------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python27-2.7.18.txz ===== Message from python27-2.7.18: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Installing /packages/All/icu-67.1,1.txz Installing /packages/All/boost-libs-1.72.0_2.txz ===== Message from boost-libs-1.72.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/tbb-2020.2.txz Installing /packages/All/bash-5.0.17.txz Installing /packages/All/python37-3.7.7_1.txz ===== Message from python37-3.7.7_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/perl5-5.30.3.txz ===== Message from perl5-5.30.3: -- The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Installing /packages/All/bowtie2-2.4.1_1.txz SUCCEEDED 00:00:35 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- /!\ tophat-2.1.1_1: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- /!\ tophat-2.1.1_1: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by tophat-2.1.1_1 for building SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- /!\ tophat-2.1.1_1: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by tophat-2.1.1_1 for building => SHA256 Checksum OK for tophat-2.1.1.tar.gz. SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- /!\ tophat-2.1.1_1: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by tophat-2.1.1_1 for building ===> Extracting for tophat-2.1.1_1 => SHA256 Checksum OK for tophat-2.1.1.tar.gz. Extracted Memory Use: 14.64M SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for tophat-2.1.1_1 ===> Applying ports patches for tophat-2.1.1_1 from /xports/biology/tophat/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> tophat-2.1.1_1 depends on package: gmake>=4.3 - found ===> tophat-2.1.1_1 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> tophat-2.1.1_1 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> tophat-2.1.1_1 depends on package: gmake>=4.3 - found ===> tophat-2.1.1_1 depends on file: /usr/local/bin/python2.7 - found ===> tophat-2.1.1_1 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so) ===> Configuring for tophat-2.1.1_1 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes 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 c++ accepts -g... yes checking for style of include used by gmake... GNU checking dependency style of c++... gcc3 checking for ar... ar checking the archiver (ar) interface... ar checking for gawk... (cached) /usr/bin/awk checking whether we are using the GNU C++ compiler... (cached) yes checking whether c++ accepts -g... (cached) yes checking dependency style of c++... (cached) gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking dependency style of cc... gcc3 checking whether gmake sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking whether /usr/local/bin/python2.7 version is >= 2.4... yes checking for /usr/local/bin/python2.7 version... 2.7 checking for /usr/local/bin/python2.7 platform... dragonfly5 checking for /usr/local/bin/python2.7 script directory... ${prefix}/lib/python2.7/site-packages checking for /usr/local/bin/python2.7 extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for boostlib >= 1.38.0... yes checking whether the compiler implements namespaces... yes checking whether the Boost::Thread library is available... yes checking for main in -lboost_thread... yes checking whether Boost::Thread needs Boost::System library... no checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for inline... inline checking for pid_t... (cached) yes checking for size_t... (cached) yes checking for ptrdiff_t... (cached) yes checking for an ANSI C-conforming const... 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 gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for memset... (cached) yes checking for strdup... (cached) yes checking for strrchr... (cached) yes checking for strtol... (cached) yes checking for strsep... (cached) yes checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 checking how to create a pax tar archive... gnutar checking dependency style of cc... (cached) gcc3 checking dependency style of c++... (cached) gcc3 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 config.h config.status: executing depfiles commands -- tophat 2.1.1 Configuration Results -- C++ compiler: c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include Linker flags: -L./samtools-0.1.18 -L/usr/local/lib BOOST libraries: -lboost_thread GCC version: cc 8.3 [DragonFly] Release/2019-02-22 Host System type: x86_64-portbld-dragonfly5.9 Install prefix: /usr/local Install eprefix: ${prefix} See config.h for further configuration information. Email bug reports to . SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for tophat-2.1.1_1 gmake[1]: Entering directory '/construction/biology/tophat/tophat-2.1.1' gmake all-recursive gmake[2]: Entering directory '/construction/biology/tophat/tophat-2.1.1' Making all in src gmake[3]: Entering directory '/construction/biology/tophat/tophat-2.1.1/src' Makefile:1679: warning: overriding recipe for target 'libbam.a' Makefile:1203: warning: ignoring old recipe for target 'libbam.a' cd ./samtools-0.1.18 && gmake samtools_0.1.18 gmake[4]: Entering directory '/construction/biology/tophat/tophat-2.1.1/src/samtools-0.1.18' gmake[5]: Entering directory '/construction/biology/tophat/tophat-2.1.1/src/samtools-0.1.18' cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam.c -o bam.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam.c -o sam.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. razf.c -o razf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. knetfile.c -o knetfile.o knetfile.c: In function 'socket_wait': knetfile.c:70:8: warning: implicit declaration of function 'select'; did you mean 'exect'? [-Wimplicit-function-declaration] ret = select(fd+1, fdr, fdw, 0, &tv); ^~~~~~ exect cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o In file included from bam_sort.c:9: bam_sort.c:309:26: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static KSORT_INIT(sort, bam1_p, bam1_lt) ^~~~~~~ ksort.h:148:25: note: in definition of macro 'KSORT_INIT' for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ ^~~~~~~~~ bam_sort.c:53:27: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static KSORT_INIT(heap, heap1_t, heap_lt) ^~~~~~~ ksort.h:148:25: note: in definition of macro 'KSORT_INIT' for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ ^~~~~~~~~ cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o ar cr libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o /usr/bin/ranlib libbam.a gmake[5]: Leaving directory '/construction/biology/tophat/tophat-2.1.1/src/samtools-0.1.18' gmake[5]: Entering directory '/construction/biology/tophat/tophat-2.1.1/src/samtools-0.1.18/bcftools' cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf.c -o bcf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. vcf.c -o vcf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcfutils.c -o bcfutils.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. prob1.c -o prob1.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. em.c -o em.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kfunc.c -o kfunc.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kmin.c -o kmin.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. index.c -o index.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. fet.c -o fet.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. mut.c -o mut.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') gmake[5]: Leaving directory '/construction/biology/tophat/tophat-2.1.1/src/samtools-0.1.18/bcftools' cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview.c -o bam_tview.o bam_tview.c:434:2: warning: #warning "No curses library is available; tview is disabled." [-Wcpp] #warning "No curses library is available; tview is disabled." ^~~~~~~ cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_plcmd.c -o bam_plcmd.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_view.c -o sam_view.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdup.c -o bam_rmdup.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdupse.c -o bam_rmdupse.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_mate.c -o bam_mate.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_stat.c -o bam_stat.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_color.c -o bam_color.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bamtk.c -o bamtk.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 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Leaving directory '/construction/biology/tophat/tophat-2.1.1/src/samtools-0.1.18' cp ./samtools-0.1.18/libbam.a ./samtools-0.1.18/samtools_0.1.18 . c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT GBase.o -MD -MP -MF .deps/GBase.Tpo -c -o GBase.o GBase.cpp mv -f .deps/GBase.Tpo .deps/GBase.Po c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT codons.o -MD -MP -MF .deps/codons.Tpo -c -o codons.o codons.cpp mv -f .deps/codons.Tpo .deps/codons.Po c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include 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gff.o gff.cpp mv -f .deps/gff.Tpo .deps/gff.Po rm -f libgc.a ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgc.a c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp mv -f .deps/reads.Tpo .deps/reads.Po cc -DHAVE_CONFIG_H -I. -I.. -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -MT alphabet.o -MD -MP -MF .deps/alphabet.Tpo -c -o alphabet.o alphabet.c mv -f .deps/alphabet.Tpo .deps/alphabet.Po c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread 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-L./samtools-0.1.18 -L/usr/local/lib -o bam2fastx bam2fastx.o ../src/libgc.a -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT segment_juncs.o -MD -MP -MF .deps/segment_juncs.Tpo -c -o segment_juncs.o segment_juncs.cpp mv -f .deps/segment_juncs.Tpo .deps/segment_juncs.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o segment_juncs segment_juncs.o ../src/libtophat.a -lboost_thread -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT gtf_juncs.o -MD -MP -MF .deps/gtf_juncs.Tpo -c -o gtf_juncs.o gtf_juncs.cpp mv -f .deps/gtf_juncs.Tpo .deps/gtf_juncs.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o gtf_juncs gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT juncs_db.o -MD -MP -MF .deps/juncs_db.Tpo -c -o juncs_db.o juncs_db.cpp mv -f .deps/juncs_db.Tpo .deps/juncs_db.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o juncs_db juncs_db.o ../src/libtophat.a -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT long_spanning_reads.o -MD -MP -MF .deps/long_spanning_reads.Tpo -c -o long_spanning_reads.o long_spanning_reads.cpp mv -f .deps/long_spanning_reads.Tpo .deps/long_spanning_reads.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o long_spanning_reads long_spanning_reads.o ../src/libtophat.a -lboost_thread -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT bam_merge.o -MD -MP -MF .deps/bam_merge.Tpo -c -o bam_merge.o bam_merge.cpp mv -f .deps/bam_merge.Tpo .deps/bam_merge.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o bam_merge bam_merge.o ../src/libtophat.a ../src/libgc.a -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT map2gtf.o -MD -MP -MF .deps/map2gtf.Tpo -c -o map2gtf.o map2gtf.cpp mv -f .deps/map2gtf.Tpo .deps/map2gtf.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o map2gtf map2gtf.o ../src/libtophat.a libgc.a -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT tophat_reports.o -MD -MP -MF .deps/tophat_reports.Tpo -c -o tophat_reports.o tophat_reports.cpp mv -f .deps/tophat_reports.Tpo .deps/tophat_reports.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o tophat_reports tophat_reports.o ../src/libtophat.a -lboost_thread -lbam -lz c++ -DHAVE_CONFIG_H -I. -I.. -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -MT sam_juncs.o -MD -MP -MF .deps/sam_juncs.Tpo -c -o sam_juncs.o sam_juncs.cpp mv -f .deps/sam_juncs.Tpo .deps/sam_juncs.Po c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -pipe -Wno-unused -O2 -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/local/lib -L./samtools-0.1.18 -L/usr/local/lib -o sam_juncs sam_juncs.o ../src/libtophat.a -lbam -lz cp tophat2.sh tophat2 && chmod 755 tophat2 sed -e 's|__VERSION__|2.1.1|' tophat.py > tophat && chmod 755 tophat gmake[3]: Leaving directory '/construction/biology/tophat/tophat-2.1.1/src' gmake[3]: Entering directory '/construction/biology/tophat/tophat-2.1.1' gmake[3]: Leaving directory '/construction/biology/tophat/tophat-2.1.1' gmake[2]: Leaving directory '/construction/biology/tophat/tophat-2.1.1' gmake[1]: Leaving directory '/construction/biology/tophat/tophat-2.1.1' SUCCEEDED 00:03:32 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> tophat-2.1.1_1 depends on executable: bowtie2 - found ===> tophat-2.1.1_1 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for tophat-2.1.1_1 ===> tophat-2.1.1_1 depends on executable: bowtie2 - found ===> tophat-2.1.1_1 depends on file: /usr/local/bin/python2.7 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/tophat/tophat-2.1.1' if test -z ''; then \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/tophat/tophat-2.1.1/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/tophat/tophat-2.1.1/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/tophat/tophat-2.1.1/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/tophat/tophat-2.1.1/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG=''" install; \ fi gmake[2]: Entering directory '/construction/biology/tophat/tophat-2.1.1' Making install in src gmake[3]: Entering directory '/construction/biology/tophat/tophat-2.1.1/src' Makefile:1679: warning: overriding recipe for target 'libbam.a' Makefile:1203: warning: ignoring old recipe for target 'libbam.a' gmake[4]: Entering directory '/construction/biology/tophat/tophat-2.1.1/src' Makefile:1679: warning: overriding recipe for target 'libbam.a' Makefile:1203: warning: ignoring old recipe for target 'libbam.a' /bin/mkdir -p '/construction/biology/tophat/stage/usr/local/bin' /bin/sh /construction/biology/tophat/tophat-2.1.1/install-sh -c -s samtools_0.1.18 prep_reads gtf_to_fasta fix_map_ordering bam2fastx segment_juncs gtf_juncs juncs_db long_spanning_reads bam_merge map2gtf tophat_reports sam_juncs '/construction/biology/tophat/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/tophat/stage/usr/local/bin' install -m 555 tophat2 tophat '/construction/biology/tophat/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/tophat/stage/usr/local/bin' install -m 555 contig_to_chr_coords bed_to_juncs sra_to_solid tophat-fusion-post '/construction/biology/tophat/stage/usr/local/bin' gmake install-data-hook gmake[5]: Entering directory '/construction/biology/tophat/tophat-2.1.1/src' Makefile:1679: warning: overriding recipe for target 'libbam.a' Makefile:1203: warning: ignoring old recipe for target 'libbam.a' cp -r intervaltree sortedcontainers /construction/biology/tophat/stage/usr/local/bin gmake[5]: Leaving directory '/construction/biology/tophat/tophat-2.1.1/src' gmake[4]: Leaving directory '/construction/biology/tophat/tophat-2.1.1/src' gmake[3]: Leaving directory '/construction/biology/tophat/tophat-2.1.1/src' gmake[3]: Entering directory '/construction/biology/tophat/tophat-2.1.1' gmake[4]: Entering directory '/construction/biology/tophat/tophat-2.1.1' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/tophat/tophat-2.1.1' gmake[3]: Leaving directory '/construction/biology/tophat/tophat-2.1.1' gmake[2]: Leaving directory '/construction/biology/tophat/tophat-2.1.1' gmake[1]: Leaving directory '/construction/biology/tophat/tophat-2.1.1' install -m 555 /xports/biology/tophat/files/tophat-test /construction/biology/tophat/stage/usr/local/bin ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for tophat-2.1.1_1 file sizes/checksums [29]: 0% file sizes/checksums [29]: 100% packing files [29]: 0% packing files [29]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:05:05