch-rmark/rmk_files/inf_qdb-72.rmk infernal-1.0.2/benchmarks/cmsearch-rmark/rmark.pl infernal-1.0.2/benchmarks/cmsearch-rmark/duplicate_blast_bm.sh infernal-1.0.2/configure infernal-1.0.2/install-sh infernal-1.0.2/aclocal.m4 infernal-1.0.2/LICENSE infernal-1.0.2/Makefile.in infernal-1.0.2/configure.ac infernal-1.0.2/config.sub infernal-1.0.2/Userguide.pdf sudo -u fink-bld [ENV] sh -c /tmp/fink.e_lOE ./configure --prefix=/sw/build.build/root-infernal-1.0.2-1/sw configure: Configuring Infernal for your system. checking build system type... i686-apple-darwin13.3.0 checking host system type... i686-apple-darwin13.3.0 configure: Full Infernal source distribution - using full configuration checking for gcc... gcc checking for C compiler default output file name... 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for C compiler vendor... gnu checking for gcc option to accept ISO C99... none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether your make is GNU make... yes, it is. checking whether C compiler accepts -malign-double... yes checking whether C compiler accepts -fstrict-aliasing... yes checking for gcc architecture flag... checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69 checking for x86 cpuid 1 output... 206a7:100800:1fbae3bf:bfebfbff checking whether C compiler accepts -march=pentium2... no checking whether C compiler accepts -mcpu=pentium2... yes checking for gcc architecture flag... -mcpu=pentium2 checking whether C compiler accepts -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -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 emmintrin.h usability... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking if platform can run SSE/SSE2 instructions... yes checking whether C compiler accepts -msse2... yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking whether byte ordering is bigendian... no checking for int8_t... yes checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for off_t... yes checking for mkstemp... yes checking for popen... yes checking for strcasecmp... yes checking for times... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating Makefile config.status: creating src/config.h config.status: creating easel/esl_config.h make (cd easel; make CC="gcc" CFLAGS="-O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2"; make) gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c easel.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_alphabet.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_cluster.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_dirichlet.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_distance.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_dmatrix.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_exponential.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_fileparser.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_gamma.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_getopts.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_gev.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_gumbel.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' esl_getopts.c:1273:60: warning: format string is not a string literal (potentially insecure) [-Wformat-security] ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name); ^~~~~~~~~~~~~~~~~ ./easel.h:47:58: note: expanded from macro 'ESL_FAIL' if (errbuf != NULL) snprintf(errbuf, eslERRBUFSIZE, __VA_ARGS__);\ ^ /usr/include/secure/_stdio.h:57:62: note: expanded from macro 'snprintf' __builtin___snprintf_chk (str, len, 0, __darwin_obsz(str), __VA_ARGS__) ^ gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_histogram.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_hyperexp.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_keyhash.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_minimizer.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_mixgev.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_mpi.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_msa.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_msacluster.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_msashuffle.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_msaweight.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' 1 warning generated. gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_normal.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_paml.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_random.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' esl_msa.c:3617:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(fp, s); ^ gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_randomseq.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_ratematrix.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_regexp.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_rootfinder.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_scorematrix.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_sq.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_sqio.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_sse.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_ssi.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_stack.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_stats.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_stopwatch.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_stretchexp.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_swat.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_tree.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_vectorops.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_vmx.c gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_weibull.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -I. -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -msse2 -c esl_wuss.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' esl_tree.c:152:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(fp, s); ^ 1 warning generated. 1 warning generated. /usr/bin/ar rcv libeasel.a easel.o esl_alphabet.o esl_cluster.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_getopts.o esl_gev.o esl_gumbel.o esl_histogram.o esl_hyperexp.o esl_keyhash.o esl_minimizer.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_random.o esl_randomseq.o esl_ratematrix.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_swat.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_wuss.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libeasel.a(esl_mpi.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libeasel.a(esl_vmx.o) has no symbols a - easel.o a - esl_alphabet.o a - esl_cluster.o a - esl_dirichlet.o a - esl_distance.o a - esl_dmatrix.o a - esl_exponential.o a - esl_fileparser.o a - esl_gamma.o a - esl_getopts.o a - esl_gev.o a - esl_gumbel.o a - esl_histogram.o a - esl_hyperexp.o a - esl_keyhash.o a - esl_minimizer.o a - esl_mixgev.o a - esl_mpi.o a - esl_msa.o a - esl_msacluster.o a - esl_msashuffle.o a - esl_msaweight.o a - esl_normal.o a - esl_paml.o a - esl_random.o a - esl_randomseq.o a - esl_ratematrix.o a - esl_regexp.o a - esl_rootfinder.o a - esl_scorematrix.o a - esl_sq.o a - esl_sqio.o a - esl_sse.o a - esl_ssi.o a - esl_stack.o a - esl_stats.o a - esl_stopwatch.o a - esl_stretchexp.o a - esl_swat.o a - esl_tree.o a - esl_vectorops.o a - esl_vmx.o a - esl_weibull.o a - esl_wuss.o ranlib libeasel.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libeasel.a(esl_mpi.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libeasel.a(esl_vmx.o) has no symbols chmod 644 libeasel.a (cd miniapps; make) gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-afetch.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-alimanip.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-alimap.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-alistat.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-compalign.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-compstruct.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-construct.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-histplot.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: warning: clang: note: this will be a hard error (cannot be downgraded to a warning) in the future unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: clang: note: this will be a hard error (cannot be downgraded to a warning) in the future this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-reformat.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-selectn.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-seqstat.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-sfetch.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-shuffle.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-ssdraw.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I.. -c esl-weight.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-afetch esl-afetch.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-alistat esl-alistat.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-compstruct esl-compstruct.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-histplot esl-histplot.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-reformat esl-reformat.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-selectn esl-selectn.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-seqstat esl-seqstat.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-sfetch esl-sfetch.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-shuffle esl-shuffle.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-weight esl-weight.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-alimap esl-alimap.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-compalign esl-compalign.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-construct esl-construct.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-alimanip esl-alimanip.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L/sw/lib -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' (cd miniapps; make) make[2]: Nothing to be done for `all'. (cd src; make CC="gcc" CFLAGS="-O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2"; make module) gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cmalign.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_dpalign.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_dpsearch.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_dpsmall.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_io.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_modelconfig.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_modelmaker.c clang: warning: clangunknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future]: warningclang: note: this will be a hard error (cannot be downgraded to a warning) in the future : unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the futureclang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' cmalign.c:337:23: warning: while loop has empty body [-Wempty-body] while (cfg.do_stall); ^ cmalign.c:337:23: note: put the semicolon on a separate line to silence this warning gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_mx.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_parsetree.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_qdband.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' 1 warning generated. gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cm_submodel.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cp9.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cp9_dp.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cp9_modelconfig.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cp9_modelmaker.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cp9_mx.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cp9_trace.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c alphabet.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c dispatch.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c display.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c eweight.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c errors.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c hmmband.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c hybridsearch.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c logsum.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c mpisupport.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c prior.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c rnamat.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c searchinfo.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' searchinfo.c:110:22: warning: if statement has empty body [-Wempty-body] if(cyk_filter) ;/* do nothing, CYK is default */ ^ searchinfo.c:110:22: note: put the semicolon on a separate line to silence this warning gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c seqstoaln.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c stats.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c truncyk.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cmbuild.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cmcalibrate.c 1 warning generated. gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cmemit.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cmscore.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' cmcalibrate.c:410:23: warning: while loop has empty body [-Wempty-body] while (cfg.do_stall); ^ cmcalibrate.c:410:23: note: put the semicolon on a separate line to silence this warning cmscore.c:305:23: warning: while loop has empty body [-Wempty-body] while (cfg.do_stall); ^ cmscore.c:305:23: note: put the semicolon on a separate line to silence this warning gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cmsearch.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c cmstat.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' cmsearch.c:334:23: warning: while loop has empty body [-Wempty-body] while (cfg.do_stall); ^ cmsearch.c:334:23: note: put the semicolon on a separate line to silence this warning gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c trcyk.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' 1 warning generated. gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel -c truncyk_check.c clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' 1 warning generated. 1 warning generated. gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o cmalign cmalign.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o cmbuild cmbuild.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o cmcalibrate cmcalibrate.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o cmemit cmemit.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o cmscore cmscore.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o cmsearch cmsearch.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o cmstat cmstat.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o trcyk trcyk.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clangclang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-malign-double' : warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -L../easel -o truncyk_check truncyk_check.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' /usr/bin/ar rcv libinfernal.a cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libinfernal.a(mpisupport.o) has no symbols a - cm.o a - cm_dpalign.o a - cm_dpsearch.o a - cm_dpsmall.o a - cm_io.o a - cm_modelconfig.o a - cm_modelmaker.o a - cm_mx.o a - cm_parsetree.o a - cm_qdband.o a - cm_submodel.o a - cp9.o a - cp9_dp.o a - cp9_modelconfig.o a - cp9_modelmaker.o a - cp9_mx.o a - cp9_trace.o a - alphabet.o a - dispatch.o a - display.o a - eweight.o a - errors.o a - hmmband.o a - hybridsearch.o a - logsum.o a - mpisupport.o a - prior.o a - rnamat.o a - searchinfo.o a - seqstoaln.o a - stats.o a - truncyk.o ranlib libinfernal.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libinfernal.a(mpisupport.o) has no symbols chmod 644 libinfernal.a (cd testsuite; make CC="gcc" CFLAGS="-O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2") gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel/ -I../src -c bandcyk-montecarlo-test.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel/ -I../src -c bandcyk-truncation-test.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel/ -I../src -c cp9-test.c gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -DHAVE_CONFIG_H -I../easel/ -I../src -c sub_cm-test.c clangclang: : warning: warningunknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future]: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future]clangclangclang: : warning: warning: note: this will be a hard error (cannot be downgraded to a warning) in the futureunknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] : clang: note: this will be a hard error (cannot be downgraded to a warning) in the future unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future]clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2'clang: warning: argument unused during compilation: '-malign-double' clang: warning: clang: warning: argument unused during compilation: '-malign-double' clang: warning: argument unused during compilation: '-mcpu=pentium2' argument unused during compilation: '-mcpu=pentium2' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -L/sw/lib -DHAVE_CONFIG_H -L../easel/ -L../src -o bandcyk-truncation-test bandcyk-truncation-test.o -linfernal -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -L/sw/lib -DHAVE_CONFIG_H -L../easel/ -L../src -o cp9-test cp9-test.o -linfernal -leasel -lm gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -L/sw/lib -DHAVE_CONFIG_H -L../easel/ -L../src -o bandcyk-montecarlo-test bandcyk-montecarlo-test.o -linfernal -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' gcc -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -mcpu=pentium2 -L/sw/lib -DHAVE_CONFIG_H -L../easel/ -L../src -o sub_cm-test sub_cm-test.o -linfernal -leasel -lm clang: warning: unknown argument: '-malign-double' [-Wunused-command-line-argument-hard-error-in-future] clang: note: this will be a hard error (cannot be downgraded to a warning) in the future clang: warning: argument unused during compilation: '-malign-double' /bin/rm -rf /sw/build.build/root-infernal-1.0.2-1 /bin/mkdir -p /sw/build.build/root-infernal-1.0.2-1/sw /bin/mkdir -p /sw/build.build/root-infernal-1.0.2-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-infernal-1.0.2-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.m9s4p mkdir -p /sw/build.build/root-infernal-1.0.2-1/sw/bin mkdir -p /sw/build.build/root-infernal-1.0.2-1/sw/share/infernal mkdir -p /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1 make install mkdir -p /sw/build.build/root-infernal-1.0.2-1/sw/bin for file in cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat; do\ cp src/$file /sw/build.build/root-infernal-1.0.2-1/sw/bin/;\ done cp documentation/manpages/cmalign.man /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1/cmalign.1 cp documentation/manpages/cmbuild.man /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1/cmbuild.1 cp documentation/manpages/cmsearch.man /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1/cmsearch.1 cp documentation/manpages/cmscore.man /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1/cmscore.1 cp documentation/manpages/cm2hmm.man /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1/cm2hmm.1 cp documentation/manpages/cmemit.man /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1/cmemit.1 cp documentation/manpages/cm2hmmsearch.man /sw/build.build/root-infernal-1.0.2-1/sw/share/man/man1/cm2hmmsearch.1 cp -R documentation/release-notes /sw/build.build/root-infernal-1.0.2-1/sw/share/infernal/. cp -R testsuite /sw/build.build/root-infernal-1.0.2-1/sw/share/infernal/. cp -R intro /sw/build.build/root-infernal-1.0.2-1/sw/share/infernal/. cp Userguide.pdf /sw/build.build/root-infernal-1.0.2-1/sw/share/infernal/. sudo -u fink-bld [ENV] sh -c /tmp/fink.2IlGh /usr/bin/install -d -m 700 /sw/build.build/root-infernal-1.0.2-1/sw/share/doc/infernal /bin/cp -r COPYRIGHT /sw/build.build/root-infernal-1.0.2-1/sw/share/doc/infernal/ /bin/cp -r 00README /sw/build.build/root-infernal-1.0.2-1/sw/share/doc/infernal/ /bin/cp -r LICENSE /sw/build.build/root-infernal-1.0.2-1/sw/share/doc/infernal/ /bin/cp -r Userguide.pdf /sw/build.build/root-infernal-1.0.2-1/sw/share/doc/infernal/ /bin/cp -r 00README-MPI /sw/build.build/root-infernal-1.0.2-1/sw/share/doc/infernal/ /bin/chmod -R go=u-w /sw/build.build/root-infernal-1.0.2-1/sw/share/doc/infernal /bin/rm -f /sw/build.build/root-infernal-1.0.2-1/sw/info/dir /sw/build.build/root-infernal-1.0.2-1/sw/info/dir.old /sw/build.build/root-infernal-1.0.2-1/sw/share/info/dir /sw/build.build/root-infernal-1.0.2-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-infernal-1.0.2-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `infernal' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/infernal_1.0.2-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-infernal-1.0.2-1 (Reading database ... 4297 files and directories currently installed.) Removing fink-buildlock-infernal-1.0.2-1 ...