{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wed Apr 6 11:53:38 PDT 2016\r\n" ] } ], "source": [ "!date" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Software:\n", "\n", " System Software Overview:\n", "\n", " System Version: OS X 10.9.5 (13F34)\n", " Kernel Version: Darwin 13.4.0\n", " Boot Volume: Hummingbird\n", " Boot Mode: Normal\n", " Computer Name: hummingbird\n", " User Name: Sam (Sam)\n", " Secure Virtual Memory: Enabled\n", " Time since boot: 137 days 20:44\n", "\n" ] } ], "source": [ "%%bash\n", "system_profiler SPSoftwareDataType" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "--2016-04-06 11:55:33-- http://catchenlab.life.illinois.edu/stacks/source/stacks-1.37.tar.gz\n", "Resolving catchenlab.life.illinois.edu... 130.126.48.94\n", "Connecting to catchenlab.life.illinois.edu|130.126.48.94|:80... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 504569 (493K) [application/x-gzip]\n", "Saving to: 'stacks-1.37.tar.gz'\n", "\n", " 0K .......... .......... .......... .......... .......... 10% 508K 1s\n", " 50K .......... .......... .......... .......... .......... 20% 1018K 1s\n", " 100K .......... .......... .......... .......... .......... 30% 28.5M 0s\n", " 150K .......... .......... .......... .......... .......... 40% 43.0M 0s\n", " 200K .......... .......... .......... .......... .......... 50% 1.01M 0s\n", " 250K .......... .......... .......... .......... .......... 60% 18.9M 0s\n", " 300K .......... .......... .......... .......... .......... 71% 1.06M 0s\n", " 350K .......... .......... .......... .......... .......... 81% 4.78M 0s\n", " 400K .......... .......... .......... .......... .......... 91% 41.6M 0s\n", " 450K .......... .......... .......... .......... .. 100% 1.08M=0.3s\n", "\n", "2016-04-06 11:55:35 (1.62 MB/s) - 'stacks-1.37.tar.gz' saved [504569/504569]\n", "\n" ] } ], "source": [ "%%bash\n", "wget http://catchenlab.life.illinois.edu/stacks/source/stacks-1.37.tar.gz" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "cp: /usr/local/bioinformatics/stacks-1.37.tar.gz: Permission denied\r\n" ] } ], "source": [ "cp stacks-1.37.tar.gz /usr/local/bioinformatics/" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[35m/usr/local/bioinformatics/stacks\u001b[m\u001b[m@ /usr/local/bioinformatics/stacks-1.37.tar.gz\r\n", "\r\n", "/usr/local/bioinformatics/stacks-1.13:\r\n", "\u001b[34mbin\u001b[m\u001b[m/ \u001b[34mshare\u001b[m\u001b[m/\r\n" ] } ], "source": [ "ls /usr/local/bioinformatics/stacks*" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "ename": "NameError", "evalue": "name 'tar' is not defined", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mtar\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0mzxvf\u001b[0m \u001b[0;34m/\u001b[0m\u001b[0musr\u001b[0m\u001b[0;34m/\u001b[0m\u001b[0mlocal\u001b[0m\u001b[0;34m/\u001b[0m\u001b[0mbioinformatics\u001b[0m\u001b[0;34m/\u001b[0m\u001b[0mstacks\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1.37\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtar\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgz\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", "\u001b[0;31mNameError\u001b[0m: name 'tar' is not defined" ] } ], "source": [ "tar -zxvf /usr/local/bioinformatics/stacks-1.37.tar.gz" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "x stacks-1.37/\n", "x stacks-1.37/acinclude.m4\n", "x stacks-1.37/aclocal.m4\n", "x stacks-1.37/autogen.sh\n", "x stacks-1.37/ChangeLog\n", "x stacks-1.37/config/\n", "x stacks-1.37/config.h.in\n", "x stacks-1.37/configure\n", "x stacks-1.37/configure.ac\n", "x stacks-1.37/INSTALL\n", "x stacks-1.37/LICENSE\n", "x stacks-1.37/Makefile.am\n", "x stacks-1.37/Makefile.in\n", "x stacks-1.37/php/\n", "x stacks-1.37/README\n", "x stacks-1.37/scripts/\n", "x stacks-1.37/sql/\n", "x stacks-1.37/src/\n", "x stacks-1.37/tests/\n", "x stacks-1.37/tests/kmer_filter.t\n", "x stacks-1.37/tests/process_radtags.t\n", "x stacks-1.37/tests/pstacks.t\n", "x stacks-1.37/tests/ustacks.t\n", "x stacks-1.37/src/BamI.h\n", "x stacks-1.37/src/BamUnalignedI.h\n", "x stacks-1.37/src/bootstrap.h\n", "x stacks-1.37/src/BowtieI.h\n", "x stacks-1.37/src/BustardI.h\n", "x stacks-1.37/src/catalog_utils.cc\n", "x stacks-1.37/src/catalog_utils.h\n", "x stacks-1.37/src/clean.cc\n", "x stacks-1.37/src/clean.h\n", "x stacks-1.37/src/clone_filter.cc\n", "x stacks-1.37/src/clone_filter.h\n", "x stacks-1.37/src/cmb.cc\n", "x stacks-1.37/src/cmb.h\n", "x stacks-1.37/src/constants.h\n", "x stacks-1.37/src/cstacks.cc\n", "x stacks-1.37/src/cstacks.h\n", "x stacks-1.37/src/DNANSeq.cc\n", "x stacks-1.37/src/DNANSeq.h\n", "x stacks-1.37/src/DNASeq.cc\n", "x stacks-1.37/src/DNASeq.h\n", "x stacks-1.37/src/estacks.cc\n", "x stacks-1.37/src/estacks.h\n", "x stacks-1.37/src/FastaI.h\n", "x stacks-1.37/src/FastqI.h\n", "x stacks-1.37/src/file_io.cc\n", "x stacks-1.37/src/file_io.h\n", "x stacks-1.37/src/genotype_dictionaries.h\n", "x stacks-1.37/src/genotypes.cc\n", "x stacks-1.37/src/genotypes.h\n", "x stacks-1.37/src/gzFasta.h\n", "x stacks-1.37/src/gzFastq.h\n", "x stacks-1.37/src/hstacks.cc\n", "x stacks-1.37/src/hstacks.h\n", "x stacks-1.37/src/input.cc\n", "x stacks-1.37/src/input.h\n", "x stacks-1.37/src/kmer_filter.cc\n", "x stacks-1.37/src/kmer_filter.h\n", "x stacks-1.37/src/kmers.cc\n", "x stacks-1.37/src/kmers.h\n", "x stacks-1.37/src/locus.cc\n", "x stacks-1.37/src/locus.h\n", "x stacks-1.37/src/log_utils.cc\n", "x stacks-1.37/src/log_utils.h\n", "x stacks-1.37/src/models.cc\n", "x stacks-1.37/src/models.h\n", "x stacks-1.37/src/mst.cc\n", "x stacks-1.37/src/mst.h\n", "x stacks-1.37/src/mstack.cc\n", "x stacks-1.37/src/mstack.h\n", "x stacks-1.37/src/ordered.h\n", "x stacks-1.37/src/phasedstacks.cc\n", "x stacks-1.37/src/phasedstacks.h\n", "x stacks-1.37/src/PopMap.h\n", "x stacks-1.37/src/PopSum.h\n", "x stacks-1.37/src/populations.cc\n", "x stacks-1.37/src/populations.h\n", "x stacks-1.37/src/process_radtags.cc\n", "x stacks-1.37/src/process_radtags.h\n", "x stacks-1.37/src/process_shortreads.cc\n", "x stacks-1.37/src/process_shortreads.h\n", "x stacks-1.37/src/pstacks.cc\n", "x stacks-1.37/src/pstacks.h\n", "x stacks-1.37/src/renz.h\n", "x stacks-1.37/src/rxstacks.cc\n", "x stacks-1.37/src/rxstacks.h\n", "x stacks-1.37/src/SamI.h\n", "x stacks-1.37/src/smoothing.h\n", "x stacks-1.37/src/smoothing_utils.h\n", "x stacks-1.37/src/sql_utilities.h\n", "x stacks-1.37/src/sstacks.cc\n", "x stacks-1.37/src/sstacks.h\n", "x stacks-1.37/src/stacks.cc\n", "x stacks-1.37/src/stacks.h\n", "x stacks-1.37/src/Tsv.h\n", "x stacks-1.37/src/ustacks.cc\n", "x stacks-1.37/src/ustacks.h\n", "x stacks-1.37/src/utils.cc\n", "x stacks-1.37/src/utils.h\n", "x stacks-1.37/src/write.cc\n", "x stacks-1.37/src/write.h\n", "x stacks-1.37/sql/catalog_index.sql\n", "x stacks-1.37/sql/chr_index.sql\n", "x stacks-1.37/sql/mysql.cnf.dist\n", "x stacks-1.37/sql/stacks.sql\n", "x stacks-1.37/sql/tag_index.sql\n", "x stacks-1.37/scripts/convert_stacks.pl\n", "x stacks-1.37/scripts/denovo_map.pl\n", "x stacks-1.37/scripts/exec_velvet.pl\n", "x stacks-1.37/scripts/export_sql.pl\n", "x stacks-1.37/scripts/extract_interpop_chars.pl\n", "x stacks-1.37/scripts/index_radtags.pl\n", "x stacks-1.37/scripts/load_radtags.pl\n", "x stacks-1.37/scripts/load_sequences.pl\n", "x stacks-1.37/scripts/ref_map.pl\n", "x stacks-1.37/scripts/sort_read_pairs.pl\n", "x stacks-1.37/scripts/stacks_export_notify.pl\n", "x stacks-1.37/php/ajax.js\n", "x stacks-1.37/php/annotate.js\n", "x stacks-1.37/php/annotate_marker.php\n", "x stacks-1.37/php/catalog.php\n", "x stacks-1.37/php/catalog_genotypes.php\n", "x stacks-1.37/php/CatalogClass.php\n", "x stacks-1.37/php/constants.php.dist\n", "x stacks-1.37/php/correct_genotype.php\n", "x stacks-1.37/php/correct_genotypes.php\n", "x stacks-1.37/php/db_functions.php\n", "x stacks-1.37/php/export.js\n", "x stacks-1.37/php/export_batch.php\n", "x stacks-1.37/php/fst_view.php\n", "x stacks-1.37/php/hapstat_view.php\n", "x stacks-1.37/php/header.php\n", "x stacks-1.37/php/images/\n", "x stacks-1.37/php/index.php\n", "x stacks-1.37/php/last_modified.php\n", "x stacks-1.37/php/Locus.php\n", "x stacks-1.37/php/phist_view.php\n", "x stacks-1.37/php/pop_view.php\n", "x stacks-1.37/php/population_view.js\n", "x stacks-1.37/php/samples.php\n", "x stacks-1.37/php/sequence_blast.php\n", "x stacks-1.37/php/stack_view.php\n", "x stacks-1.37/php/stacks.css\n", "x stacks-1.37/php/stacks.js\n", "x stacks-1.37/php/stacks_functions.php\n", "x stacks-1.37/php/sumstat_view.php\n", "x stacks-1.37/php/tag.php\n", "x stacks-1.37/php/tags.php\n", "x stacks-1.37/php/version.php\n", "x stacks-1.37/php/view_sequence.php\n", "x stacks-1.37/php/images/caret-d.png\n", "x stacks-1.37/php/images/caret-u.png\n", "x stacks-1.37/php/images/excel_icon.png\n", "x stacks-1.37/php/images/l-arrow-disabled.png\n", "x stacks-1.37/php/images/l-arrow.png\n", "x stacks-1.37/php/images/r-arrow-disabled.png\n", "x stacks-1.37/php/images/r-arrow.png\n", "x stacks-1.37/php/images/stacks_bg.png\n", "x stacks-1.37/php/images/stacks_logo_rev_small.png\n", "x stacks-1.37/config/compile\n", "x stacks-1.37/config/depcomp\n", "x stacks-1.37/config/install-sh\n", "x stacks-1.37/config/missing\n", "x stacks-1.37/config/test-driver\n" ] } ], "source": [ "%%bash\n", "tar -zxvf /usr/local/bioinformatics/stacks-1.37.tar.gz" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "--2016-04-06 12:09:13-- https://github.com/sparsehash/sparsehash/archive/master.zip\n", "Resolving github.com... 192.30.252.120\n", "Connecting to github.com|192.30.252.120|:443... connected.\n", "HTTP request sent, awaiting response... 302 Found\n", "Location: https://codeload.github.com/sparsehash/sparsehash/zip/master [following]\n", "--2016-04-06 12:09:13-- https://codeload.github.com/sparsehash/sparsehash/zip/master\n", "Resolving codeload.github.com... 192.30.252.161\n", "Connecting to codeload.github.com|192.30.252.161|:443... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [application/zip]\n", "Saving to: 'master.zip'\n", "\n", " 0K .......... .......... .......... .......... .......... 327K\n", " 50K .......... .......... .......... .......... .......... 655K\n", " 100K .......... .......... .......... .......... .......... 26.1M\n", " 150K .......... .......... .......... .......... .......... 26.7M\n", " 200K .......... .......... .......... .......... .......... 671K\n", " 250K .......... .......... .......... .......... .......... 28.8M\n", " 300K .......... .......... .......... .......... .......... 677K\n", " 350K .......... .......... .......... ....... 31.8M=0.4s\n", "\n", "2016-04-06 12:09:14 (1009 KB/s) - 'master.zip' saved [397003]\n", "\n" ] } ], "source": [ "%%bash\n", "wget https://github.com/sparsehash/sparsehash/archive/master.zip" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Archive: master.zip\n", "4a36398d442cc86f47d2d7e751596cc2430ad135\n", " creating: sparsehash-master/\n", " inflating: sparsehash-master/.gitignore \n", " inflating: sparsehash-master/AUTHORS \n", " inflating: sparsehash-master/COPYING \n", " inflating: sparsehash-master/ChangeLog \n", " inflating: sparsehash-master/INSTALL \n", " inflating: sparsehash-master/Makefile.am \n", " inflating: sparsehash-master/Makefile.in \n", " inflating: sparsehash-master/NEWS \n", " inflating: sparsehash-master/README \n", " inflating: sparsehash-master/README_windows.txt \n", " inflating: sparsehash-master/TODO \n", " inflating: sparsehash-master/aclocal.m4 \n", " inflating: sparsehash-master/autogen.sh \n", " inflating: sparsehash-master/config.guess \n", " inflating: sparsehash-master/config.sub \n", " inflating: sparsehash-master/configure \n", " inflating: sparsehash-master/configure.ac \n", " inflating: sparsehash-master/depcomp \n", " creating: sparsehash-master/doc/\n", " inflating: sparsehash-master/doc/dense_hash_map.html \n", " inflating: sparsehash-master/doc/dense_hash_set.html \n", " inflating: sparsehash-master/doc/designstyle.css \n", " inflating: sparsehash-master/doc/implementation.html \n", " inflating: sparsehash-master/doc/index.html \n", " inflating: sparsehash-master/doc/performance.html \n", " inflating: sparsehash-master/doc/sparse_hash_map.html \n", " inflating: sparsehash-master/doc/sparse_hash_set.html \n", " inflating: sparsehash-master/doc/sparsetable.html \n", " creating: sparsehash-master/experimental/\n", " inflating: sparsehash-master/experimental/Makefile \n", " inflating: sparsehash-master/experimental/README \n", " inflating: sparsehash-master/experimental/example.c \n", " inflating: sparsehash-master/experimental/libchash.c \n", " inflating: sparsehash-master/experimental/libchash.h \n", " inflating: sparsehash-master/google-sparsehash.sln \n", " inflating: sparsehash-master/install-sh \n", " creating: sparsehash-master/m4/\n", " inflating: sparsehash-master/m4/acx_pthread.m4 \n", " inflating: sparsehash-master/m4/google_namespace.m4 \n", " inflating: sparsehash-master/m4/namespaces.m4 \n", " inflating: sparsehash-master/m4/stl_hash.m4 \n", " inflating: sparsehash-master/m4/stl_hash_fun.m4 \n", " inflating: sparsehash-master/missing \n", " creating: sparsehash-master/packages/\n", " inflating: sparsehash-master/packages/deb.sh \n", " creating: sparsehash-master/packages/deb/\n", " inflating: sparsehash-master/packages/deb/README \n", " inflating: sparsehash-master/packages/deb/changelog \n", " extracting: sparsehash-master/packages/deb/compat \n", " inflating: sparsehash-master/packages/deb/control \n", " inflating: sparsehash-master/packages/deb/copyright \n", " inflating: sparsehash-master/packages/deb/docs \n", " inflating: sparsehash-master/packages/deb/rules \n", " inflating: sparsehash-master/packages/deb/sparsehash.dirs \n", " inflating: sparsehash-master/packages/deb/sparsehash.install \n", " inflating: sparsehash-master/packages/rpm.sh \n", " creating: sparsehash-master/packages/rpm/\n", " inflating: sparsehash-master/packages/rpm/rpm.spec \n", " inflating: sparsehash-master/sparsehash.sln \n", " creating: sparsehash-master/src/\n", " inflating: sparsehash-master/src/config.h.in \n", " inflating: sparsehash-master/src/config.h.include \n", " creating: sparsehash-master/src/google/\n", " inflating: sparsehash-master/src/google/dense_hash_map \n", " inflating: sparsehash-master/src/google/dense_hash_set \n", " inflating: sparsehash-master/src/google/sparse_hash_map \n", " inflating: sparsehash-master/src/google/sparse_hash_set \n", " creating: sparsehash-master/src/google/sparsehash/\n", " inflating: sparsehash-master/src/google/sparsehash/densehashtable.h \n", " inflating: sparsehash-master/src/google/sparsehash/hashtable-common.h \n", " inflating: sparsehash-master/src/google/sparsehash/libc_allocator_with_realloc.h \n", " inflating: sparsehash-master/src/google/sparsehash/sparsehashtable.h \n", " inflating: sparsehash-master/src/google/sparsetable \n", " inflating: sparsehash-master/src/google/template_util.h \n", " inflating: sparsehash-master/src/google/type_traits.h \n", " inflating: sparsehash-master/src/hash_test_interface.h \n", " inflating: sparsehash-master/src/hashtable_test.cc \n", " inflating: sparsehash-master/src/libc_allocator_with_realloc_test.cc \n", " inflating: sparsehash-master/src/simple_compat_test.cc \n", " inflating: sparsehash-master/src/simple_test.cc \n", " creating: sparsehash-master/src/sparsehash/\n", " inflating: sparsehash-master/src/sparsehash/dense_hash_map \n", " inflating: sparsehash-master/src/sparsehash/dense_hash_set \n", " creating: sparsehash-master/src/sparsehash/internal/\n", " inflating: sparsehash-master/src/sparsehash/internal/densehashtable.h \n", " inflating: sparsehash-master/src/sparsehash/internal/hashtable-common.h \n", " inflating: sparsehash-master/src/sparsehash/internal/libc_allocator_with_realloc.h \n", " inflating: sparsehash-master/src/sparsehash/internal/sparsehashtable.h \n", " inflating: sparsehash-master/src/sparsehash/sparse_hash_map \n", " inflating: sparsehash-master/src/sparsehash/sparse_hash_set \n", " inflating: sparsehash-master/src/sparsehash/sparsetable \n", " inflating: sparsehash-master/src/sparsehash/template_util.h \n", " inflating: sparsehash-master/src/sparsehash/type_traits.h \n", " inflating: sparsehash-master/src/sparsetable_unittest.cc \n", " inflating: sparsehash-master/src/template_util_unittest.cc \n", " inflating: sparsehash-master/src/testutil.h \n", " inflating: sparsehash-master/src/time_hash_map.cc \n", " inflating: sparsehash-master/src/type_traits_unittest.cc \n", " creating: sparsehash-master/src/windows/\n", " inflating: sparsehash-master/src/windows/config.h \n", " creating: sparsehash-master/src/windows/google/\n", " creating: sparsehash-master/src/windows/google/sparsehash/\n", " inflating: sparsehash-master/src/windows/google/sparsehash/sparseconfig.h \n", " inflating: sparsehash-master/src/windows/port.cc \n", " inflating: sparsehash-master/src/windows/port.h \n", " creating: sparsehash-master/src/windows/sparsehash/\n", " creating: sparsehash-master/src/windows/sparsehash/internal/\n", " inflating: sparsehash-master/src/windows/sparsehash/internal/sparseconfig.h \n", " creating: sparsehash-master/vsprojects/\n", " creating: sparsehash-master/vsprojects/hashtable_test/\n", " inflating: sparsehash-master/vsprojects/hashtable_test/hashtable_test.vcproj \n", " creating: sparsehash-master/vsprojects/libc_allocator_with_realloc_test/\n", " inflating: sparsehash-master/vsprojects/libc_allocator_with_realloc_test/libc_allocator_with_realloc_test.vcproj \n", " creating: sparsehash-master/vsprojects/simple_test/\n", " inflating: sparsehash-master/vsprojects/simple_test/simple_test.vcproj \n", " creating: sparsehash-master/vsprojects/sparsetable_unittest/\n", " inflating: sparsehash-master/vsprojects/sparsetable_unittest/sparsetable_unittest.vcproj \n", " creating: sparsehash-master/vsprojects/template_util_unittest/\n", " inflating: sparsehash-master/vsprojects/template_util_unittest/template_util_unittest.vcproj \n", " creating: sparsehash-master/vsprojects/time_hash_map/\n", " inflating: sparsehash-master/vsprojects/time_hash_map/time_hash_map.vcproj \n", " creating: sparsehash-master/vsprojects/type_traits_unittest/\n", " inflating: sparsehash-master/vsprojects/type_traits_unittest/type_traits_unittest.vcproj \n" ] } ], "source": [ "%%bash\n", "unzip master.zip" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/Sam/sparsehash-master\n" ] } ], "source": [ "cd sparsehash-master/" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "checking for a BSD-compatible install... /usr/bin/install -c\n", "checking whether build environment is sane... yes\n", "checking for a thread-safe mkdir -p... ./install-sh -c -d\n", "checking for gawk... no\n", "checking for mawk... no\n", "checking for nawk... no\n", "checking for awk... awk\n", "checking whether make sets $(MAKE)... yes\n", "checking for g++... g++\n", "checking whether the C++ compiler works... yes\n", "checking for C++ compiler default output file name... a.out\n", "checking for suffix of executables... \n", "checking whether we are cross compiling... no\n", "checking for suffix of object files... o\n", "checking whether we are using the GNU C++ compiler... yes\n", "checking whether g++ accepts -g... yes\n", "checking for style of include used by make... GNU\n", "checking dependency style of g++... gcc3\n", "checking for gcc... gcc\n", "checking whether we are using the GNU C compiler... yes\n", "checking whether gcc accepts -g... yes\n", "checking for gcc option to accept ISO C89... none needed\n", "checking dependency style of gcc... gcc3\n", "checking how to run the C preprocessor... gcc -E\n", "checking for grep that handles long lines and -e... /usr/bin/grep\n", "checking for egrep... /usr/bin/grep -E\n", "checking for ANSI C header files... yes\n", "checking for memcpy... yes\n", "checking for memmove... yes\n", "checking for sys/types.h... yes\n", "checking for sys/stat.h... yes\n", "checking for stdlib.h... yes\n", "checking for string.h... yes\n", "checking for memory.h... yes\n", "checking for strings.h... yes\n", "checking for inttypes.h... yes\n", "checking for stdint.h... yes\n", "checking for unistd.h... yes\n", "checking for uint16_t... yes\n", "checking for u_int16_t... yes\n", "checking for __uint16... no\n", "checking for long long... yes\n", "checking sys/resource.h usability... yes\n", "checking sys/resource.h presence... yes\n", "checking for sys/resource.h... yes\n", "checking for unistd.h... (cached) yes\n", "checking sys/time.h usability... yes\n", "checking sys/time.h presence... yes\n", "checking for sys/time.h... yes\n", "checking sys/utsname.h usability... yes\n", "checking sys/utsname.h presence... yes\n", "checking for sys/utsname.h... yes\n", "checking how to run the C++ preprocessor... g++ -E\n", "checking google/malloc_extension.h usability... no\n", "checking google/malloc_extension.h presence... no\n", "checking for google/malloc_extension.h... no\n", "checking whether the compiler implements namespaces... yes\n", "checking the location of hash_map... \n", "checking how to include hash_fun directly... \n", "configure: creating ./config.status\n", "config.status: creating Makefile\n", "config.status: creating src/config.h\n", "config.status: executing depfiles commands\n" ] } ], "source": [ "%%bash\n", "./configure" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[ -d src/sparsehash/internal ] || mkdir -p src/sparsehash/internal\n", "echo \"/*\" > src/sparsehash/internal/_sparsehash_config\n", "echo \" * NOTE: This file is for internal use only.\" >> src/sparsehash/internal/_sparsehash_config\n", "echo \" * Do not use these #defines in your own program!\" >> src/sparsehash/internal/_sparsehash_config\n", "echo \" */\" >> src/sparsehash/internal/_sparsehash_config\n", "awk '{prevline=currline; currline=$0;} \\\n", "\t /^#/ {in_second_file = 1;} \\\n", "\t !in_second_file {if (currline !~ /^ *$/) {inc[currline]=0}}; \\\n", "\t \tin_second_file { for (i in inc) { \\\n", "\t \t if (index(currline, i) != 0) { \\\n", "\t \t print \"\\n\"prevline\"\\n\"currline; \\\n", "\t \t delete inc[i]; \\\n", "\t \t } \\\n", "\t \t } }' \\\n", "\t./src/config.h.include ./src/config.h \\\n", "\t>> src/sparsehash/internal/_sparsehash_config\n", "mv -f src/sparsehash/internal/_sparsehash_config src/sparsehash/internal/sparseconfig.h\n", "/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am\n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT template_util_unittest.o -MD -MP -MF .deps/template_util_unittest.Tpo -c -o template_util_unittest.o `test -f 'src/template_util_unittest.cc' || echo './'`src/template_util_unittest.cc\n", "mv -f .deps/template_util_unittest.Tpo .deps/template_util_unittest.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o template_util_unittest template_util_unittest.o \n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT type_traits_unittest.o -MD -MP -MF .deps/type_traits_unittest.Tpo -c -o type_traits_unittest.o `test -f 'src/type_traits_unittest.cc' || echo './'`src/type_traits_unittest.cc\n", "mv -f .deps/type_traits_unittest.Tpo .deps/type_traits_unittest.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o type_traits_unittest type_traits_unittest.o \n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT libc_allocator_with_realloc_test.o -MD -MP -MF .deps/libc_allocator_with_realloc_test.Tpo -c -o libc_allocator_with_realloc_test.o `test -f 'src/libc_allocator_with_realloc_test.cc' || echo './'`src/libc_allocator_with_realloc_test.cc\n", "mv -f .deps/libc_allocator_with_realloc_test.Tpo .deps/libc_allocator_with_realloc_test.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o libc_allocator_with_realloc_test libc_allocator_with_realloc_test.o \n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT sparsetable_unittest.o -MD -MP -MF .deps/sparsetable_unittest.Tpo -c -o sparsetable_unittest.o `test -f 'src/sparsetable_unittest.cc' || echo './'`src/sparsetable_unittest.cc\n", "mv -f .deps/sparsetable_unittest.Tpo .deps/sparsetable_unittest.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o sparsetable_unittest sparsetable_unittest.o \n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT hashtable_test.o -MD -MP -MF .deps/hashtable_test.Tpo -c -o hashtable_test.o `test -f 'src/hashtable_test.cc' || echo './'`src/hashtable_test.cc\n", "mv -f .deps/hashtable_test.Tpo .deps/hashtable_test.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o hashtable_test hashtable_test.o \n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT simple_test.o -MD -MP -MF .deps/simple_test.Tpo -c -o simple_test.o `test -f 'src/simple_test.cc' || echo './'`src/simple_test.cc\n", "mv -f .deps/simple_test.Tpo .deps/simple_test.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o simple_test simple_test.o \n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT simple_compat_test.o -MD -MP -MF .deps/simple_compat_test.Tpo -c -o simple_compat_test.o `test -f 'src/simple_compat_test.cc' || echo './'`src/simple_compat_test.cc\n", "mv -f .deps/simple_compat_test.Tpo .deps/simple_compat_test.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o simple_compat_test simple_compat_test.o \n", "g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -MT time_hash_map-time_hash_map.o -MD -MP -MF .deps/time_hash_map-time_hash_map.Tpo -c -o time_hash_map-time_hash_map.o `test -f 'src/time_hash_map.cc' || echo './'`src/time_hash_map.cc\n", "mv -f .deps/time_hash_map-time_hash_map.Tpo .deps/time_hash_map-time_hash_map.Po\n", "g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o time_hash_map time_hash_map-time_hash_map.o \n", "echo 'prefix=/usr/local' > \"libsparsehash.pc\".tmp\n", "echo 'exec_prefix='`echo '/usr/local' | sed 's@^/usr/local@${prefix}@'` >> \"libsparsehash.pc\".tmp\n", "echo 'libdir='`echo '/usr/local/lib' | sed 's@^/usr/local@${exec_prefix}@'` >> \"libsparsehash.pc\".tmp\n", "echo 'includedir='`echo '/usr/local/include' | sed 's@^/usr/local@${prefix}@'` >> \"libsparsehash.pc\".tmp\n", "echo '' >> \"libsparsehash.pc\".tmp\n", "echo 'Name: sparsehash' >> \"libsparsehash.pc\".tmp\n", "echo 'Version: 2.0.2' >> \"libsparsehash.pc\".tmp\n", "grep '^Summary:' ./packages/rpm/rpm.spec | sed s/^Summary:/Description:/ | head -n1 >> \"libsparsehash.pc\".tmp\n", "grep '^URL: ' ./packages/rpm/rpm.spec >> \"libsparsehash.pc\".tmp\n", "echo 'Requires:' >> \"libsparsehash.pc\".tmp\n", "echo 'Libs:' >> \"libsparsehash.pc\".tmp\n", "echo 'Cflags: -I${includedir}' >> \"libsparsehash.pc\".tmp\n", "mv -f \"libsparsehash.pc\".tmp \"libsparsehash.pc\"\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "src/type_traits_unittest.cc:88:7: warning: private field 'n_' is not used [-Wunused-private-field]\n", " int n_;\n", " ^\n", "src/type_traits_unittest.cc:98:7: warning: private field 'n_' is not used [-Wunused-private-field]\n", " int n_;\n", " ^\n", "src/type_traits_unittest.cc:112:7: warning: private field 'n_' is not used [-Wunused-private-field]\n", " int n_;\n", " ^\n", "src/type_traits_unittest.cc:138:7: warning: private field 'n_' is not used [-Wunused-private-field]\n", " int n_;\n", " ^\n", "4 warnings generated.\n", "src/hashtable_test.cc:520:1: warning: unused variable 'HashtableCharStarTest_numtypes' [-Wunused-const-variable]\n", "TYPED_TEST_CASE_6(HashtableCharStarTest, CharStarHashtables);\n", "^\n", "./src/testutil.h:106:20: note: expanded from macro 'TYPED_TEST_CASE_6'\n", " static const int classname##_numtypes = 6; \\\n", " ^\n", ":67:1: note: expanded from here\n", "HashtableCharStarTest_numtypes\n", "^\n", "1 warning generated.\n" ] } ], "source": [ "%%bash\n", "make" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Applications/Xcode.app/Contents/Developer/usr/bin/make install-am\n", "test -z \"/usr/local/lib\" || ./install-sh -c -d \"/usr/local/lib\"\n", "test -z \"/usr/local/share/doc/sparsehash-2.0.2\" || ./install-sh -c -d \"/usr/local/share/doc/sparsehash-2.0.2\"\n", " /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog INSTALL NEWS README README_windows.txt TODO doc/dense_hash_map.html doc/dense_hash_set.html doc/sparse_hash_map.html doc/sparse_hash_set.html doc/sparsetable.html doc/implementation.html doc/performance.html doc/index.html doc/designstyle.css '/usr/local/share/doc/sparsehash-2.0.2'\n", "test -z \"/usr/local/include/google\" || ./install-sh -c -d \"/usr/local/include/google\"\n", " /usr/bin/install -c -m 644 src/google/dense_hash_map src/google/dense_hash_set src/google/sparse_hash_map src/google/sparse_hash_set src/google/sparsetable src/google/template_util.h src/google/type_traits.h '/usr/local/include/google'\n", "test -z \"/usr/local/include/google/sparsehash\" || ./install-sh -c -d \"/usr/local/include/google/sparsehash\"\n", " /usr/bin/install -c -m 644 src/google/sparsehash/densehashtable.h src/google/sparsehash/sparsehashtable.h src/google/sparsehash/hashtable-common.h src/google/sparsehash/libc_allocator_with_realloc.h '/usr/local/include/google/sparsehash'\n", "test -z \"/usr/local/include/sparsehash/internal\" || ./install-sh -c -d \"/usr/local/include/sparsehash/internal\"\n", " /usr/bin/install -c -m 644 src/sparsehash/internal/densehashtable.h src/sparsehash/internal/sparsehashtable.h src/sparsehash/internal/hashtable-common.h src/sparsehash/internal/libc_allocator_with_realloc.h '/usr/local/include/sparsehash/internal'\n", "test -z \"/usr/local/include/sparsehash/internal\" || ./install-sh -c -d \"/usr/local/include/sparsehash/internal\"\n", " /usr/bin/install -c -m 644 src/sparsehash/internal/sparseconfig.h '/usr/local/include/sparsehash/internal'\n", "test -z \"/usr/local/lib/pkgconfig\" || ./install-sh -c -d \"/usr/local/lib/pkgconfig\"\n", " /usr/bin/install -c -m 644 libsparsehash.pc '/usr/local/lib/pkgconfig'\n", "test -z \"/usr/local/include/sparsehash\" || ./install-sh -c -d \"/usr/local/include/sparsehash\"\n", " /usr/bin/install -c -m 644 src/sparsehash/dense_hash_map src/sparsehash/dense_hash_set src/sparsehash/sparse_hash_map src/sparsehash/sparse_hash_set src/sparsehash/sparsetable src/sparsehash/template_util.h src/sparsehash/type_traits.h '/usr/local/include/sparsehash'\n" ] } ], "source": [ "%%bash\n", "make install" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bioinformatics\n" ] } ], "source": [ "cd /usr/local/bioinformatics/" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "x stacks-1.37/: Can't create 'stacks-1.37'\n", "x stacks-1.37/acinclude.m4: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/acinclude.m4'\n", "x stacks-1.37/aclocal.m4: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/aclocal.m4'\n", "x stacks-1.37/autogen.sh: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/autogen.sh'\n", "x stacks-1.37/ChangeLog: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/ChangeLog'\n", "x stacks-1.37/config/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config'\n", "x stacks-1.37/config.h.in: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config.h.in'\n", "x stacks-1.37/configure: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/configure'\n", "x stacks-1.37/configure.ac: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/configure.ac'\n", "x stacks-1.37/INSTALL: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/INSTALL'\n", "x stacks-1.37/LICENSE: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/LICENSE'\n", "x stacks-1.37/Makefile.am: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/Makefile.am'\n", "x stacks-1.37/Makefile.in: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/Makefile.in'\n", "x stacks-1.37/php/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php'\n", "x stacks-1.37/README: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/README'\n", "x stacks-1.37/scripts/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts'\n", "x stacks-1.37/sql/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql'\n", "x stacks-1.37/src/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src'\n", "x stacks-1.37/tests/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests'\n", "x stacks-1.37/tests/kmer_filter.t: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests/kmer_filter.t'\n", "x stacks-1.37/tests/process_radtags.t: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests/process_radtags.t'\n", "x stacks-1.37/tests/pstacks.t: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests/pstacks.t'\n", "x stacks-1.37/tests/ustacks.t: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests/ustacks.t'\n", "x stacks-1.37/src/BamI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BamI.h'\n", "x stacks-1.37/src/BamUnalignedI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BamUnalignedI.h'\n", "x stacks-1.37/src/bootstrap.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/bootstrap.h'\n", "x stacks-1.37/src/BowtieI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BowtieI.h'\n", "x stacks-1.37/src/BustardI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BustardI.h'\n", "x stacks-1.37/src/catalog_utils.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/catalog_utils.cc'\n", "x stacks-1.37/src/catalog_utils.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/catalog_utils.h'\n", "x stacks-1.37/src/clean.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/clean.cc'\n", "x stacks-1.37/src/clean.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/clean.h'\n", "x stacks-1.37/src/clone_filter.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/clone_filter.cc'\n", "x stacks-1.37/src/clone_filter.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/clone_filter.h'\n", "x stacks-1.37/src/cmb.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cmb.cc'\n", "x stacks-1.37/src/cmb.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cmb.h'\n", "x stacks-1.37/src/constants.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/constants.h'\n", "x stacks-1.37/src/cstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cstacks.cc'\n", "x stacks-1.37/src/cstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cstacks.h'\n", "x stacks-1.37/src/DNANSeq.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNANSeq.cc'\n", "x stacks-1.37/src/DNANSeq.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNANSeq.h'\n", "x stacks-1.37/src/DNASeq.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNASeq.cc'\n", "x stacks-1.37/src/DNASeq.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNASeq.h'\n", "x stacks-1.37/src/estacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/estacks.cc'\n", "x stacks-1.37/src/estacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/estacks.h'\n", "x stacks-1.37/src/FastaI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/FastaI.h'\n", "x stacks-1.37/src/FastqI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/FastqI.h'\n", "x stacks-1.37/src/file_io.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/file_io.cc'\n", "x stacks-1.37/src/file_io.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/file_io.h'\n", "x stacks-1.37/src/genotype_dictionaries.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/genotype_dictionaries.h'\n", "x stacks-1.37/src/genotypes.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/genotypes.cc'\n", "x stacks-1.37/src/genotypes.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/genotypes.h'\n", "x stacks-1.37/src/gzFasta.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/gzFasta.h'\n", "x stacks-1.37/src/gzFastq.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/gzFastq.h'\n", "x stacks-1.37/src/hstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/hstacks.cc'\n", "x stacks-1.37/src/hstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/hstacks.h'\n", "x stacks-1.37/src/input.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/input.cc'\n", "x stacks-1.37/src/input.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/input.h'\n", "x stacks-1.37/src/kmer_filter.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/kmer_filter.cc'\n", "x stacks-1.37/src/kmer_filter.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/kmer_filter.h'\n", "x stacks-1.37/src/kmers.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/kmers.cc'\n", "x stacks-1.37/src/kmers.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/kmers.h'\n", "x stacks-1.37/src/locus.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/locus.cc'\n", "x stacks-1.37/src/locus.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/locus.h'\n", "x stacks-1.37/src/log_utils.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/log_utils.cc'\n", "x stacks-1.37/src/log_utils.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/log_utils.h'\n", "x stacks-1.37/src/models.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/models.cc'\n", "x stacks-1.37/src/models.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/models.h'\n", "x stacks-1.37/src/mst.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mst.cc'\n", "x stacks-1.37/src/mst.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mst.h'\n", "x stacks-1.37/src/mstack.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mstack.cc'\n", "x stacks-1.37/src/mstack.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mstack.h'\n", "x stacks-1.37/src/ordered.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/ordered.h'\n", "x stacks-1.37/src/phasedstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/phasedstacks.cc'\n", "x stacks-1.37/src/phasedstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/phasedstacks.h'\n", "x stacks-1.37/src/PopMap.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/PopMap.h'\n", "x stacks-1.37/src/PopSum.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/PopSum.h'\n", "x stacks-1.37/src/populations.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/populations.cc'\n", "x stacks-1.37/src/populations.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/populations.h'\n", "x stacks-1.37/src/process_radtags.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/process_radtags.cc'\n", "x stacks-1.37/src/process_radtags.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/process_radtags.h'\n", "x stacks-1.37/src/process_shortreads.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/process_shortreads.cc'\n", "x stacks-1.37/src/process_shortreads.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/process_shortreads.h'\n", "x stacks-1.37/src/pstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/pstacks.cc'\n", "x stacks-1.37/src/pstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/pstacks.h'\n", "x stacks-1.37/src/renz.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/renz.h'\n", "x stacks-1.37/src/rxstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/rxstacks.cc'\n", "x stacks-1.37/src/rxstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/rxstacks.h'\n", "x stacks-1.37/src/SamI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/SamI.h'\n", "x stacks-1.37/src/smoothing.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/smoothing.h'\n", "x stacks-1.37/src/smoothing_utils.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/smoothing_utils.h'\n", "x stacks-1.37/src/sql_utilities.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/sql_utilities.h'\n", "x stacks-1.37/src/sstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/sstacks.cc'\n", "x stacks-1.37/src/sstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/sstacks.h'\n", "x stacks-1.37/src/stacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/stacks.cc'\n", "x stacks-1.37/src/stacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/stacks.h'\n", "x stacks-1.37/src/Tsv.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/Tsv.h'\n", "x stacks-1.37/src/ustacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/ustacks.cc'\n", "x stacks-1.37/src/ustacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/ustacks.h'\n", "x stacks-1.37/src/utils.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/utils.cc'\n", "x stacks-1.37/src/utils.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/utils.h'\n", "x stacks-1.37/src/write.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/write.cc'\n", "x stacks-1.37/src/write.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/write.h'\n", "x stacks-1.37/sql/catalog_index.sql: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql/catalog_index.sql'\n", "x stacks-1.37/sql/chr_index.sql: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql/chr_index.sql'\n", "x stacks-1.37/sql/mysql.cnf.dist: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql/mysql.cnf.dist'\n", "x stacks-1.37/sql/stacks.sql: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql/stacks.sql'\n", "x stacks-1.37/sql/tag_index.sql: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql/tag_index.sql'\n", "x stacks-1.37/scripts/convert_stacks.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/convert_stacks.pl'\n", "x stacks-1.37/scripts/denovo_map.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/denovo_map.pl'\n", "x stacks-1.37/scripts/exec_velvet.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/exec_velvet.pl'\n", "x stacks-1.37/scripts/export_sql.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/export_sql.pl'\n", "x stacks-1.37/scripts/extract_interpop_chars.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/extract_interpop_chars.pl'\n", "x stacks-1.37/scripts/index_radtags.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/index_radtags.pl'\n", "x stacks-1.37/scripts/load_radtags.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/load_radtags.pl'\n", "x stacks-1.37/scripts/load_sequences.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/load_sequences.pl'\n", "x stacks-1.37/scripts/ref_map.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/ref_map.pl'\n", "x stacks-1.37/scripts/sort_read_pairs.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/sort_read_pairs.pl'\n", "x stacks-1.37/scripts/stacks_export_notify.pl: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts/stacks_export_notify.pl'\n", "x stacks-1.37/php/ajax.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/ajax.js'\n", "x stacks-1.37/php/annotate.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/annotate.js'\n", "x stacks-1.37/php/annotate_marker.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/annotate_marker.php'\n", "x stacks-1.37/php/catalog.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/catalog.php'\n", "x stacks-1.37/php/catalog_genotypes.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/catalog_genotypes.php'\n", "x stacks-1.37/php/CatalogClass.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/CatalogClass.php'\n", "x stacks-1.37/php/constants.php.dist: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/constants.php.dist'\n", "x stacks-1.37/php/correct_genotype.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/correct_genotype.php'\n", "x stacks-1.37/php/correct_genotypes.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/correct_genotypes.php'\n", "x stacks-1.37/php/db_functions.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/db_functions.php'\n", "x stacks-1.37/php/export.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/export.js'\n", "x stacks-1.37/php/export_batch.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/export_batch.php'\n", "x stacks-1.37/php/fst_view.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/fst_view.php'\n", "x stacks-1.37/php/hapstat_view.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/hapstat_view.php'\n", "x stacks-1.37/php/header.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/header.php'\n", "x stacks-1.37/php/images/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images'\n", "x stacks-1.37/php/index.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/index.php'\n", "x stacks-1.37/php/last_modified.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/last_modified.php'\n", "x stacks-1.37/php/Locus.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/Locus.php'\n", "x stacks-1.37/php/phist_view.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/phist_view.php'\n", "x stacks-1.37/php/pop_view.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/pop_view.php'\n", "x stacks-1.37/php/population_view.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/population_view.js'\n", "x stacks-1.37/php/samples.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/samples.php'\n", "x stacks-1.37/php/sequence_blast.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/sequence_blast.php'\n", "x stacks-1.37/php/stack_view.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/stack_view.php'\n", "x stacks-1.37/php/stacks.css: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/stacks.css'\n", "x stacks-1.37/php/stacks.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/stacks.js'\n", "x stacks-1.37/php/stacks_functions.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/stacks_functions.php'\n", "x stacks-1.37/php/sumstat_view.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/sumstat_view.php'\n", "x stacks-1.37/php/tag.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/tag.php'\n", "x stacks-1.37/php/tags.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/tags.php'\n", "x stacks-1.37/php/version.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/version.php'\n", "x stacks-1.37/php/view_sequence.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/view_sequence.php'\n", "x stacks-1.37/php/images/caret-d.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/caret-d.png'\n", "x stacks-1.37/php/images/caret-u.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/caret-u.png'\n", "x stacks-1.37/php/images/excel_icon.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/excel_icon.png'\n", "x stacks-1.37/php/images/l-arrow-disabled.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/l-arrow-disabled.png'\n", "x stacks-1.37/php/images/l-arrow.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/l-arrow.png'\n", "x stacks-1.37/php/images/r-arrow-disabled.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/r-arrow-disabled.png'\n", "x stacks-1.37/php/images/r-arrow.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/r-arrow.png'\n", "x stacks-1.37/php/images/stacks_bg.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/stacks_bg.png'\n", "x stacks-1.37/php/images/stacks_logo_rev_small.png: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images/stacks_logo_rev_small.png'\n", "x stacks-1.37/config/compile: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/compile'\n", "x stacks-1.37/config/depcomp: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/depcomp'\n", "x stacks-1.37/config/install-sh: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/install-sh'\n", "x stacks-1.37/config/missing: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/missing'\n", "x stacks-1.37/config/test-driver: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/test-driver'\n", "tar: Error exit delayed from previous errors.\n" ] } ], "source": [ "%%bash\n", "tar -zxvf stacks-1.37.tar.gz" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[35mstacks\u001b[m\u001b[m@ stacks-1.37.tar.gz\r\n", "\r\n", "stacks-1.13:\r\n", "\u001b[34mbin\u001b[m\u001b[m/ \u001b[34mshare\u001b[m\u001b[m/\r\n", "\r\n", "stacks-1.37:\r\n", "ChangeLog LICENSE Makefile.in acinclude.m4 \u001b[31mautogen.sh\u001b[m\u001b[m* config.h.in configure.ac \u001b[34mscripts\u001b[m\u001b[m/ \u001b[34msrc\u001b[m\u001b[m/\r\n", "INSTALL Makefile.am README aclocal.m4 \u001b[34mconfig\u001b[m\u001b[m/ \u001b[31mconfigure\u001b[m\u001b[m* \u001b[34mphp\u001b[m\u001b[m/ \u001b[34msql\u001b[m\u001b[m/ \u001b[34mtests\u001b[m\u001b[m/\r\n" ] } ], "source": [ "ls stack*" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "--2016-04-06 12:19:29-- https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2\n", "Resolving sourceforge.net... 216.34.181.60\n", "Connecting to sourceforge.net|216.34.181.60|:443... connected.\n", "HTTP request sent, awaiting response... 302 Found\n", "Location: https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download [following]\n", "--2016-04-06 12:19:29-- https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download\n", "Connecting to sourceforge.net|216.34.181.60|:443... connected.\n", "HTTP request sent, awaiting response... 302 Found\n", "Location: http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2?r=&ts=1459970470&use_mirror=iweb [following]\n", "--2016-04-06 12:19:30-- http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2?r=&ts=1459970470&use_mirror=iweb\n", "Resolving downloads.sourceforge.net... 216.34.181.59\n", "Connecting to downloads.sourceforge.net|216.34.181.59|:80... connected.\n", "HTTP request sent, awaiting response... 302 Found\n", "Location: http://iweb.dl.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 [following]\n", "--2016-04-06 12:19:30-- http://iweb.dl.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2\n", "Resolving iweb.dl.sourceforge.net... 70.38.0.134, 2607:f748:10:12::5f:2\n", "Connecting to iweb.dl.sourceforge.net|70.38.0.134|:80... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 514507 (502K) [application/octet-stream]\n", "samtools-0.1.19.tar.bz2: Permission denied\n", "\n", "Cannot write to 'samtools-0.1.19.tar.bz2' (Success).\n" ] } ], "source": [ "%%bash\n", "wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/Sam/samtools-0.1.19.tar.bz2\r\n" ] } ], "source": [ "ls /Users/Sam/samtools-0.1.19.tar.bz2" ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "bunzip2 /Users/Sam/samtools-0.1.19.tar.bz2" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/Sam/samtools-0.1.19.tar\r\n" ] } ], "source": [ "ls /Users/Sam/samtools-0.1.19*" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "samtools-0.1.19/: Can't create 'samtools-0.1.19'\n", "samtools-0.1.19/.gitignore: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/.gitignore'\n", "samtools-0.1.19/AUTHORS: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/AUTHORS'\n", "samtools-0.1.19/COPYING: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/COPYING'\n", "samtools-0.1.19/ChangeLog.old: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/ChangeLog.old'\n", "samtools-0.1.19/INSTALL: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/INSTALL'\n", "samtools-0.1.19/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/Makefile'\n", "samtools-0.1.19/Makefile.mingw: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/Makefile.mingw'\n", "samtools-0.1.19/NEWS: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/NEWS'\n", "samtools-0.1.19/bam.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam.c'\n", "samtools-0.1.19/bam.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam.h'\n", "samtools-0.1.19/bam2bcf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam2bcf.c'\n", "samtools-0.1.19/bam2bcf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam2bcf.h'\n", "samtools-0.1.19/bam2bcf_indel.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam2bcf_indel.c'\n", "samtools-0.1.19/bam2depth.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam2depth.c'\n", "samtools-0.1.19/bam_aux.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_aux.c'\n", "samtools-0.1.19/bam_cat.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_cat.c'\n", "samtools-0.1.19/bam_color.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_color.c'\n", "samtools-0.1.19/bam_endian.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_endian.h'\n", "samtools-0.1.19/bam_import.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_import.c'\n", "samtools-0.1.19/bam_index.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_index.c'\n", "samtools-0.1.19/bam_lpileup.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_lpileup.c'\n", "samtools-0.1.19/bam_mate.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_mate.c'\n", "samtools-0.1.19/bam_md.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_md.c'\n", "samtools-0.1.19/bam_pileup.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_pileup.c'\n", "samtools-0.1.19/bam_plcmd.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_plcmd.c'\n", "samtools-0.1.19/bam_reheader.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_reheader.c'\n", "samtools-0.1.19/bam_rmdup.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_rmdup.c'\n", "samtools-0.1.19/bam_rmdupse.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_rmdupse.c'\n", "samtools-0.1.19/bam_sort.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_sort.c'\n", "samtools-0.1.19/bam_stat.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_stat.c'\n", "samtools-0.1.19/bam_tview.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_tview.c'\n", "samtools-0.1.19/bam_tview.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_tview.h'\n", "samtools-0.1.19/bam_tview_curses.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_tview_curses.c'\n", "samtools-0.1.19/bam_tview_html.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam_tview_html.c'\n", "samtools-0.1.19/bamshuf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bamshuf.c'\n", "samtools-0.1.19/bamtk.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bamtk.c'\n", "samtools-0.1.19/bcftools/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools'\n", "samtools-0.1.19/bcftools/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/Makefile'\n", "samtools-0.1.19/bcftools/README: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/README'\n", "samtools-0.1.19/bcftools/bcf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/bcf.c'\n", "samtools-0.1.19/bcftools/bcf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/bcf.h'\n", "samtools-0.1.19/bcftools/bcf.tex: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/bcf.tex'\n", "samtools-0.1.19/bcftools/bcf2qcall.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/bcf2qcall.c'\n", "samtools-0.1.19/bcftools/bcfutils.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/bcfutils.c'\n", "samtools-0.1.19/bcftools/call1.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/call1.c'\n", "samtools-0.1.19/bcftools/em.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/em.c'\n", "samtools-0.1.19/bcftools/fet.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/fet.c'\n", "samtools-0.1.19/bcftools/index.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/index.c'\n", "samtools-0.1.19/bcftools/kfunc.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/kfunc.c'\n", "samtools-0.1.19/bcftools/kmin.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/kmin.c'\n", "samtools-0.1.19/bcftools/kmin.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/kmin.h'\n", "samtools-0.1.19/bcftools/main.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/main.c'\n", "samtools-0.1.19/bcftools/mut.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/mut.c'\n", "samtools-0.1.19/bcftools/prob1.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/prob1.c'\n", "samtools-0.1.19/bcftools/prob1.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/prob1.h'\n", "samtools-0.1.19/bcftools/vcf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/vcf.c'\n", "samtools-0.1.19/bcftools/vcfutils.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/vcfutils.pl'\n", "samtools-0.1.19/bcftools/bcf.h~: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/bcf.h~'\n", "samtools-0.1.19/bedcov.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bedcov.c'\n", "samtools-0.1.19/bedidx.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bedidx.c'\n", "samtools-0.1.19/bgzf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bgzf.c'\n", "samtools-0.1.19/bgzf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bgzf.h'\n", "samtools-0.1.19/bgzip.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bgzip.c'\n", "samtools-0.1.19/cut_target.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/cut_target.c'\n", "samtools-0.1.19/errmod.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/errmod.c'\n", "samtools-0.1.19/errmod.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/errmod.h'\n", "samtools-0.1.19/examples/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples'\n", "samtools-0.1.19/examples/00README.txt: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/00README.txt'\n", "samtools-0.1.19/examples/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/Makefile'\n", "samtools-0.1.19/examples/bam2bed.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/bam2bed.c'\n", "samtools-0.1.19/examples/calDepth.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/calDepth.c'\n", "samtools-0.1.19/examples/chk_indel.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/chk_indel.c'\n", "samtools-0.1.19/examples/ex1.fa: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/ex1.fa'\n", "samtools-0.1.19/examples/ex1.sam.gz: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/ex1.sam.gz'\n", "samtools-0.1.19/examples/toy.fa: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/toy.fa'\n", "samtools-0.1.19/examples/toy.sam: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/toy.sam'\n", "samtools-0.1.19/faidx.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/faidx.c'\n", "samtools-0.1.19/faidx.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/faidx.h'\n", "samtools-0.1.19/kaln.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kaln.c'\n", "samtools-0.1.19/kaln.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kaln.h'\n", "samtools-0.1.19/khash.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/khash.h'\n", "samtools-0.1.19/klist.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/klist.h'\n", "samtools-0.1.19/knetfile.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/knetfile.c'\n", "samtools-0.1.19/knetfile.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/knetfile.h'\n", "samtools-0.1.19/kprobaln.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kprobaln.c'\n", "samtools-0.1.19/kprobaln.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kprobaln.h'\n", "samtools-0.1.19/kseq.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kseq.h'\n", "samtools-0.1.19/ksort.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/ksort.h'\n", "samtools-0.1.19/kstring.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kstring.c'\n", "samtools-0.1.19/kstring.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kstring.h'\n", "samtools-0.1.19/misc/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc'\n", "samtools-0.1.19/misc/HmmGlocal.java: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/HmmGlocal.java'\n", "samtools-0.1.19/misc/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/Makefile'\n", "samtools-0.1.19/misc/ace2sam.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/ace2sam.c'\n", "samtools-0.1.19/misc/bamcheck.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/bamcheck.c'\n", "samtools-0.1.19/misc/blast2sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/blast2sam.pl'\n", "samtools-0.1.19/misc/bowtie2sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/bowtie2sam.pl'\n", "samtools-0.1.19/misc/export2sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/export2sam.pl'\n", "samtools-0.1.19/misc/interpolate_sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/interpolate_sam.pl'\n", "samtools-0.1.19/misc/maq2sam.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/maq2sam.c'\n", "samtools-0.1.19/misc/md5.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/md5.c'\n", "samtools-0.1.19/misc/md5.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/md5.h'\n", "samtools-0.1.19/misc/md5fa.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/md5fa.c'\n", "samtools-0.1.19/misc/novo2sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/novo2sam.pl'\n", "samtools-0.1.19/misc/plot-bamcheck: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/plot-bamcheck'\n", "samtools-0.1.19/misc/psl2sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/psl2sam.pl'\n", "samtools-0.1.19/misc/r2plot.lua: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/r2plot.lua'\n", "samtools-0.1.19/misc/sam2vcf.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/sam2vcf.pl'\n", "samtools-0.1.19/misc/samtools.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/samtools.pl'\n", "samtools-0.1.19/misc/soap2sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/soap2sam.pl'\n", "samtools-0.1.19/misc/varfilter.py: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/varfilter.py'\n", "samtools-0.1.19/misc/vcfutils.lua: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/vcfutils.lua'\n", "samtools-0.1.19/misc/wgsim.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/wgsim.c'\n", "samtools-0.1.19/misc/wgsim_eval.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/wgsim_eval.pl'\n", "samtools-0.1.19/misc/zoom2sam.pl: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/zoom2sam.pl'\n", "samtools-0.1.19/padding.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/padding.c'\n", "samtools-0.1.19/phase.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/phase.c'\n", "samtools-0.1.19/razf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/razf.c'\n", "samtools-0.1.19/razf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/razf.h'\n", "samtools-0.1.19/razip.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/razip.c'\n", "samtools-0.1.19/sam.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sam.c'\n", "samtools-0.1.19/sam.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sam.h'\n", "samtools-0.1.19/sam_header.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sam_header.c'\n", "samtools-0.1.19/sam_header.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sam_header.h'\n", "samtools-0.1.19/sam_view.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sam_view.c'\n", "samtools-0.1.19/sample.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sample.c'\n", "samtools-0.1.19/sample.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sample.h'\n", "samtools-0.1.19/samtools.1: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/samtools.1'\n", "samtools-0.1.19/win32/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/win32'\n", "samtools-0.1.19/win32/libcurses.a: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/win32/libcurses.a'\n", "samtools-0.1.19/win32/libz.a: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/win32/libz.a'\n", "samtools-0.1.19/win32/xcurses.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/win32/xcurses.h'\n", "samtools-0.1.19/win32/zconf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/win32/zconf.h'\n", "samtools-0.1.19/win32/zlib.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/win32/zlib.h'\n", "samtools-0.1.19/bam.h~: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam.h~'\n", "tar: Error exit delayed from previous errors.\n" ] } ], "source": [ "%%bash\n", "tar -xjf /Users/Sam/samtools-0.1.19.tar" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[34mFastQC\u001b[m\u001b[m/ \u001b[34mbismark_v0.14.2\u001b[m\u001b[m/ \u001b[35mfastx_toolkit\u001b[m\u001b[m@ \u001b[35mngsplot\u001b[m\u001b[m@ \u001b[35mstacks\u001b[m\u001b[m@\r\n", "\u001b[35mTrimmomatic\u001b[m\u001b[m@ \u001b[35mbowtie\u001b[m\u001b[m@ \u001b[34mfastx_toolkit-0.0.13.2\u001b[m\u001b[m/ \u001b[34mngsplot-2.08\u001b[m\u001b[m/ \u001b[34mstacks-1.13\u001b[m\u001b[m/\r\n", "\u001b[34mTrimmomatic-0.30\u001b[m\u001b[m/ \u001b[34mbowtie-1.0.0\u001b[m\u001b[m/ \u001b[35mhmmer\u001b[m\u001b[m@ \u001b[35mrsem\u001b[m\u001b[m@ \u001b[34mstacks-1.37\u001b[m\u001b[m/\r\n", "\u001b[35mTrinotate\u001b[m\u001b[m@ \u001b[35mbowtie2\u001b[m\u001b[m@ \u001b[34mhmmer-3.1b1\u001b[m\u001b[m/ \u001b[34mrsem-1.2.10\u001b[m\u001b[m/ stacks-1.37.tar.gz\r\n", "\u001b[34mTrinotate_r20140708\u001b[m\u001b[m/ \u001b[34mbowtie2-2.1.0\u001b[m\u001b[m/ \u001b[34mlibgtextutils-0.6.1\u001b[m\u001b[m/ \u001b[34msamtools-0.1.19\u001b[m\u001b[m/ \u001b[34mtophat-2.0.13.OSX_x86_64\u001b[m\u001b[m/\r\n", "\u001b[34manaconda\u001b[m\u001b[m/ \u001b[34mcufflinks-2.2.1.OSX_x86_64\u001b[m\u001b[m/ \u001b[35mncbi-blast\u001b[m\u001b[m@ \u001b[34msignalp-4.1\u001b[m\u001b[m/ \u001b[35mtrinity\u001b[m\u001b[m@\r\n", "\u001b[34mbedtools-2.22.1\u001b[m\u001b[m/ \u001b[34mdbs\u001b[m\u001b[m/ \u001b[34mncbi-blast-2.2.29+\u001b[m\u001b[m/ source.sh \u001b[34mtrinityrnaseq_r20131110\u001b[m\u001b[m/\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[Errno 13] Permission denied: 'samtools-0.1.19/'\n", "/usr/local/bioinformatics\n" ] } ], "source": [ "cd samtools-0.1.19/" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bioinformatics/samtools-0.1.19\n" ] } ], "source": [ "cd samtools-0.1.19/" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "bash: line 1: ./configure: No such file or directory\n" ] } ], "source": [ "%%bash\n", "./configure" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "AUTHORS bam2bcf.h bam_md.c bam_tview_html.c errmod.h kprobaln.h sam.c\r\n", "COPYING bam2bcf_indel.c bam_pileup.c bamshuf.c \u001b[34mexamples\u001b[m\u001b[m/ kseq.h sam.h\r\n", "ChangeLog.old bam2depth.c bam_plcmd.c bamtk.c faidx.c ksort.h sam_header.c\r\n", "INSTALL bam_aux.c bam_reheader.c \u001b[34mbcftools\u001b[m\u001b[m/ faidx.h kstring.c sam_header.h\r\n", "Makefile bam_cat.c bam_rmdup.c bedcov.c kaln.c kstring.h sam_view.c\r\n", "Makefile.mingw bam_color.c bam_rmdupse.c bedidx.c kaln.h \u001b[34mmisc\u001b[m\u001b[m/ sample.c\r\n", "NEWS bam_endian.h bam_sort.c bgzf.c khash.h padding.c sample.h\r\n", "bam.c bam_import.c bam_stat.c bgzf.h klist.h phase.c samtools.1\r\n", "bam.h bam_index.c bam_tview.c bgzip.c knetfile.c razf.c \u001b[34mwin32\u001b[m\u001b[m/\r\n", "bam.h~ bam_lpileup.c bam_tview.h cut_target.c knetfile.h razf.h\r\n", "bam2bcf.c bam_mate.c bam_tview_curses.c errmod.c kprobaln.c razip.c\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o\n", "ar -csru 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\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o\n", "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\n", "make[2]: Nothing to be done for `lib'.\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o\n", "gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o\n", "gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread\n", "gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c\n", "gcc -g -Wall -O2 -o md5sum-lite md5sum-lite.o\n", "gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o\n", "gcc -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c\n", "gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz\n", "gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz\n", "gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz\n", "gcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c\n", "gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz\n", "gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c\n", "gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz\n", "gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c\n", "gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "bgzf.c:82:1: warning: unused function 'kh_clear_cache' [-Wunused-function]\n", "KHASH_MAP_INIT_INT64(cache, cache_t)\n", "^\n", "./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'\n", " KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":98:1: note: expanded from here\n", "kh_clear_cache\n", "^\n", "1 warning generated.\n", "bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(s, int)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":200:1: note: expanded from here\n", "kh_clear_s\n", "^\n", "bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":214:1: note: expanded from here\n", "kh_del_s\n", "^\n", "bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(r2l, str_p)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:168:23: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE kh_##name##_t *kh_init_##name() { \\\n", " ^\n", ":221:1: note: expanded from here\n", "kh_init_r2l\n", "^\n", "bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:171:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_destroy_##name(kh_##name##_t *h) \\\n", " ^\n", ":226:1: note: expanded from here\n", "kh_destroy_r2l\n", "^\n", "bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":229:1: note: expanded from here\n", "kh_clear_r2l\n", "^\n", "bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \\\n", " ^\n", ":232:1: note: expanded from here\n", "kh_get_r2l\n", "^\n", "bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:260:16: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \\\n", " ^\n", ":238:1: note: expanded from here\n", "kh_put_r2l\n", "^\n", "bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":243:1: note: expanded from here\n", "kh_del_r2l\n", "^\n", "8 warnings generated.\n", "bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(ref, uint64_t)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":200:1: note: expanded from here\n", "kh_clear_ref\n", "^\n", "bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \\\n", " ^\n", ":203:1: note: expanded from here\n", "kh_get_ref\n", "^\n", "bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":214:1: note: expanded from here\n", "kh_del_ref\n", "^\n", "3 warnings generated.\n", "bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function]\n", "KHASH_MAP_INIT_INT(i, bam_binlist_t)\n", "^\n", "./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'\n", " KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":218:1: note: expanded from here\n", "kh_clear_i\n", "^\n", "bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]\n", "./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'\n", " KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":232:1: note: expanded from here\n", "kh_del_i\n", "^\n", "2 warnings generated.\n", "faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(s, faidx1_t)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":154:1: note: expanded from here\n", "kh_clear_s\n", "^\n", "faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":168:1: note: expanded from here\n", "kh_del_s\n", "^\n", "2 warnings generated.\n", "bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(reg, bed_reglist_t)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":214:1: note: expanded from here\n", "kh_clear_reg\n", "^\n", "bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":228:1: note: expanded from here\n", "kh_del_reg\n", "^\n", "2 warnings generated.\n", "sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(str, const char *)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":154:1: note: expanded from here\n", "kh_clear_str\n", "^\n", "sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":168:1: note: expanded from here\n", "kh_del_str\n", "^\n", "2 warnings generated.\n", "vcf.c:243:15: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]\n", " endblock: i = i;\n", " ~ ^ ~\n", "vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function]\n", "KSTREAM_INIT(gzFile, gzread, 4096)\n", "^\n", "../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'\n", " __KS_GETC(__read, __bufsize) \\\n", " ^\n", "../kseq.h:67:20: note: expanded from macro '__KS_GETC'\n", " static inline int ks_getc(kstream_t *ks) \\\n", " ^\n", "2 warnings generated.\n", "bcfutils.c:7:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(str2id, int)\n", "^\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":51:1: note: expanded from here\n", "kh_clear_str2id\n", "^\n", "bcfutils.c:7:1: warning: unused function 'kh_del_str2id' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":65:1: note: expanded from here\n", "kh_del_str2id\n", "^\n", "2 warnings generated.\n", "prob1.c:13:1: warning: unused function 'ks_getc' [-Wunused-function]\n", "KSTREAM_INIT(gzFile, gzread, 16384)\n", "^\n", "../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'\n", " __KS_GETC(__read, __bufsize) \\\n", " ^\n", "../kseq.h:67:20: note: expanded from macro '__KS_GETC'\n", " static inline int ks_getc(kstream_t *ks) \\\n", " ^\n", "1 warning generated.\n", "sam_view.c:12:1: warning: unused function 'kh_clear_rg' [-Wunused-function]\n", "KHASH_SET_INIT_STR(rg)\n", "^\n", "./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":41:1: note: expanded from here\n", "kh_clear_rg\n", "^\n", "sam_view.c:12:1: warning: unused function 'kh_del_rg' [-Wunused-function]\n", "./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":55:1: note: expanded from here\n", "kh_del_rg\n", "^\n", "2 warnings generated.\n", "bam_rmdup.c:12:1: warning: unused function 'kh_get_pos' [-Wunused-function]\n", "KHASH_MAP_INIT_INT64(pos, bam1_p)\n", "^\n", "./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'\n", " KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \\\n", " ^\n", ":232:1: note: expanded from here\n", "kh_get_pos\n", "^\n", "bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function]\n", "./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'\n", " KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":243:1: note: expanded from here\n", "kh_del_pos\n", "^\n", "bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(lib, lib_aux_t)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":260:1: note: expanded from here\n", "kh_clear_lib\n", "^\n", "bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":274:1: note: expanded from here\n", "kh_del_lib\n", "^\n", "4 warnings generated.\n", "bam_rmdupse.c:18:1: warning: unused function 'kh_clear_best' [-Wunused-function]\n", "KHASH_MAP_INIT_INT(best, elem_p)\n", "^\n", "./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'\n", " KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":103:1: note: expanded from here\n", "kh_clear_best\n", "^\n", "bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function]\n", "./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'\n", " KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \\\n", " ^\n", ":106:1: note: expanded from here\n", "kh_get_best\n", "^\n", "bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(lib, lib_aux_t)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":134:1: note: expanded from here\n", "kh_clear_lib\n", "^\n", "bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":148:1: note: expanded from here\n", "kh_del_lib\n", "^\n", "4 warnings generated.\n", "bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body]\n", " for (r = p; *r && *r != '\\t' && *r != '\\n'; ++r); lp = r - p;\n", " ^\n", "bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence this warning\n", "bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body]\n", " for (r = q; *r && *r != '\\t' && *r != '\\n'; ++r); lq = r - q;\n", " ^\n", "bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence this warning\n", "bam2bcf_indel.c:9:1: warning: unused function 'kh_clear_rg' [-Wunused-function]\n", "KHASH_SET_INIT_STR(rg)\n", "^\n", "./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":200:1: note: expanded from here\n", "kh_clear_rg\n", "^\n", "bam2bcf_indel.c:9:1: warning: unused function 'kh_del_rg' [-Wunused-function]\n", "./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":214:1: note: expanded from here\n", "kh_del_rg\n", "^\n", "4 warnings generated.\n", "errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]\n", " if (m > m) return -1;\n", " ^\n", "1 warning generated.\n", "sample.c:5:1: warning: unused function 'kh_clear_sm' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(sm, int)\n", "^\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":136:1: note: expanded from here\n", "kh_clear_sm\n", "^\n", "sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function]\n", "./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":150:1: note: expanded from here\n", "kh_del_sm\n", "^\n", "2 warnings generated.\n", "phase.c:45:1: warning: unused function 'kh_clear_set64' [-Wunused-function]\n", "KHASH_SET_INIT_INT64(set64)\n", "^\n", "./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'\n", " KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":49:1: note: expanded from here\n", "kh_clear_set64\n", "^\n", "phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function]\n", "./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'\n", " KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":63:1: note: expanded from here\n", "kh_del_set64\n", "^\n", "phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function]\n", "KHASH_MAP_INIT_INT64(64, frag_t)\n", "^\n", "./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'\n", " KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)\n", " ^\n", "./khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":78:1: note: expanded from here\n", "kh_clear_64\n", "^\n", "3 warnings generated.\n", "bedcov.c:12:1: warning: unused function 'ks_getc' [-Wunused-function]\n", "KSTREAM_INIT(gzFile, gzread, 16384)\n", "^\n", "./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'\n", " __KS_GETC(__read, __bufsize) \\\n", " ^\n", "./kseq.h:67:20: note: expanded from macro '__KS_GETC'\n", " static inline int ks_getc(kstream_t *ks) \\\n", " ^\n", "1 warning generated.\n", "call1.c:17:1: warning: unused function 'ks_getc' [-Wunused-function]\n", "KSTREAM_INIT(gzFile, gzread, 16384)\n", "^\n", "../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'\n", " __KS_GETC(__read, __bufsize) \\\n", " ^\n", "../kseq.h:67:20: note: expanded from macro '__KS_GETC'\n", " static inline int ks_getc(kstream_t *ks) \\\n", " ^\n", "1 warning generated.\n", "main.c:9:1: warning: unused function 'ks_getc' [-Wunused-function]\n", "KSTREAM_INIT(gzFile, gzread, 0x10000)\n", "^\n", "../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'\n", " __KS_GETC(__read, __bufsize) \\\n", " ^\n", "../kseq.h:67:20: note: expanded from macro '__KS_GETC'\n", " static inline int ks_getc(kstream_t *ks) \\\n", " ^\n", "1 warning generated.\n", "md5.c:155:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess]\n", " memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */\n", " ~~~ ^~~\n", "md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)?\n", " memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */\n", " ^~~\n", "1 warning generated.\n", "md5.c:155:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess]\n", " memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */\n", " ~~~ ^~~\n", "md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)?\n", " memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */\n", " ^~~\n", "1 warning generated.\n", "ace2sam.c:33:1: warning: unused function 'ks_getc' [-Wunused-function]\n", "KSTREAM_INIT(gzFile, gzread, 16384)\n", "^\n", "../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'\n", " __KS_GETC(__read, __bufsize) \\\n", " ^\n", "../kseq.h:67:20: note: expanded from macro '__KS_GETC'\n", " static inline int ks_getc(kstream_t *ks) \\\n", " ^\n", "1 warning generated.\n", "bamcheck.c:52:1: warning: unused function 'kh_init_kh_faidx' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)\n", "^\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE kh_##name##_t *kh_init_##name() { \\\n", " ^\n", ":42:1: note: expanded from here\n", "kh_init_kh_faidx\n", "^\n", "bamcheck.c:52:1: warning: unused function 'kh_destroy_kh_faidx' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_destroy_##name(kh_##name##_t *h) \\\n", " ^\n", ":47:1: note: expanded from here\n", "kh_destroy_kh_faidx\n", "^\n", "bamcheck.c:52:1: warning: unused function 'kh_clear_kh_faidx' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":50:1: note: expanded from here\n", "kh_clear_kh_faidx\n", "^\n", "bamcheck.c:52:1: warning: unused function 'kh_put_kh_faidx' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \\\n", " ^\n", ":59:1: note: expanded from here\n", "kh_put_kh_faidx\n", "^\n", "bamcheck.c:52:1: warning: unused function 'kh_del_kh_faidx' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":64:1: note: expanded from here\n", "kh_del_kh_faidx\n", "^\n", "bamcheck.c:53:1: warning: unused function 'kh_init_kh_bam_tid' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(kh_bam_tid, int)\n", "^\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE kh_##name##_t *kh_init_##name() { \\\n", " ^\n", ":71:1: note: expanded from here\n", "kh_init_kh_bam_tid\n", "^\n", "bamcheck.c:53:1: warning: unused function 'kh_destroy_kh_bam_tid' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_destroy_##name(kh_##name##_t *h) \\\n", " ^\n", ":76:1: note: expanded from here\n", "kh_destroy_kh_bam_tid\n", "^\n", "bamcheck.c:53:1: warning: unused function 'kh_clear_kh_bam_tid' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":79:1: note: expanded from here\n", "kh_clear_kh_bam_tid\n", "^\n", "bamcheck.c:53:1: warning: unused function 'kh_put_kh_bam_tid' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \\\n", " ^\n", ":88:1: note: expanded from here\n", "kh_put_kh_bam_tid\n", "^\n", "bamcheck.c:53:1: warning: unused function 'kh_del_kh_bam_tid' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":93:1: note: expanded from here\n", "kh_del_kh_bam_tid\n", "^\n", "bamcheck.c:54:1: warning: unused function 'kh_clear_kh_rg' [-Wunused-function]\n", "KHASH_MAP_INIT_STR(kh_rg, const char *)\n", "^\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_clear_##name(kh_##name##_t *h) \\\n", " ^\n", ":108:1: note: expanded from here\n", "kh_clear_kh_rg\n", "^\n", "bamcheck.c:54:1: warning: unused function 'kh_del_kh_rg' [-Wunused-function]\n", "../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'\n", " KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)\n", " ^\n", "../khash.h:307:2: note: expanded from macro 'KHASH_INIT'\n", " KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)\n", " ^\n", "../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'\n", " SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \\\n", " ^\n", ":122:1: note: expanded from here\n", "kh_del_kh_rg\n", "^\n", "12 warnings generated.\n" ] } ], "source": [ "%%bash\n", "make" ] }, { "cell_type": "code", "execution_count": 34, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bioinformatics/stacks-1.37\n" ] } ], "source": [ "cd ../stacks-1.37/" ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "checking for a BSD-compatible install... /usr/bin/install -c\n", "checking whether build environment is sane... yes\n", "checking for a thread-safe mkdir -p... config/install-sh -c -d\n", "checking for gawk... no\n", "checking for mawk... no\n", "checking for nawk... no\n", "checking for awk... awk\n", "checking whether make sets $(MAKE)... yes\n", "checking whether make supports nested variables... yes\n", "checking for g++... g++\n", "checking whether the C++ compiler works... yes\n", "checking for C++ compiler default output file name... a.out\n", "checking for suffix of executables... \n", "checking whether we are cross compiling... no\n", "checking for suffix of object files... o\n", "checking whether we are using the GNU C++ compiler... yes\n", "checking whether g++ accepts -g... yes\n", "checking for style of include used by make... GNU\n", "checking dependency style of g++... gcc3\n", "checking for gcc... gcc\n", "checking whether we are using the GNU C compiler... yes\n", "checking whether gcc accepts -g... yes\n", "checking for gcc option to accept ISO C89... none needed\n", "checking whether gcc understands -c and -o together... yes\n", "checking dependency style of gcc... gcc3\n", "checking whether g++ supports C++11 features by default... no\n", "checking whether g++ supports C++11 features with -std=gnu++11... yes\n", "checking for omp_set_num_threads in -lgomp... no\n", "checking for gzread in -lz... yes\n", "checking for dirent.h that defines DIR... yes\n", "checking for library containing opendir... none required\n", "checking how to run the C preprocessor... gcc -E\n", "checking for grep that handles long lines and -e... /usr/bin/grep\n", "checking for egrep... /usr/bin/grep -E\n", "checking for ANSI C header files... yes\n", "checking for sys/types.h... yes\n", "checking for sys/stat.h... yes\n", "checking for stdlib.h... yes\n", "checking for string.h... yes\n", "checking for memory.h... yes\n", "checking for strings.h... yes\n", "checking for inttypes.h... yes\n", "checking for stdint.h... yes\n", "checking for unistd.h... yes\n", "checking float.h usability... yes\n", "checking float.h presence... yes\n", "checking for float.h... yes\n", "checking limits.h usability... yes\n", "checking limits.h presence... yes\n", "checking for limits.h... yes\n", "checking for stdlib.h... (cached) yes\n", "checking for string.h... (cached) yes\n", "checking for stdbool.h that conforms to C99... yes\n", "checking for _Bool... yes\n", "checking for an ANSI C-conforming const... yes\n", "checking for size_t... yes\n", "checking whether closedir returns void... no\n", "checking for stdlib.h... (cached) yes\n", "checking for GNU libc compatible malloc... yes\n", "checking for stdlib.h... (cached) yes\n", "checking for GNU libc compatible realloc... yes\n", "checking for floor... yes\n", "checking for memset... yes\n", "checking for pow... yes\n", "checking for sqrt... yes\n", "checking for gawk... (cached) awk\n", "checking that generated files are newer than configure... done\n", "configure: creating ./config.status\n", "config.status: creating Makefile\n", "config.status: creating config.h\n", "config.status: executing depfiles commands\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "configure: WARNING: Unable to locate OpenMP library, you should probably specify '--disable-openmp'.\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/clone_filter-clean.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/clone_filter-clone_filter.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/clone_filter-file_io.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/clone_filter-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/clone_filter-kmers.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/clone_filter-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/clone_filter-write.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-cstacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-kmers.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-locus.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/cstacks-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-estacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-models.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-mstack.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/estacks-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-catalog_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-genotypes.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-locus.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-log_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/genotypes-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-hstacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-kmers.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-locus.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/hstacks-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/kmer_filter-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/kmer_filter-kmer_filter.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/kmer_filter-kmers.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/kmer_filter-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/kmer_filter-write.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/phasedstacks-catalog_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/phasedstacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/phasedstacks-locus.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/phasedstacks-log_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/phasedstacks-phasedstacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/phasedstacks-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-catalog_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-locus.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-log_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-populations.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/populations-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_radtags-clean.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_radtags-file_io.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_radtags-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_radtags-log_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_radtags-process_radtags.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_radtags-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_radtags-write.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-clean.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-file_io.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-kmers.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-log_utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-process_shortreads.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/process_shortreads-write.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-models.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-mstack.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-pstacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/pstacks-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-locus.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-models.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-mst.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-rxstacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/rxstacks-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/sstacks-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/sstacks-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/sstacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/sstacks-locus.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/sstacks-sstacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/sstacks-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/sstacks-utils.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-DNANSeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-DNASeq.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-cmb.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-input.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-kmers.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-models.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-mst.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-mstack.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-stacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-ustacks.Po: No such file or directory\n", "mkdir: ./src/.deps: Permission denied\n", "mkdir: ./src/.deps: Permission denied\n", "./config.status: line 1206: ./src/.deps/ustacks-utils.Po: No such file or directory\n" ] } ], "source": [ "%%bash\n", "./configure --disable-openmp --enable-sparsehash --enable-bam" ] }, { "cell_type": "code", "execution_count": 36, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/bin/sh: src/.dirstamp: Permission denied\n", "make[1]: *** [src/.dirstamp] Error 1\n", "make: *** [all] Error 2\n" ] } ], "source": [ "%%bash\n", "make" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "./configure --with-bam-include-path=/usr/local/bionformatics/samtools-0.1.19" ] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }