printf ' ' | fink --no-use-binary-dist --yes rebuild mira 2>&1 WARNING: your info file index has not been updated for 16 days. You should run 'fink selfupdate' to get the latest package descriptions. The package 'mira' will be built without being installed. Reading build dependency for mira-3.4.1.1-1002... Reading dependency for mira-3.4.1.1-1002... Reading build conflict for mira-3.4.1.1-1002... The following package will be rebuilt: mira Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-mira-3.4.1.1-1002 /sw/build.build dpkg-deb: building package `fink-buildlock-mira-3.4.1.1-1002' in `/sw/build.build/fink-buildlock-mira-3.4.1.1-1002_2014.08.10-17.49.14_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-mira-3.4.1.1-1002_2014.08.10-17.49.14_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-mira-3.4.1.1-1002. (Reading database ... 158016 files and directories currently installed.) Unpacking fink-buildlock-mira-3.4.1.1-1002 (from .../fink-buildlock-mira-3.4.1.1-1002_2014.08.10-17.49.14_darwin-x86_64.deb) ... Setting up fink-buildlock-mira-3.4.1.1-1002 (2014.08.10-17.49.14) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.srOCF env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/mira-3.4.1.1.tar.gz mira-3.4.1.1/ mira-3.4.1.1/config/ mira-3.4.1.1/config/m4/ mira-3.4.1.1/config/m4/ltversion.m4 mira-3.4.1.1/config/m4/ltsugar.m4 mira-3.4.1.1/config/m4/ax_check_zlib.m4 mira-3.4.1.1/config/m4/ltoptions.m4 mira-3.4.1.1/config/m4/lt~obsolete.m4 mira-3.4.1.1/config/m4/ax_boost_filesystem.m4 mira-3.4.1.1/config/m4/ax_boost_iostreams.m4 mira-3.4.1.1/config/m4/ax_boost_thread.m4 mira-3.4.1.1/config/m4/ax_boost_regex.m4 mira-3.4.1.1/config/m4/ax_cxx_have_std.m4 mira-3.4.1.1/config/m4/ax_with_prog.m4 mira-3.4.1.1/config/m4/ax_cxx_namespaces.m4 mira-3.4.1.1/config/m4/libtool.m4 mira-3.4.1.1/config/m4/ax_lib_expat.m4 mira-3.4.1.1/config/m4/ax_boost_base.m4 mira-3.4.1.1/config/m4/ax_boost_system.m4 mira-3.4.1.1/config/m4/ax_with_perl.m4 mira-3.4.1.1/config/m4/ax_cxx_have_stl.m4 mira-3.4.1.1/minidemo/ mira-3.4.1.1/minidemo/demo4/ mira-3.4.1.1/minidemo/demo4/runme.sh mira-3.4.1.1/minidemo/solexa1/ mira-3.4.1.1/minidemo/solexa1/README.txt mira-3.4.1.1/minidemo/solexa1/runme.sh mira-3.4.1.1/minidemo/data/ mira-3.4.1.1/minidemo/data/solexa_eco_art/ mira-3.4.1.1/minidemo/data/solexa_eco_art/ecoli_straindata_in.txt mira-3.4.1.1/minidemo/data/solexa_eco_art/ecoli_backbone_in.gbf mira-3.4.1.1/minidemo/data/solexa_eco_art/ecoli_in.solexa.fasta mira-3.4.1.1/minidemo/data/solexa_eco_art/ecoli_in.solexa.fasta.qual mira-3.4.1.1/minidemo/data/bbdataset1/ mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_NCTC11168_first40kb.gbf mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_in.sanger.fasta.qual mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_in.fasta.qual mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_in.sanger.fasta mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_backbone_in.gbf mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_in.fasta mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_traceinfo_in.sanger.xml mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_straindata_in.txt mira-3.4.1.1/minidemo/data/bbdataset1/cjejuni_demo_traceinfo_in.xml mira-3.4.1.1/minidemo/data/fasta_estset1/ mira-3.4.1.1/minidemo/data/fasta_estset1/tvc_mini.fasta.qual mira-3.4.1.1/minidemo/data/fasta_estset1/triphysaria_versicolor.fasta.qual mira-3.4.1.1/minidemo/data/fasta_estset1/tvc_mini.fasta mira-3.4.1.1/minidemo/data/fasta_estset1/triphysaria_versicolor.masked.fasta mira-3.4.1.1/minidemo/data/fasta_estset1/README mira-3.4.1.1/minidemo/data/fasta_estset1/triphysaria_versicolor.fasta mira-3.4.1.1/minidemo/data/fasta_set1/ mira-3.4.1.1/minidemo/data/fasta_set1/U13small_m.fasta.qual mira-3.4.1.1/minidemo/data/fasta_set1/U13small_nm.fasta.qual mira-3.4.1.1/minidemo/data/fasta_set1/U13small_nm.fasta mira-3.4.1.1/minidemo/data/fasta_set1/U13small_m.fasta mira-3.4.1.1/minidemo/data/exp_set1/ mira-3.4.1.1/minidemo/data/exp_set1/U13a03g02.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a03e10.p2.exp mira-3.4.1.1/minidemo/data/exp_set1/fofn mira-3.4.1.1/minidemo/data/exp_set1/U13a05b10.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/122533c.t3.exp mira-3.4.1.1/minidemo/data/exp_set1/122533c.t7.exp mira-3.4.1.1/minidemo/data/exp_set1/230375b.t3.exp mira-3.4.1.1/minidemo/data/exp_set1/230375a.t7.exp mira-3.4.1.1/minidemo/data/exp_set1/230375b.t7.exp mira-3.4.1.1/minidemo/data/exp_set1/122533a.t7.exp mira-3.4.1.1/minidemo/data/exp_set1/U13e07d02.t2.exp mira-3.4.1.1/minidemo/data/exp_set1/230375b.t2.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a08b04.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/230375b.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/230375c.t3.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a08f11.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a03e10.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/122533b.t7.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a03c03.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/U13e07f02.t2.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a04c06.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a06d03.t1.exp mira-3.4.1.1/minidemo/data/exp_set1/U13a08f10.p2.exp mira-3.4.1.1/minidemo/data/exp_set1/122533b.t3.exp mira-3.4.1.1/minidemo/data/exp_set1/230375a.t3.exp mira-3.4.1.1/minidemo/data/exp_set1/230375c.t7.exp mira-3.4.1.1/minidemo/data/exp_set1/122533a.t3.exp mira-3.4.1.1/minidemo/data/screendata_454/ mira-3.4.1.1/minidemo/data/screendata_454/msd_testFrags454.fna mira-3.4.1.1/minidemo/data/screendata_454/msd_uFrag1_454.fna mira-3.4.1.1/minidemo/data/screendata_454/msd_minimum454screen.fna mira-3.4.1.1/minidemo/data/screendata_454/msd_primer454.fna mira-3.4.1.1/minidemo/data/spneu_t4_40k_454/ mira-3.4.1.1/minidemo/data/spneu_t4_40k_454/spneu_t4_40k_in.454.fasta.qual mira-3.4.1.1/minidemo/data/spneu_t4_40k_454/spneu_t4_40k.gbf mira-3.4.1.1/minidemo/data/spneu_t4_40k_454/spneu_t4_40k_in.454.fasta mira-3.4.1.1/minidemo/data/scf/ mira-3.4.1.1/minidemo/data/scf/U13a03g02.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/230375c.t7.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a08f11.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a08b04.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/122533a.t7.scf.gz mira-3.4.1.1/minidemo/data/scf/122533a.t3.scf.gz mira-3.4.1.1/minidemo/data/scf/230375a.t7.scf.gz mira-3.4.1.1/minidemo/data/scf/122533c.t7.scf.gz mira-3.4.1.1/minidemo/data/scf/230375c.t3.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a03e10.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/230375b.t3.scf.gz mira-3.4.1.1/minidemo/data/scf/122533b.t7.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a06d03.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/U13e07f02.t2.scf.gz mira-3.4.1.1/minidemo/data/scf/122533c.t3.scf.gz mira-3.4.1.1/minidemo/data/scf/230375b.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/U13e07d02.t2.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a05b10.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a04c06.t1.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a08f10.p2.scf.gz mira-3.4.1.1/minidemo/data/scf/230375a.t3.scf.gz mira-3.4.1.1/minidemo/data/scf/230375b.t7.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a03e10.p2.scf.gz mira-3.4.1.1/minidemo/data/scf/122533b.t3.scf.gz mira-3.4.1.1/minidemo/data/scf/230375b.t2.scf.gz mira-3.4.1.1/minidemo/data/scf/U13a03c03.t1.scf.gz mira-3.4.1.1/minidemo/demo2/ mira-3.4.1.1/minidemo/demo2/runme.sh mira-3.4.1.1/minidemo/demo5/ mira-3.4.1.1/minidemo/demo5/runme.sh mira-3.4.1.1/minidemo/estdemo1/ mira-3.4.1.1/minidemo/estdemo1/README mira-3.4.1.1/minidemo/estdemo1/runme.sh mira-3.4.1.1/minidemo/bbdemo2/ mira-3.4.1.1/minidemo/bbdemo2/parameters.par mira-3.4.1.1/minidemo/bbdemo2/runme.sh mira-3.4.1.1/minidemo/solexa2/ mira-3.4.1.1/minidemo/solexa2/README.txt mira-3.4.1.1/minidemo/solexa2/runme.sh mira-3.4.1.1/minidemo/README.txt mira-3.4.1.1/minidemo/demo3/ mira-3.4.1.1/minidemo/demo3/demo3.par mira-3.4.1.1/minidemo/demo3/runme.sh mira-3.4.1.1/minidemo/demo1/ mira-3.4.1.1/minidemo/demo1/runme.sh mira-3.4.1.1/minidemo/solexa3_lenski/ mira-3.4.1.1/minidemo/solexa3_lenski/3_runassembly.sh mira-3.4.1.1/minidemo/solexa3_lenski/1_fetchdata.sh mira-3.4.1.1/minidemo/solexa3_lenski/README.txt mira-3.4.1.1/minidemo/solexa3_lenski/2_prepdata.sh mira-3.4.1.1/minidemo/estdemo2/ mira-3.4.1.1/minidemo/estdemo2/step1_straindata_in.txt mira-3.4.1.1/minidemo/estdemo2/tvc_straindata_in.txt mira-3.4.1.1/minidemo/estdemo2/README mira-3.4.1.1/minidemo/estdemo2/runme.sh mira-3.4.1.1/minidemo/bbdemo1/ mira-3.4.1.1/minidemo/bbdemo1/runme.sh mira-3.4.1.1/ChangeLog mira-3.4.1.1/config.guess mira-3.4.1.1/mkinstalldirs mira-3.4.1.1/config.sub mira-3.4.1.1/aclocal.m4 mira-3.4.1.1/ylwrap mira-3.4.1.1/configure mira-3.4.1.1/ltmain.sh mira-3.4.1.1/THANKS mira-3.4.1.1/Makefile.in mira-3.4.1.1/doc/ mira-3.4.1.1/doc/Makefile.in mira-3.4.1.1/doc/docbook/ mira-3.4.1.1/doc/docbook/chap_preface_part.xml mira-3.4.1.1/doc/docbook/versionfile mira-3.4.1.1/doc/docbook/chap_intro_part.xml mira-3.4.1.1/doc/docbook/chap_seqadvice_part.xml mira-3.4.1.1/doc/docbook/chap_pacbio_part.xml mira-3.4.1.1/doc/docbook/bookfigures/ mira-3.4.1.1/doc/docbook/bookfigures/sxa_sroc_lenski1.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_gcbias_comp20082009.png mira-3.4.1.1/doc/docbook/bookfigures/haf2_haf5_clearshortrepeat.png mira-3.4.1.1/doc/docbook/bookfigures/454san_stmu_hybdenovo.png mira-3.4.1.1/doc/docbook/bookfigures/pb_c227-11-clcr_res.png mira-3.4.1.1/doc/docbook/bookfigures/454sxa_stms_hybdenovo.png mira-3.4.1.1/doc/docbook/bookfigures/pb_elasticdarkinserts03.png mira-3.4.1.1/doc/docbook/bookfigures/haf_danger_join_ok.png mira-3.4.1.1/doc/docbook/bookfigures/ion_dh10bdirdepindel.png mira-3.4.1.1/doc/docbook/bookfigures/srmc_in_454sxahyb_1stpass.png mira-3.4.1.1/doc/docbook/bookfigures/454_autoedit1.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_unsc_ggcxg2_lenski.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_unsc_ggc4_lenski.png mira-3.4.1.1/doc/docbook/bookfigures/srmc_in_454sxahyb_lastpass2.png mira-3.4.1.1/doc/docbook/bookfigures/haf5_repend_rrna.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_unsc_ggc2_lenski.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_unsc_ggc3_lenski.png mira-3.4.1.1/doc/docbook/bookfigures/iontor_indelhpexample.png mira-3.4.1.1/doc/docbook/bookfigures/454sxa_hybdenovo.png mira-3.4.1.1/doc/docbook/bookfigures/gcb99_edit.png mira-3.4.1.1/doc/docbook/bookfigures/pb_elasticdarkinserts04.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_sroc_lenski2.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_cer_reads1.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_gcbias_bias2009.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_cer_reads2.png mira-3.4.1.1/doc/docbook/bookfigures/ion_dh10bcovB13_320kb.png mira-3.4.1.1/doc/docbook/bookfigures/gcb99_replocator.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_gcbias_nobias2008.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_unsc_ggc1_lenski.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_wrmcsrmc_hiding_lenski1.png mira-3.4.1.1/doc/docbook/bookfigures/haf5_haf2_contigcoverage_ovals.png mira-3.4.1.1/doc/docbook/bookfigures/454_autoedit2.png mira-3.4.1.1/doc/docbook/bookfigures/haf_danger_join_notok.png mira-3.4.1.1/doc/docbook/bookfigures/pb_elasticdarkinserts02.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_mcvc_lenski.png mira-3.4.1.1/doc/docbook/bookfigures/ion_dh10bgoodB13.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_unsc_ggcxg1_lenski.png mira-3.4.1.1/doc/docbook/bookfigures/haf5_haf2_contigcoverage.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_xmastree_lenski1.png mira-3.4.1.1/doc/docbook/bookfigures/454_stacks_join.png mira-3.4.1.1/doc/docbook/bookfigures/san_autoedit1.png mira-3.4.1.1/doc/docbook/bookfigures/srmc_in_454sxahyb_lastpass1.png mira-3.4.1.1/doc/docbook/bookfigures/san_autoedit2.png mira-3.4.1.1/doc/docbook/bookfigures/sxa_xmastree_lenski2.png mira-3.4.1.1/doc/docbook/bookfigures/haf2_end_nomoredata.png mira-3.4.1.1/doc/docbook/bookfigures/ion_dh10bcovB13_12kb.png mira-3.4.1.1/doc/docbook/bookfigures/pb_elasticdarkinserts01.png mira-3.4.1.1/doc/docbook/chap_maf_part.xml mira-3.4.1.1/doc/docbook/chap_faq_part.xml mira-3.4.1.1/doc/docbook/chap_sanger_part.xml mira-3.4.1.1/doc/docbook/book.xsl mira-3.4.1.1/doc/docbook/chap_mirautils_part.xml mira-3.4.1.1/doc/docbook/doccss/ mira-3.4.1.1/doc/docbook/doccss/miradocstyle.css mira-3.4.1.1/doc/docbook/chap_solexa_part.xml mira-3.4.1.1/doc/docbook/chap_installation_part.xml mira-3.4.1.1/doc/docbook/chap_bonus_part.xml mira-3.4.1.1/doc/docbook/chap_logfiles_part.xml mira-3.4.1.1/doc/docbook/chap_iontor_part.xml mira-3.4.1.1/doc/docbook/Makefile.in mira-3.4.1.1/doc/docbook/mira.xsl mira-3.4.1.1/doc/docbook/figures_other/ mira-3.4.1.1/doc/docbook/figures_other/iontor_indelhpexample_orig.png mira-3.4.1.1/doc/docbook/chap_reference_part.xml mira-3.4.1.1/doc/docbook/chap_hard_part.xml mira-3.4.1.1/doc/docbook/chap_results_part.xml mira-3.4.1.1/doc/docbook/Makefile.am mira-3.4.1.1/doc/docbook/Makefile mira-3.4.1.1/doc/docbook/images/ mira-3.4.1.1/doc/docbook/images/warning.png.orig mira-3.4.1.1/doc/docbook/images/note.png.orig mira-3.4.1.1/doc/docbook/images/warning.png mira-3.4.1.1/doc/docbook/images/README.txt mira-3.4.1.1/doc/docbook/images/note.png mira-3.4.1.1/doc/docbook/book_definitiveguide.xml mira-3.4.1.1/doc/docbook/chap_454_part.xml mira-3.4.1.1/doc/docbook/chap_est_part.xml mira-3.4.1.1/doc/Makefile.am mira-3.4.1.1/doc/3rdparty/ mira-3.4.1.1/doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf mira-3.4.1.1/doc/Makefile mira-3.4.1.1/GETTING_STARTED mira-3.4.1.1/Makefile.am mira-3.4.1.1/COPYING mira-3.4.1.1/configure.in mira-3.4.1.1/HELP_WANTED mira-3.4.1.1/INSTALL mira-3.4.1.1/README mira-3.4.1.1/distribution/ mira-3.4.1.1/distribution/LICENCE mira-3.4.1.1/distribution/Makefile.in mira-3.4.1.1/distribution/Makefile.am mira-3.4.1.1/distribution/Makefile mira-3.4.1.1/distribution/README mira-3.4.1.1/AUTHORS mira-3.4.1.1/install-sh mira-3.4.1.1/src/ mira-3.4.1.1/src/errorhandling/ mira-3.4.1.1/src/errorhandling/errorhandling.H mira-3.4.1.1/src/errorhandling/Makefile.in mira-3.4.1.1/src/errorhandling/Makefile.am mira-3.4.1.1/src/errorhandling/errorhandling.C mira-3.4.1.1/src/knn_abi373/ mira-3.4.1.1/src/knn_abi373/over.c mira-3.4.1.1/src/knn_abi373/under.h mira-3.4.1.1/src/knn_abi373/add.h mira-3.4.1.1/src/knn_abi373/missing.h mira-3.4.1.1/src/knn_abi373/under.c mira-3.4.1.1/src/knn_abi373/Makefile.in mira-3.4.1.1/src/knn_abi373/nplus.c mira-3.4.1.1/src/knn_abi373/ncall.h mira-3.4.1.1/src/knn_abi373/over.h mira-3.4.1.1/src/knn_abi373/ncall.c mira-3.4.1.1/src/knn_abi373/Makefile.am mira-3.4.1.1/src/knn_abi373/nplus.h mira-3.4.1.1/src/knn_abi373/add.c mira-3.4.1.1/src/knn_abi373/wrong.h mira-3.4.1.1/src/knn_abi373/wrong.c mira-3.4.1.1/src/knn_abi373/missing.c mira-3.4.1.1/src/stdinc/ mira-3.4.1.1/src/stdinc/template.H mira-3.4.1.1/src/stdinc/stlincludes.H mira-3.4.1.1/src/stdinc/foolcompiler.C mira-3.4.1.1/src/stdinc/template.C mira-3.4.1.1/src/stdinc/Makefile.in mira-3.4.1.1/src/stdinc/defines.H mira-3.4.1.1/src/stdinc/types.H mira-3.4.1.1/src/stdinc/Makefile.am mira-3.4.1.1/src/EdIt/ mira-3.4.1.1/src/EdIt/parameters_flexer.cc mira-3.4.1.1/src/EdIt/hypothesen.C mira-3.4.1.1/src/EdIt/parameters.C mira-3.4.1.1/src/EdIt/hypothesen.H mira-3.4.1.1/src/EdIt/Makefile.in mira-3.4.1.1/src/EdIt/parameters_tokens.h mira-3.4.1.1/src/EdIt/Makefile.am mira-3.4.1.1/src/EdIt/parameters.H mira-3.4.1.1/src/EdIt/faultRegion.C mira-3.4.1.1/src/EdIt/parameters_flexer.ll mira-3.4.1.1/src/examples_programming/ mira-3.4.1.1/src/examples_programming/Makefile.in mira-3.4.1.1/src/examples_programming/Makefile.am mira-3.4.1.1/src/examples_programming/readpool_101.C mira-3.4.1.1/src/examples_programming/README mira-3.4.1.1/src/examples_programming/mira_101.C mira-3.4.1.1/src/examples_programming/read_101.C mira-3.4.1.1/src/scripts/ mira-3.4.1.1/src/scripts/fasta2frag.tcl mira-3.4.1.1/src/scripts/Makefile.in mira-3.4.1.1/src/scripts/fastqselect.tcl mira-3.4.1.1/src/scripts/Makefile.am mira-3.4.1.1/src/scripts/fixACE4consed.tcl mira-3.4.1.1/src/scripts/fastaselect.tcl mira-3.4.1.1/src/progs/ mira-3.4.1.1/src/progs/convert_project.C mira-3.4.1.1/src/progs/scftool.C mira-3.4.1.1/src/progs/par2c.pl mira-3.4.1.1/src/progs/mira.C mira-3.4.1.1/src/progs/Makefile.in mira-3.4.1.1/src/progs/version.H mira-3.4.1.1/src/progs/me_step2.par mira-3.4.1.1/src/progs/me_step1.par mira-3.4.1.1/src/progs/Makefile.am mira-3.4.1.1/src/progs/dbgreplay.C mira-3.4.1.1/src/progs/me_step3.par mira-3.4.1.1/src/progs/sw.C mira-3.4.1.1/src/progs/fastatool.C mira-3.4.1.1/src/progs/miratest.C mira-3.4.1.1/src/examine/ mira-3.4.1.1/src/examine/afh_info.C mira-3.4.1.1/src/examine/globals.H mira-3.4.1.1/src/examine/buffer.C mira-3.4.1.1/src/examine/prescan.H mira-3.4.1.1/src/examine/Makefile.in mira-3.4.1.1/src/examine/scfbuffer.H mira-3.4.1.1/src/examine/misc.H mira-3.4.1.1/src/examine/cfh.C mira-3.4.1.1/src/examine/ranges.C mira-3.4.1.1/src/examine/scf_look.C mira-3.4.1.1/src/examine/Makefile.am mira-3.4.1.1/src/examine/calc.C mira-3.4.1.1/src/examine/buffer.H mira-3.4.1.1/src/examine/misc.C mira-3.4.1.1/src/examine/scf_look.H mira-3.4.1.1/src/examine/prescan.C mira-3.4.1.1/src/support/ mira-3.4.1.1/src/support/Makefile.in mira-3.4.1.1/src/support/Makefile.am mira-3.4.1.1/src/support/consedrc.13.0 mira-3.4.1.1/src/support/consedtaglib.txt mira-3.4.1.1/src/support/README mira-3.4.1.1/src/support/GTAGDB mira-3.4.1.1/src/Makefile.in mira-3.4.1.1/src/util/ mira-3.4.1.1/src/util/dptools.C mira-3.4.1.1/src/util/progressindic.H mira-3.4.1.1/src/util/dptools.H mira-3.4.1.1/src/util/memusage.H mira-3.4.1.1/src/util/Makefile.in mira-3.4.1.1/src/util/misc.H mira-3.4.1.1/src/util/Makefile.am mira-3.4.1.1/src/util/misc.C mira-3.4.1.1/src/Makefile.am mira-3.4.1.1/src/caf/ mira-3.4.1.1/src/caf/caf.C mira-3.4.1.1/src/caf/caf.H mira-3.4.1.1/src/caf/Makefile.in mira-3.4.1.1/src/caf/caf_tokens.h mira-3.4.1.1/src/caf/Makefile.am mira-3.4.1.1/src/caf/caf_flexer.cc mira-3.4.1.1/src/caf/caf_flexer.ll mira-3.4.1.1/src/knn_alf/ mira-3.4.1.1/src/knn_alf/over.c mira-3.4.1.1/src/knn_alf/under.h mira-3.4.1.1/src/knn_alf/add.h mira-3.4.1.1/src/knn_alf/missing.h mira-3.4.1.1/src/knn_alf/under.c mira-3.4.1.1/src/knn_alf/Makefile.in mira-3.4.1.1/src/knn_alf/nplus.c mira-3.4.1.1/src/knn_alf/ncall.h mira-3.4.1.1/src/knn_alf/over.h mira-3.4.1.1/src/knn_alf/ncall.c mira-3.4.1.1/src/knn_alf/Makefile.am mira-3.4.1.1/src/knn_alf/nplus.h mira-3.4.1.1/src/knn_alf/add.c mira-3.4.1.1/src/knn_alf/wrong.h mira-3.4.1.1/src/knn_alf/wrong.c mira-3.4.1.1/src/knn_alf/missing.c mira-3.4.1.1/src/lec/ mira-3.4.1.1/src/lec/Makefile.in mira-3.4.1.1/src/lec/Makefile.am mira-3.4.1.1/src/io/ mira-3.4.1.1/src/io/generalio.C mira-3.4.1.1/src/io/fastq-lh.H mira-3.4.1.1/src/io/ncbiinfoxml.C mira-3.4.1.1/src/io/phd.C mira-3.4.1.1/src/io/gbf.C mira-3.4.1.1/src/io/scf.H mira-3.4.1.1/src/io/tokens.h mira-3.4.1.1/src/io/exp_flexer.cc mira-3.4.1.1/src/io/fastq-mira.H mira-3.4.1.1/src/io/Makefile.in mira-3.4.1.1/src/io/exp.H mira-3.4.1.1/src/io/ncbiinfoxml.H mira-3.4.1.1/src/io/Makefile.am mira-3.4.1.1/src/io/generalio.H mira-3.4.1.1/src/io/exp_flexer.ll mira-3.4.1.1/src/io/fasta.C mira-3.4.1.1/src/io/fastq-mira.C mira-3.4.1.1/src/io/scf.C mira-3.4.1.1/src/io/fasta.H mira-3.4.1.1/src/io/exp.C mira-3.4.1.1/src/io/phd.H mira-3.4.1.1/src/io/gbf.H mira-3.4.1.1/src/README mira-3.4.1.1/src/test/ mira-3.4.1.1/src/test/Makefile.in mira-3.4.1.1/src/test/Makefile.am mira-3.4.1.1/src/test/io/ mira-3.4.1.1/src/test/io/generalio/ mira-3.4.1.1/src/test/io/generalio/Makefile.in mira-3.4.1.1/src/test/io/generalio/tstgeneralio.C mira-3.4.1.1/src/test/io/generalio/Makefile.am mira-3.4.1.1/src/test/io/Makefile.in mira-3.4.1.1/src/test/io/Makefile.am mira-3.4.1.1/src/test/io/fasta/ mira-3.4.1.1/src/test/io/fasta/tstFASTA.C mira-3.4.1.1/src/test/io/fasta/Makefile.in mira-3.4.1.1/src/test/io/fasta/Makefile.am mira-3.4.1.1/src/test/io/scf/ mira-3.4.1.1/src/test/io/scf/Makefile.in mira-3.4.1.1/src/test/io/scf/tstSCF.C mira-3.4.1.1/src/test/io/scf/Makefile.am mira-3.4.1.1/src/test/mira/ mira-3.4.1.1/src/test/mira/read/ mira-3.4.1.1/src/test/mira/read/Makefile.in mira-3.4.1.1/src/test/mira/read/Makefile.am mira-3.4.1.1/src/test/mira/read/tstRead.C mira-3.4.1.1/src/test/mira/readpool/ mira-3.4.1.1/src/test/mira/readpool/Makefile.in mira-3.4.1.1/src/test/mira/readpool/Makefile.am mira-3.4.1.1/src/test/mira/readpool/tstReadPool.C mira-3.4.1.1/src/test/mira/Makefile.in mira-3.4.1.1/src/test/mira/align/ mira-3.4.1.1/src/test/mira/align/Makefile.in mira-3.4.1.1/src/test/mira/align/Makefile.am mira-3.4.1.1/src/test/mira/align/tstAlign.C mira-3.4.1.1/src/test/mira/Makefile.am mira-3.4.1.1/src/mira/ mira-3.4.1.1/src/mira/estassembly.C mira-3.4.1.1/src/mira/skim.H mira-3.4.1.1/src/mira/scaffolder.C mira-3.4.1.1/src/mira/assembly_output.C mira-3.4.1.1/src/mira/dynamic.H mira-3.4.1.1/src/mira/readpool.H mira-3.4.1.1/src/mira/assembly.H mira-3.4.1.1/src/mira/assembly.C mira-3.4.1.1/src/mira/ads.H mira-3.4.1.1/src/mira/assembly_info.H mira-3.4.1.1/src/mira/parameters_flexer.cc mira-3.4.1.1/src/mira/contig_edit.C mira-3.4.1.1/src/mira/enums.H mira-3.4.1.1/src/mira/dataprocessing.C mira-3.4.1.1/src/mira/maf_parse.C mira-3.4.1.1/src/mira/CHANGES_old.txt mira-3.4.1.1/src/mira/parameters.C mira-3.4.1.1/src/mira/newpathfinder.H mira-3.4.1.1/src/mira/Makefile.in mira-3.4.1.1/src/mira/adaptorsforclip.solexa.xxd mira-3.4.1.1/src/mira/contig.H mira-3.4.1.1/src/mira/CHANGES.txt mira-3.4.1.1/src/mira/structs.H mira-3.4.1.1/src/mira/adaptorsforclip.iontor.xxd mira-3.4.1.1/src/mira/adsfacts.C mira-3.4.1.1/src/mira/indexed_deque.H mira-3.4.1.1/src/mira/gff_parse.C mira-3.4.1.1/src/mira/read.H mira-3.4.1.1/src/mira/TODO mira-3.4.1.1/src/mira/multitag.H mira-3.4.1.1/src/mira/parameters_tokens.h mira-3.4.1.1/src/mira/assembly_swalign.C mira-3.4.1.1/src/mira/read.C mira-3.4.1.1/src/mira/scaffolder.H mira-3.4.1.1/src/mira/Makefile.am mira-3.4.1.1/src/mira/skim.C mira-3.4.1.1/src/mira/assembly_output.H mira-3.4.1.1/src/mira/parameters.H mira-3.4.1.1/src/mira/contig_analysis.C mira-3.4.1.1/src/mira/multitag.C mira-3.4.1.1/src/mira/contig_output.C mira-3.4.1.1/src/mira/parameters_flexer.ll mira-3.4.1.1/src/mira/align.H mira-3.4.1.1/src/mira/adaptorsforclip.454.xxd mira-3.4.1.1/src/mira/readpool.C mira-3.4.1.1/src/mira/assembly_info.C mira-3.4.1.1/src/mira/maf_parse.H mira-3.4.1.1/src/mira/demoparam.prm mira-3.4.1.1/src/mira/gff_parse.H mira-3.4.1.1/src/mira/assembly_repeatresolve.C mira-3.4.1.1/src/mira/dynamic.C mira-3.4.1.1/src/mira/newpathfinder.C mira-3.4.1.1/src/mira/adaptorsregex.iontor.xxd mira-3.4.1.1/src/mira/stringcontainer.H mira-3.4.1.1/src/mira/assembly_reduceskimhits.C mira-3.4.1.1/src/mira/ads.C mira-3.4.1.1/src/mira/adaptorsregex.solexa.xxd mira-3.4.1.1/src/mira/adsfacts.H mira-3.4.1.1/src/mira/align.C mira-3.4.1.1/src/mira/contig.C mira-3.4.1.1/src/mira/assembly_io.C mira-3.4.1.1/src/mira/timerestrict.H mira-3.4.1.1/depcomp mira-3.4.1.1/NEWS mira-3.4.1.1/missing sudo -u fink-bld [ENV] sh -c /tmp/fink.LFp7J mv config/m4 m4 perl -pi -e "s,-pthread,-lpthread,g" configure configure.in m4/ax_boost_thread.m4 ltmain.sh perl -pi -e 's|-mmacosx-version-min\=10\.5||g' configure configure.in mv configure.in configure.ac sudo -u fink-bld [ENV] sh -c /tmp/fink.3nxeY /tmp/fink.MAG9t #!/bin/sh -ev export PERL=/usr/bin/perl export PATH=/sw/lib/flex/bin:/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/fink:$PATH export AUTOCONF=/sw/bin/autoconf export ACLOCAL=/sw/bin/aclocal-1.14 export AUTOMAKE=/sw/bin/automake-1.14 mkdir fink ln -s /sw/lib/flex/bin/flex /sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/fink/flex++ autoreconf -vfi autoreconf: Entering directory `.' autoreconf: configure.ac: not using Gettext autoreconf: running: /sw/bin/aclocal-1.14 --force autoreconf: configure.ac: tracing autoreconf: running: libtoolize --copy --force libtoolize: putting auxiliary files in `.'. libtoolize: copying file `./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'. libtoolize: copying file `m4/libtool.m4' libtoolize: copying file `m4/ltoptions.m4' libtoolize: copying file `m4/ltsugar.m4' libtoolize: copying file `m4/ltversion.m4' libtoolize: copying file `m4/lt~obsolete.m4' libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am. autoreconf: running: /sw/bin/autoconf --force autoreconf: configure.ac: not using Autoheader autoreconf: running: /sw/bin/automake-1.14 --add-missing --copy --force-missing configure.ac:82: installing './compile' doc/docbook/Makefile.am:5: warning: ':='-style assignments are not portable doc/docbook/Makefile.am:6: warning: ':='-style assignments are not portable doc/docbook/Makefile.am:15: warning: '%'-style pattern rules are a GNU make extension src/EdIt/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/caf/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/errorhandling/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/examine/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/examples_programming/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/io/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/knn_abi373/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/knn_alf/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/lec/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/mira/Makefile.am:6: warning: '%'-style pattern rules are a GNU make extension src/mira/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/progs/Makefile.am:7: warning: '%'-style pattern rules are a GNU make extension src/progs/Makefile.am:21: warning: '%'-style pattern rules are a GNU make extension src/progs/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/progs/Makefile.am:102: warning: variable 'ace2caf_SOURCES' is defined but no program or src/progs/Makefile.am:102: library has 'ace2caf' as canonical name (possible typo) src/progs/Makefile.am:81: warning: variable 'nodist_mirazip_SOURCES' is defined but no program or src/progs/Makefile.am:81: library has 'mirazip' as canonical name (possible typo) src/progs/Makefile.am:105: warning: variable 'tagsnp_SOURCES' is defined but no program or src/progs/Makefile.am:105: library has 'tagsnp' as canonical name (possible typo) src/progs/Makefile.am:89: warning: variable 'uncover_at_SOURCES' is defined but no program or src/progs/Makefile.am:89: library has 'uncover_at' as canonical name (possible typo) src/progs/Makefile.am:103: warning: variable 'ace2caf_LDADD' is defined but no program or src/progs/Makefile.am:103: library has 'ace2caf' as canonical name (possible typo) src/progs/Makefile.am:82: warning: variable 'mirazip_LDADD' is defined but no program or src/progs/Makefile.am:82: library has 'mirazip' as canonical name (possible typo) src/progs/Makefile.am:106: warning: variable 'tagsnp_LDADD' is defined but no program or src/progs/Makefile.am:106: library has 'tagsnp' as canonical name (possible typo) src/progs/Makefile.am:90: warning: variable 'uncover_at_LDADD' is defined but no program or src/progs/Makefile.am:90: library has 'uncover_at' as canonical name (possible typo) src/test/io/fasta/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/test/io/generalio/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/test/io/scf/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/test/mira/align/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/test/mira/read/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/test/mira/readpool/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/util/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') autoreconf: Leaving directory `.' ./configure --prefix=/sw --mandir=/sw/share/man \ --enable-dependency-tracking \ --with-boost=/sw \ --with-boost-thread=boost_thread-mt \ --with-boost-regex=boost_regex-mt \ --with-boost-filesystem=boost_filesystem-mt \ --with-boost-iostreams=boost_iostreams-mt \ --with-boost-system=boost_system-mt \ --with-expat=/sw \ --disable-static checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '600' is supported by ustar format... yes checking whether GID '600' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether to add --prefix as include path... yes +++++++++++++++++++++++++++++++++++++ systemuname: Darwin CFLAGS now: -I/sw/include CXXFLAGS now: -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 +++++++++++++++++++++++++++++++++++++ systemuname: Darwin CFLAGS now: -I/sw/include CXXFLAGS now: -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ checking how to run the C preprocessor... gcc -E 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 for int64_t... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -I/sw/include CXXFLAGS now: -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ checking whether long has 64bit... yes checking whether enabling 64bit compilation support... yes checking build system type... x86_64-apple-darwin13.3.0 checking for compiler optimisation settings... -O3 -funroll-loops +++++++++++++++++++++++++++++++++++++ CFLAGS now: -I/sw/include -O3 -funroll-loops CXXFLAGS now: -I/sw/include -O3 -funroll-loops LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ checking host system type... x86_64-apple-darwin13.3.0 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin13.3.0 file names to x86_64-apple-darwin13.3.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.3.0 file names to toolchain format... func_convert_file_noop checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for flex... no checking for flex... flex checking lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking for flex++... yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for C/C++ restrict keyword... __restrict checking whether struct tm is in sys/time.h or time.h... time.h checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... no checking whether stat accepts an empty string... no checking for strftime... yes checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for isblank... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -I/sw/include -O3 -funroll-loops CXXFLAGS now: -I/sw/include -O3 -funroll-loops LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ checking whether the compiler implements namespaces... yes checking whether the compiler supports ISO C++ standard library... yes checking whether the compiler supports Standard Template Library... yes checking for boostlib >= 1.46.0... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/sw/include BOOST LDFLAGS: -L/sw/lib ac_boost_path: /sw ac_boost_lib_path: CFLAGS now: -I/sw/include -O3 -funroll-loops CXXFLAGS now: -I/sw/include -O3 -funroll-loops LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ Setting rescue value for ac_boost_lib_path: /sw/lib +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/sw/include BOOST LDFLAGS: -L/sw/lib CFLAGS now: -I/sw/include -O3 -funroll-loops -Wl,-rpath,/sw/lib CXXFLAGS now: -I/sw/include -O3 -funroll-loops LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread-mt... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -lpthread -I/sw/include BOOST LDFLAGS: -L/sw/lib ac_boost_path: /sw ac_boost_lib_path: /sw/lib BOOST_THREAD_LIB: -lboost_thread-mt CFLAGS now: -I/sw/include -O3 -funroll-loops -Wl,-rpath,/sw/lib CXXFLAGS now: -I/sw/include -O3 -funroll-loops LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -lpthread -I/sw/include BOOST LDFLAGS: -L/sw/lib ac_boost_path: /sw ac_boost_lib_path: /sw/lib BOOST_THREAD_LIB: -lboost_thread-mt CFLAGS now: -I/sw/include -O3 -funroll-loops -Wl,-rpath,/sw/lib CXXFLAGS now: -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Regex library is available... yes checking for main in -lboost_regex-mt... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -lpthread -I/sw/include BOOST LDFLAGS: -L/sw/lib ac_boost_path: /sw ac_boost_lib_path: /sw/lib BOOST_REGEX_LIB: -lboost_regex-mt CFLAGS now: -I/sw/include -O3 -funroll-loops -Wl,-rpath,/sw/lib CXXFLAGS now: -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt -lboost_regex-mt +++++++++++++++++++++++++++++++++++++ checking whether the Boost::System library is available... yes checking for exit in -lboost_system-mt... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -lpthread -I/sw/include BOOST LDFLAGS: -L/sw/lib ac_boost_path: /sw ac_boost_lib_path: /sw/lib BOOST_SYSTEM_LIB: -lboost_system-mt CFLAGS now: -I/sw/include -O3 -funroll-loops -Wl,-rpath,/sw/lib CXXFLAGS now: -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt -lboost_regex-mt -lboost_system-mt +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Filesystem library is available... yes checking for exit in -lboost_filesystem-mt... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -lpthread -I/sw/include BOOST LDFLAGS: -L/sw/lib ac_boost_path: /sw ac_boost_lib_path: /sw/lib BOOST_FILESYSTEM_LIB: -lboost_filesystem-mt CFLAGS now: -I/sw/include -O3 -funroll-loops -Wl,-rpath,/sw/lib CXXFLAGS now: -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt -lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt +++++++++++++++++++++++++++++++++++++ checking whether the Boost::IOStreams library is available... yes checking for main in -lboost_iostreams-mt... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -lpthread -I/sw/include BOOST LDFLAGS: -L/sw/lib ac_boost_path: /sw ac_boost_lib_path: /sw/lib BOOST_IOSTREAMS_LIB: -lboost_iostreams-mt CFLAGS now: -I/sw/include -O3 -funroll-loops -Wl,-rpath,/sw/lib CXXFLAGS now: -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt -lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lz -lbz2 +++++++++++++++++++++++++++++++++++++ checking for Expat XML Parser headers in /sw/include... found checking for Expat XML Parser libraries... found checking for Expat XML Parser... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -I/sw/include -O3 -funroll-loops -I/sw/include CXXFLAGS now: -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt -lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lz -lbz2 +++++++++++++++++++++++++++++++++++++ checking if zlib is wanted... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -I/sw/include -O3 -funroll-loops -I/sw/include CXXFLAGS now: -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include LDFLAGS now: -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt -lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lz -lbz2 +++++++++++++++++++++++++++++++++++++ checking for flex version compatible with MIRA... yes checking for purify... no checking whether mira should compile in public quiet mode... yes checking whether mira should compile a development version... no checking whether mira should compile with bound tracking... yes checking whether mira should compile with bug tracking... yes checking whether mira should compile with extended bug tracking... no checking whether mira should compile with function trace... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/stdinc/Makefile config.status: creating src/lec/Makefile config.status: creating src/errorhandling/Makefile config.status: creating src/util/Makefile config.status: creating src/io/Makefile config.status: creating src/mira/Makefile config.status: creating src/EdIt/Makefile config.status: creating src/caf/Makefile config.status: creating src/examine/Makefile config.status: creating src/knn_abi373/Makefile config.status: creating src/knn_alf/Makefile config.status: creating src/support/Makefile config.status: creating src/scripts/Makefile config.status: creating src/test/Makefile config.status: creating src/test/io/Makefile config.status: creating src/test/io/scf/Makefile config.status: creating src/test/io/fasta/Makefile config.status: creating src/test/io/generalio/Makefile config.status: creating src/test/mira/Makefile config.status: creating src/test/mira/align/Makefile config.status: creating src/test/mira/read/Makefile config.status: creating src/test/mira/readpool/Makefile config.status: creating src/examples_programming/Makefile config.status: creating src/progs/Makefile config.status: creating doc/Makefile config.status: creating doc/docbook/Makefile config.status: creating distribution/Makefile config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------------------------------------- Summary of MIRA configuration -------------------------------------------------------------------------------- Linking against tcmalloc is disabled! Note that is the default for OS X, but you might want to try switching it on like this: --with-tcmalloc Building version ................................. 3.4.1.1_prod_darwin13.3.0_x86_64_dynamic Production or development version?................ production We are building on ............................... Darwin CPU supports 64 bit? ......... ................... yes Compiler ......................................... gcc Compiler optimisation flags used ................. -O3 -funroll-loops Do we compile in 64 bit? ......................... yes Building completely static? ...................... no BOOST expected to compile and link?............... yes Linking with TCmalloc library?.................... no Can MIRA be built on this system? ................ yes Using CFLAGS : -I/sw/include -O3 -funroll-loops -I/sw/include Using CXXFLAGS : -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include Using LDFLAGS : -L/sw/lib/flex/lib -L/sw/lib -L/sw/lib -L/sw/lib -lboost_thread-mt -lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lz -lbz2 Looks good, we do not expect compilation problems. -------------------------------------------------------------------------------- Type 'make' to make the binaries and then 'make install' to install them. make -w make: Entering directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1' Making all in src make[1]: Entering directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/src' Making all in lec make[2]: Entering directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/src/lec' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/src/lec' Making all in io make[2]: Entering directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/src/io' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT gbf.o -MD -MP -MF .deps/gbf.Tpo -c -o gbf.o gbf.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT generalio.o -MD -MP -MF .deps/generalio.Tpo -c -o generalio.o generalio.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT fasta.o -MD -MP -MF .deps/fasta.Tpo -c -o fasta.o fasta.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT fastq-mira.o -MD -MP -MF .deps/fastq-mira.Tpo -c -o fastq-mira.o fastq-mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT phd.o -MD -MP -MF .deps/phd.Tpo -c -o phd.o phd.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT scf.o -MD -MP -MF .deps/scf.Tpo -c -o scf.o scf.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT exp.o -MD -MP -MF .deps/exp.Tpo -c -o exp.o exp.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.1.1\" -DPACKAGE_STRING=\"mira\ 3.4.1.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.1.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -I/sw/lib/flex/include -I/sw/include -DPUBLICQUIET -I/sw/include -O3 -funroll-loops -lpthread -I/sw/include -I/sw/include -MT ncbiinfoxml.o -MD -MP -MF .deps/ncbiinfoxml.Tpo -c -o ncbiinfoxml.o ncbiinfoxml.C clangclang: warning: -lpthread: 'linker' input unused clang: warning: -lpthread: 'linker' input unused : warning: -lpthread: 'linker' input unused clang: warning: -lpthread: 'linker' input unused clang: warning: -lpthread: 'linker' input unused clang: warning: -lpthread: 'linker' input unused clang: warning: -lpthread: 'linker' input unused clang: warning: -lpthread: 'linker' input unused In file included from phd.C:31: In file included from ../../src/io/phd.H:34: ../../src/stdinc/stlincludes.H:76:10: fatal error: 'ext/slist' file not found #include ^ In file included from fasta.C:27: In file included from ../../src/io/fasta.H:40: ../../src/stdinc/stlincludes.H:76:10: fatal error: 'ext/slist' file not found #include ^ In file included from exp.C:41: In file included from ./exp.H:39: ../../src/stdinc/stlincludes.H:76:10: fatal error: 'ext/slist' file not found #include ^ In file included from ncbiinfoxml.C:37: In file included from ./ncbiinfoxml.H:35: ../../src/stdinc/stlincludes.H:76In file included from fastq-mira.C:26: In file included from ../../src/io/fastq-mira.H:31: In file included from ../../src/errorhandling/errorhandling.H:44: In file included from ../../src/util/misc.H:47: ../../src/stdinc/stlincludes.H:76:10: :10: fatal errorfatal error: 'ext/slist' file not found : #include ^ 'ext/slist' file not found #include ^ In file included from generalio.C:29: In file included from ./generalio.H:32: ../../src/stdinc/stlincludes.H:76:10: fatal error: 'ext/slist' file not found #include ^ In file included from gbf.C:28: In file included from ../../src/io/gbf.H:36: In file included from ../../src/errorhandling/errorhandling.H:44: In file included from ../../src/util/misc.H:47: ../../src/stdinc/stlincludes.H:76:10: fatal error: 'ext/slist' file not found #include ^ 1 error generated. In file included from scf.C:34: In file included from ./scf.H:67: In file included from ../../src/errorhandling/errorhandling.H:44: In file included from ../../src/util/misc.H:47: ../../src/stdinc/stlincludes.H:76:10: fatal error: 'ext/slist' file not found #include ^ make[2]: *** [generalio.o] Error 1 make[2]: *** Waiting for unfinished jobs.... 1 error generated. make[2]: *** [fastq-mira.o] Error 1 1 error generated. make[2]: *** [phd.o] Error 1 1 error generated. make[2]: *** [ncbiinfoxml.o] Error 1 1 error generated. make[2]: *** [fasta.o] Error 1 1 error generated. make[2]: *** [gbf.o] Error 1 1 error generated. make[2]: *** [exp.o] Error 1 1 error generated. make[2]: *** [scf.o] Error 1 make[2]: Leaving directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/src/io' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1/src' make: *** [all-recursive] Error 1 make: Leaving directory `/sw/build.build/mira-3.4.1.1-1002/mira-3.4.1.1' ### execution of /tmp/fink.MAG9t failed, exit code 2 ### execution of /tmp/fink.3nxeY failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-mira-3.4.1.1-1002 (Reading database ... 158017 files and directories currently installed.) Removing fink-buildlock-mira-3.4.1.1-1002 ... Failed: phase compiling: mira-3.4.1.1-1002 failed Before reporting any errors, please run "fink selfupdate" and try again. Also try using "fink configure" to set your maximum build jobs to 1 and attempt to build the package again. If you continue to have issues, please check to see if the FAQ on Fink's website solves the problem. If not, ask on one (not both, please) of these mailing lists: The Fink Users List The Fink Beginners List , with a carbon copy to the maintainer: Hanspeter Niederstrasser Note that this is preferable to emailing just the maintainer directly, since most fink package maintainers do not have access to all possible hardware and software configurations. Please try to include the complete error message in your report. This generally consists of a compiler line starting with e.g. "gcc" or "g++" followed by the actual error output from the compiler. Also include the following system information: Package manager version: 0.37.0 Distribution version: selfupdate-cvs Thu Jul 24 20:26:24 2014, 10.9, x86_64 Trees: local/main stable/main Xcode.app: 5.1.1 Xcode command-line tools: 6.0.0.0.1.1405597879 Max. Fink build jobs: 8