!date
Wed Apr 6 11:53:38 PDT 2016
%%bash
system_profiler SPSoftwareDataType
Software:
System Software Overview:
System Version: OS X 10.9.5 (13F34)
Kernel Version: Darwin 13.4.0
Boot Volume: Hummingbird
Boot Mode: Normal
Computer Name: hummingbird
User Name: Sam (Sam)
Secure Virtual Memory: Enabled
Time since boot: 137 days 20:44
%%bash
wget http://catchenlab.life.illinois.edu/stacks/source/stacks-1.37.tar.gz
--2016-04-06 11:55:33-- http://catchenlab.life.illinois.edu/stacks/source/stacks-1.37.tar.gz
Resolving catchenlab.life.illinois.edu... 130.126.48.94
Connecting to catchenlab.life.illinois.edu|130.126.48.94|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 504569 (493K) [application/x-gzip]
Saving to: 'stacks-1.37.tar.gz'
0K .......... .......... .......... .......... .......... 10% 508K 1s
50K .......... .......... .......... .......... .......... 20% 1018K 1s
100K .......... .......... .......... .......... .......... 30% 28.5M 0s
150K .......... .......... .......... .......... .......... 40% 43.0M 0s
200K .......... .......... .......... .......... .......... 50% 1.01M 0s
250K .......... .......... .......... .......... .......... 60% 18.9M 0s
300K .......... .......... .......... .......... .......... 71% 1.06M 0s
350K .......... .......... .......... .......... .......... 81% 4.78M 0s
400K .......... .......... .......... .......... .......... 91% 41.6M 0s
450K .......... .......... .......... .......... .. 100% 1.08M=0.3s
2016-04-06 11:55:35 (1.62 MB/s) - 'stacks-1.37.tar.gz' saved [504569/504569]
cp stacks-1.37.tar.gz /usr/local/bioinformatics/
cp: /usr/local/bioinformatics/stacks-1.37.tar.gz: Permission denied
ls /usr/local/bioinformatics/stacks*
/usr/local/bioinformatics/stacks@ /usr/local/bioinformatics/stacks-1.37.tar.gz /usr/local/bioinformatics/stacks-1.13: bin/ share/
tar -zxvf /usr/local/bioinformatics/stacks-1.37.tar.gz
--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-7-4e01bb15e112> in <module>() ----> 1 tar -zxvf /usr/local/bioinformatics/stacks-1.37.tar.gz NameError: name 'tar' is not defined
%%bash
tar -zxvf /usr/local/bioinformatics/stacks-1.37.tar.gz
x stacks-1.37/ x stacks-1.37/acinclude.m4 x stacks-1.37/aclocal.m4 x stacks-1.37/autogen.sh x stacks-1.37/ChangeLog x stacks-1.37/config/ x stacks-1.37/config.h.in x stacks-1.37/configure x stacks-1.37/configure.ac x stacks-1.37/INSTALL x stacks-1.37/LICENSE x stacks-1.37/Makefile.am x stacks-1.37/Makefile.in x stacks-1.37/php/ x stacks-1.37/README x stacks-1.37/scripts/ x stacks-1.37/sql/ x stacks-1.37/src/ x stacks-1.37/tests/ x stacks-1.37/tests/kmer_filter.t x stacks-1.37/tests/process_radtags.t x stacks-1.37/tests/pstacks.t x stacks-1.37/tests/ustacks.t x stacks-1.37/src/BamI.h x stacks-1.37/src/BamUnalignedI.h x stacks-1.37/src/bootstrap.h x stacks-1.37/src/BowtieI.h x stacks-1.37/src/BustardI.h x stacks-1.37/src/catalog_utils.cc x stacks-1.37/src/catalog_utils.h x stacks-1.37/src/clean.cc x stacks-1.37/src/clean.h x stacks-1.37/src/clone_filter.cc x stacks-1.37/src/clone_filter.h x stacks-1.37/src/cmb.cc x stacks-1.37/src/cmb.h x stacks-1.37/src/constants.h x stacks-1.37/src/cstacks.cc x stacks-1.37/src/cstacks.h x stacks-1.37/src/DNANSeq.cc x stacks-1.37/src/DNANSeq.h x stacks-1.37/src/DNASeq.cc x stacks-1.37/src/DNASeq.h x stacks-1.37/src/estacks.cc x stacks-1.37/src/estacks.h x stacks-1.37/src/FastaI.h x stacks-1.37/src/FastqI.h x stacks-1.37/src/file_io.cc x stacks-1.37/src/file_io.h x stacks-1.37/src/genotype_dictionaries.h x stacks-1.37/src/genotypes.cc x stacks-1.37/src/genotypes.h x stacks-1.37/src/gzFasta.h x stacks-1.37/src/gzFastq.h x stacks-1.37/src/hstacks.cc x stacks-1.37/src/hstacks.h x stacks-1.37/src/input.cc x stacks-1.37/src/input.h x stacks-1.37/src/kmer_filter.cc x stacks-1.37/src/kmer_filter.h x stacks-1.37/src/kmers.cc x stacks-1.37/src/kmers.h x stacks-1.37/src/locus.cc x stacks-1.37/src/locus.h x stacks-1.37/src/log_utils.cc x stacks-1.37/src/log_utils.h x stacks-1.37/src/models.cc x stacks-1.37/src/models.h x stacks-1.37/src/mst.cc x stacks-1.37/src/mst.h x stacks-1.37/src/mstack.cc x stacks-1.37/src/mstack.h x stacks-1.37/src/ordered.h x stacks-1.37/src/phasedstacks.cc x stacks-1.37/src/phasedstacks.h x stacks-1.37/src/PopMap.h x stacks-1.37/src/PopSum.h x stacks-1.37/src/populations.cc x stacks-1.37/src/populations.h x stacks-1.37/src/process_radtags.cc x stacks-1.37/src/process_radtags.h x stacks-1.37/src/process_shortreads.cc x stacks-1.37/src/process_shortreads.h x stacks-1.37/src/pstacks.cc x stacks-1.37/src/pstacks.h x stacks-1.37/src/renz.h x stacks-1.37/src/rxstacks.cc x stacks-1.37/src/rxstacks.h x stacks-1.37/src/SamI.h x stacks-1.37/src/smoothing.h x stacks-1.37/src/smoothing_utils.h x stacks-1.37/src/sql_utilities.h x stacks-1.37/src/sstacks.cc x stacks-1.37/src/sstacks.h x stacks-1.37/src/stacks.cc x stacks-1.37/src/stacks.h x stacks-1.37/src/Tsv.h x stacks-1.37/src/ustacks.cc x stacks-1.37/src/ustacks.h x stacks-1.37/src/utils.cc x stacks-1.37/src/utils.h x stacks-1.37/src/write.cc x stacks-1.37/src/write.h x stacks-1.37/sql/catalog_index.sql x stacks-1.37/sql/chr_index.sql x stacks-1.37/sql/mysql.cnf.dist x stacks-1.37/sql/stacks.sql x stacks-1.37/sql/tag_index.sql x stacks-1.37/scripts/convert_stacks.pl x stacks-1.37/scripts/denovo_map.pl x stacks-1.37/scripts/exec_velvet.pl x stacks-1.37/scripts/export_sql.pl x stacks-1.37/scripts/extract_interpop_chars.pl x stacks-1.37/scripts/index_radtags.pl x stacks-1.37/scripts/load_radtags.pl x stacks-1.37/scripts/load_sequences.pl x stacks-1.37/scripts/ref_map.pl x stacks-1.37/scripts/sort_read_pairs.pl x stacks-1.37/scripts/stacks_export_notify.pl x stacks-1.37/php/ajax.js x stacks-1.37/php/annotate.js x stacks-1.37/php/annotate_marker.php x stacks-1.37/php/catalog.php x stacks-1.37/php/catalog_genotypes.php x stacks-1.37/php/CatalogClass.php x stacks-1.37/php/constants.php.dist x stacks-1.37/php/correct_genotype.php x stacks-1.37/php/correct_genotypes.php x stacks-1.37/php/db_functions.php x stacks-1.37/php/export.js x stacks-1.37/php/export_batch.php x stacks-1.37/php/fst_view.php x stacks-1.37/php/hapstat_view.php x stacks-1.37/php/header.php x stacks-1.37/php/images/ x stacks-1.37/php/index.php x stacks-1.37/php/last_modified.php x stacks-1.37/php/Locus.php x stacks-1.37/php/phist_view.php x stacks-1.37/php/pop_view.php x stacks-1.37/php/population_view.js x stacks-1.37/php/samples.php x stacks-1.37/php/sequence_blast.php x stacks-1.37/php/stack_view.php x stacks-1.37/php/stacks.css x stacks-1.37/php/stacks.js x stacks-1.37/php/stacks_functions.php x stacks-1.37/php/sumstat_view.php x stacks-1.37/php/tag.php x stacks-1.37/php/tags.php x stacks-1.37/php/version.php x stacks-1.37/php/view_sequence.php x stacks-1.37/php/images/caret-d.png x stacks-1.37/php/images/caret-u.png x stacks-1.37/php/images/excel_icon.png x stacks-1.37/php/images/l-arrow-disabled.png x stacks-1.37/php/images/l-arrow.png x stacks-1.37/php/images/r-arrow-disabled.png x stacks-1.37/php/images/r-arrow.png x stacks-1.37/php/images/stacks_bg.png x stacks-1.37/php/images/stacks_logo_rev_small.png x stacks-1.37/config/compile x stacks-1.37/config/depcomp x stacks-1.37/config/install-sh x stacks-1.37/config/missing x stacks-1.37/config/test-driver
%%bash
wget https://github.com/sparsehash/sparsehash/archive/master.zip
--2016-04-06 12:09:13-- https://github.com/sparsehash/sparsehash/archive/master.zip
Resolving github.com... 192.30.252.120
Connecting to github.com|192.30.252.120|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/sparsehash/sparsehash/zip/master [following]
--2016-04-06 12:09:13-- https://codeload.github.com/sparsehash/sparsehash/zip/master
Resolving codeload.github.com... 192.30.252.161
Connecting to codeload.github.com|192.30.252.161|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/zip]
Saving to: 'master.zip'
0K .......... .......... .......... .......... .......... 327K
50K .......... .......... .......... .......... .......... 655K
100K .......... .......... .......... .......... .......... 26.1M
150K .......... .......... .......... .......... .......... 26.7M
200K .......... .......... .......... .......... .......... 671K
250K .......... .......... .......... .......... .......... 28.8M
300K .......... .......... .......... .......... .......... 677K
350K .......... .......... .......... ....... 31.8M=0.4s
2016-04-06 12:09:14 (1009 KB/s) - 'master.zip' saved [397003]
%%bash
unzip master.zip
Archive: master.zip 4a36398d442cc86f47d2d7e751596cc2430ad135 creating: sparsehash-master/ inflating: sparsehash-master/.gitignore inflating: sparsehash-master/AUTHORS inflating: sparsehash-master/COPYING inflating: sparsehash-master/ChangeLog inflating: sparsehash-master/INSTALL inflating: sparsehash-master/Makefile.am inflating: sparsehash-master/Makefile.in inflating: sparsehash-master/NEWS inflating: sparsehash-master/README inflating: sparsehash-master/README_windows.txt inflating: sparsehash-master/TODO inflating: sparsehash-master/aclocal.m4 inflating: sparsehash-master/autogen.sh inflating: sparsehash-master/config.guess inflating: sparsehash-master/config.sub inflating: sparsehash-master/configure inflating: sparsehash-master/configure.ac inflating: sparsehash-master/depcomp creating: sparsehash-master/doc/ inflating: sparsehash-master/doc/dense_hash_map.html inflating: sparsehash-master/doc/dense_hash_set.html inflating: sparsehash-master/doc/designstyle.css inflating: sparsehash-master/doc/implementation.html inflating: sparsehash-master/doc/index.html inflating: sparsehash-master/doc/performance.html inflating: sparsehash-master/doc/sparse_hash_map.html inflating: sparsehash-master/doc/sparse_hash_set.html inflating: sparsehash-master/doc/sparsetable.html creating: sparsehash-master/experimental/ inflating: sparsehash-master/experimental/Makefile inflating: sparsehash-master/experimental/README inflating: sparsehash-master/experimental/example.c inflating: sparsehash-master/experimental/libchash.c inflating: sparsehash-master/experimental/libchash.h inflating: sparsehash-master/google-sparsehash.sln inflating: sparsehash-master/install-sh creating: sparsehash-master/m4/ inflating: sparsehash-master/m4/acx_pthread.m4 inflating: sparsehash-master/m4/google_namespace.m4 inflating: sparsehash-master/m4/namespaces.m4 inflating: sparsehash-master/m4/stl_hash.m4 inflating: sparsehash-master/m4/stl_hash_fun.m4 inflating: sparsehash-master/missing creating: sparsehash-master/packages/ inflating: sparsehash-master/packages/deb.sh creating: sparsehash-master/packages/deb/ inflating: sparsehash-master/packages/deb/README inflating: sparsehash-master/packages/deb/changelog extracting: sparsehash-master/packages/deb/compat inflating: sparsehash-master/packages/deb/control inflating: sparsehash-master/packages/deb/copyright inflating: sparsehash-master/packages/deb/docs inflating: sparsehash-master/packages/deb/rules inflating: sparsehash-master/packages/deb/sparsehash.dirs inflating: sparsehash-master/packages/deb/sparsehash.install inflating: sparsehash-master/packages/rpm.sh creating: sparsehash-master/packages/rpm/ inflating: sparsehash-master/packages/rpm/rpm.spec inflating: sparsehash-master/sparsehash.sln creating: sparsehash-master/src/ inflating: sparsehash-master/src/config.h.in inflating: sparsehash-master/src/config.h.include creating: sparsehash-master/src/google/ inflating: sparsehash-master/src/google/dense_hash_map inflating: sparsehash-master/src/google/dense_hash_set inflating: sparsehash-master/src/google/sparse_hash_map inflating: sparsehash-master/src/google/sparse_hash_set creating: sparsehash-master/src/google/sparsehash/ inflating: sparsehash-master/src/google/sparsehash/densehashtable.h inflating: sparsehash-master/src/google/sparsehash/hashtable-common.h inflating: sparsehash-master/src/google/sparsehash/libc_allocator_with_realloc.h inflating: sparsehash-master/src/google/sparsehash/sparsehashtable.h inflating: sparsehash-master/src/google/sparsetable inflating: sparsehash-master/src/google/template_util.h inflating: sparsehash-master/src/google/type_traits.h inflating: sparsehash-master/src/hash_test_interface.h inflating: sparsehash-master/src/hashtable_test.cc inflating: sparsehash-master/src/libc_allocator_with_realloc_test.cc inflating: sparsehash-master/src/simple_compat_test.cc inflating: sparsehash-master/src/simple_test.cc creating: sparsehash-master/src/sparsehash/ inflating: sparsehash-master/src/sparsehash/dense_hash_map inflating: sparsehash-master/src/sparsehash/dense_hash_set creating: sparsehash-master/src/sparsehash/internal/ inflating: sparsehash-master/src/sparsehash/internal/densehashtable.h inflating: sparsehash-master/src/sparsehash/internal/hashtable-common.h inflating: sparsehash-master/src/sparsehash/internal/libc_allocator_with_realloc.h inflating: sparsehash-master/src/sparsehash/internal/sparsehashtable.h inflating: sparsehash-master/src/sparsehash/sparse_hash_map inflating: sparsehash-master/src/sparsehash/sparse_hash_set inflating: sparsehash-master/src/sparsehash/sparsetable inflating: sparsehash-master/src/sparsehash/template_util.h inflating: sparsehash-master/src/sparsehash/type_traits.h inflating: sparsehash-master/src/sparsetable_unittest.cc inflating: sparsehash-master/src/template_util_unittest.cc inflating: sparsehash-master/src/testutil.h inflating: sparsehash-master/src/time_hash_map.cc inflating: sparsehash-master/src/type_traits_unittest.cc creating: sparsehash-master/src/windows/ inflating: sparsehash-master/src/windows/config.h creating: sparsehash-master/src/windows/google/ creating: sparsehash-master/src/windows/google/sparsehash/ inflating: sparsehash-master/src/windows/google/sparsehash/sparseconfig.h inflating: sparsehash-master/src/windows/port.cc inflating: sparsehash-master/src/windows/port.h creating: sparsehash-master/src/windows/sparsehash/ creating: sparsehash-master/src/windows/sparsehash/internal/ inflating: sparsehash-master/src/windows/sparsehash/internal/sparseconfig.h creating: sparsehash-master/vsprojects/ creating: sparsehash-master/vsprojects/hashtable_test/ inflating: sparsehash-master/vsprojects/hashtable_test/hashtable_test.vcproj creating: sparsehash-master/vsprojects/libc_allocator_with_realloc_test/ inflating: sparsehash-master/vsprojects/libc_allocator_with_realloc_test/libc_allocator_with_realloc_test.vcproj creating: sparsehash-master/vsprojects/simple_test/ inflating: sparsehash-master/vsprojects/simple_test/simple_test.vcproj creating: sparsehash-master/vsprojects/sparsetable_unittest/ inflating: sparsehash-master/vsprojects/sparsetable_unittest/sparsetable_unittest.vcproj creating: sparsehash-master/vsprojects/template_util_unittest/ inflating: sparsehash-master/vsprojects/template_util_unittest/template_util_unittest.vcproj creating: sparsehash-master/vsprojects/time_hash_map/ inflating: sparsehash-master/vsprojects/time_hash_map/time_hash_map.vcproj creating: sparsehash-master/vsprojects/type_traits_unittest/ inflating: sparsehash-master/vsprojects/type_traits_unittest/type_traits_unittest.vcproj
cd sparsehash-master/
/Users/Sam/sparsehash-master
%%bash
./configure
checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for memcpy... yes checking for memmove... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for uint16_t... yes checking for u_int16_t... yes checking for __uint16... no checking for long long... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking how to run the C++ preprocessor... g++ -E checking google/malloc_extension.h usability... no checking google/malloc_extension.h presence... no checking for google/malloc_extension.h... no checking whether the compiler implements namespaces... yes checking the location of hash_map... <unordered_map> checking how to include hash_fun directly... <functional> configure: creating ./config.status config.status: creating Makefile config.status: creating src/config.h config.status: executing depfiles commands
%%bash
make
[ -d src/sparsehash/internal ] || mkdir -p src/sparsehash/internal
echo "/*" > src/sparsehash/internal/_sparsehash_config
echo " * NOTE: This file is for internal use only." >> src/sparsehash/internal/_sparsehash_config
echo " * Do not use these #defines in your own program!" >> src/sparsehash/internal/_sparsehash_config
echo " */" >> src/sparsehash/internal/_sparsehash_config
awk '{prevline=currline; currline=$0;} \
/^#/ {in_second_file = 1;} \
!in_second_file {if (currline !~ /^ *$/) {inc[currline]=0}}; \
in_second_file { for (i in inc) { \
if (index(currline, i) != 0) { \
print "\n"prevline"\n"currline; \
delete inc[i]; \
} \
} }' \
./src/config.h.include ./src/config.h \
>> src/sparsehash/internal/_sparsehash_config
mv -f src/sparsehash/internal/_sparsehash_config src/sparsehash/internal/sparseconfig.h
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
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
mv -f .deps/template_util_unittest.Tpo .deps/template_util_unittest.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o template_util_unittest template_util_unittest.o
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
mv -f .deps/type_traits_unittest.Tpo .deps/type_traits_unittest.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o type_traits_unittest type_traits_unittest.o
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
mv -f .deps/libc_allocator_with_realloc_test.Tpo .deps/libc_allocator_with_realloc_test.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o libc_allocator_with_realloc_test libc_allocator_with_realloc_test.o
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
mv -f .deps/sparsetable_unittest.Tpo .deps/sparsetable_unittest.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o sparsetable_unittest sparsetable_unittest.o
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
mv -f .deps/hashtable_test.Tpo .deps/hashtable_test.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o hashtable_test hashtable_test.o
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
mv -f .deps/simple_test.Tpo .deps/simple_test.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o simple_test simple_test.o
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
mv -f .deps/simple_compat_test.Tpo .deps/simple_compat_test.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o simple_compat_test simple_compat_test.o
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
mv -f .deps/time_hash_map-time_hash_map.Tpo .deps/time_hash_map-time_hash_map.Po
g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -g -O2 -o time_hash_map time_hash_map-time_hash_map.o
echo 'prefix=/usr/local' > "libsparsehash.pc".tmp
echo 'exec_prefix='`echo '/usr/local' | sed 's@^/usr/local@${prefix}@'` >> "libsparsehash.pc".tmp
echo 'libdir='`echo '/usr/local/lib' | sed 's@^/usr/local@${exec_prefix}@'` >> "libsparsehash.pc".tmp
echo 'includedir='`echo '/usr/local/include' | sed 's@^/usr/local@${prefix}@'` >> "libsparsehash.pc".tmp
echo '' >> "libsparsehash.pc".tmp
echo 'Name: sparsehash' >> "libsparsehash.pc".tmp
echo 'Version: 2.0.2' >> "libsparsehash.pc".tmp
grep '^Summary:' ./packages/rpm/rpm.spec | sed s/^Summary:/Description:/ | head -n1 >> "libsparsehash.pc".tmp
grep '^URL: ' ./packages/rpm/rpm.spec >> "libsparsehash.pc".tmp
echo 'Requires:' >> "libsparsehash.pc".tmp
echo 'Libs:' >> "libsparsehash.pc".tmp
echo 'Cflags: -I${includedir}' >> "libsparsehash.pc".tmp
mv -f "libsparsehash.pc".tmp "libsparsehash.pc"
src/type_traits_unittest.cc:88:7: warning: private field 'n_' is not used [-Wunused-private-field]
int n_;
^
src/type_traits_unittest.cc:98:7: warning: private field 'n_' is not used [-Wunused-private-field]
int n_;
^
src/type_traits_unittest.cc:112:7: warning: private field 'n_' is not used [-Wunused-private-field]
int n_;
^
src/type_traits_unittest.cc:138:7: warning: private field 'n_' is not used [-Wunused-private-field]
int n_;
^
4 warnings generated.
src/hashtable_test.cc:520:1: warning: unused variable 'HashtableCharStarTest_numtypes' [-Wunused-const-variable]
TYPED_TEST_CASE_6(HashtableCharStarTest, CharStarHashtables);
^
./src/testutil.h:106:20: note: expanded from macro 'TYPED_TEST_CASE_6'
static const int classname##_numtypes = 6; \
^
<scratch space>:67:1: note: expanded from here
HashtableCharStarTest_numtypes
^
1 warning generated.
%%bash
make install
/Applications/Xcode.app/Contents/Developer/usr/bin/make install-am test -z "/usr/local/lib" || ./install-sh -c -d "/usr/local/lib" test -z "/usr/local/share/doc/sparsehash-2.0.2" || ./install-sh -c -d "/usr/local/share/doc/sparsehash-2.0.2" /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' test -z "/usr/local/include/google" || ./install-sh -c -d "/usr/local/include/google" /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' test -z "/usr/local/include/google/sparsehash" || ./install-sh -c -d "/usr/local/include/google/sparsehash" /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' test -z "/usr/local/include/sparsehash/internal" || ./install-sh -c -d "/usr/local/include/sparsehash/internal" /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' test -z "/usr/local/include/sparsehash/internal" || ./install-sh -c -d "/usr/local/include/sparsehash/internal" /usr/bin/install -c -m 644 src/sparsehash/internal/sparseconfig.h '/usr/local/include/sparsehash/internal' test -z "/usr/local/lib/pkgconfig" || ./install-sh -c -d "/usr/local/lib/pkgconfig" /usr/bin/install -c -m 644 libsparsehash.pc '/usr/local/lib/pkgconfig' test -z "/usr/local/include/sparsehash" || ./install-sh -c -d "/usr/local/include/sparsehash" /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'
cd /usr/local/bioinformatics/
/usr/local/bioinformatics
%%bash
tar -zxvf stacks-1.37.tar.gz
x stacks-1.37/: Can't create 'stacks-1.37' x stacks-1.37/acinclude.m4: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/acinclude.m4' x stacks-1.37/aclocal.m4: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/aclocal.m4' x stacks-1.37/autogen.sh: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/autogen.sh' x stacks-1.37/ChangeLog: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/ChangeLog' x stacks-1.37/config/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config' x stacks-1.37/config.h.in: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config.h.in' x stacks-1.37/configure: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/configure' x stacks-1.37/configure.ac: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/configure.ac' x stacks-1.37/INSTALL: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/INSTALL' x stacks-1.37/LICENSE: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/LICENSE' x stacks-1.37/Makefile.am: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/Makefile.am' x stacks-1.37/Makefile.in: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/Makefile.in' x stacks-1.37/php/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php' x stacks-1.37/README: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/README' x stacks-1.37/scripts/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/scripts' x stacks-1.37/sql/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql' x stacks-1.37/src/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src' x stacks-1.37/tests/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests' 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' 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' x stacks-1.37/tests/pstacks.t: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests/pstacks.t' x stacks-1.37/tests/ustacks.t: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/tests/ustacks.t' x stacks-1.37/src/BamI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BamI.h' x stacks-1.37/src/BamUnalignedI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BamUnalignedI.h' x stacks-1.37/src/bootstrap.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/bootstrap.h' x stacks-1.37/src/BowtieI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BowtieI.h' x stacks-1.37/src/BustardI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/BustardI.h' 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' 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' x stacks-1.37/src/clean.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/clean.cc' x stacks-1.37/src/clean.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/clean.h' 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' 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' x stacks-1.37/src/cmb.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cmb.cc' x stacks-1.37/src/cmb.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cmb.h' x stacks-1.37/src/constants.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/constants.h' x stacks-1.37/src/cstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cstacks.cc' x stacks-1.37/src/cstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/cstacks.h' x stacks-1.37/src/DNANSeq.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNANSeq.cc' x stacks-1.37/src/DNANSeq.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNANSeq.h' x stacks-1.37/src/DNASeq.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNASeq.cc' x stacks-1.37/src/DNASeq.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/DNASeq.h' x stacks-1.37/src/estacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/estacks.cc' x stacks-1.37/src/estacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/estacks.h' x stacks-1.37/src/FastaI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/FastaI.h' x stacks-1.37/src/FastqI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/FastqI.h' 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' 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' 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' x stacks-1.37/src/genotypes.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/genotypes.cc' x stacks-1.37/src/genotypes.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/genotypes.h' x stacks-1.37/src/gzFasta.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/gzFasta.h' x stacks-1.37/src/gzFastq.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/gzFastq.h' x stacks-1.37/src/hstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/hstacks.cc' x stacks-1.37/src/hstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/hstacks.h' x stacks-1.37/src/input.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/input.cc' x stacks-1.37/src/input.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/input.h' 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' 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' x stacks-1.37/src/kmers.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/kmers.cc' x stacks-1.37/src/kmers.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/kmers.h' x stacks-1.37/src/locus.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/locus.cc' x stacks-1.37/src/locus.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/locus.h' 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' 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' x stacks-1.37/src/models.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/models.cc' x stacks-1.37/src/models.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/models.h' x stacks-1.37/src/mst.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mst.cc' x stacks-1.37/src/mst.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mst.h' x stacks-1.37/src/mstack.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mstack.cc' x stacks-1.37/src/mstack.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/mstack.h' x stacks-1.37/src/ordered.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/ordered.h' x stacks-1.37/src/phasedstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/phasedstacks.cc' x stacks-1.37/src/phasedstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/phasedstacks.h' x stacks-1.37/src/PopMap.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/PopMap.h' x stacks-1.37/src/PopSum.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/PopSum.h' x stacks-1.37/src/populations.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/populations.cc' x stacks-1.37/src/populations.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/populations.h' 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' 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' 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' 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' x stacks-1.37/src/pstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/pstacks.cc' x stacks-1.37/src/pstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/pstacks.h' x stacks-1.37/src/renz.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/renz.h' x stacks-1.37/src/rxstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/rxstacks.cc' x stacks-1.37/src/rxstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/rxstacks.h' x stacks-1.37/src/SamI.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/SamI.h' x stacks-1.37/src/smoothing.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/smoothing.h' 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' 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' x stacks-1.37/src/sstacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/sstacks.cc' x stacks-1.37/src/sstacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/sstacks.h' x stacks-1.37/src/stacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/stacks.cc' x stacks-1.37/src/stacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/stacks.h' x stacks-1.37/src/Tsv.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/Tsv.h' x stacks-1.37/src/ustacks.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/ustacks.cc' x stacks-1.37/src/ustacks.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/ustacks.h' x stacks-1.37/src/utils.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/utils.cc' x stacks-1.37/src/utils.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/utils.h' x stacks-1.37/src/write.cc: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/write.cc' x stacks-1.37/src/write.h: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/src/write.h' 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' 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' 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' x stacks-1.37/sql/stacks.sql: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/sql/stacks.sql' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' x stacks-1.37/php/ajax.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/ajax.js' x stacks-1.37/php/annotate.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/annotate.js' 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' x stacks-1.37/php/catalog.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/catalog.php' 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' x stacks-1.37/php/CatalogClass.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/CatalogClass.php' 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' 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' 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' 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' x stacks-1.37/php/export.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/export.js' 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' 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' 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' x stacks-1.37/php/header.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/header.php' x stacks-1.37/php/images/: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/images' x stacks-1.37/php/index.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/index.php' 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' x stacks-1.37/php/Locus.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/Locus.php' 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' 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' 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' x stacks-1.37/php/samples.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/samples.php' 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' 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' x stacks-1.37/php/stacks.css: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/stacks.css' x stacks-1.37/php/stacks.js: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/stacks.js' 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' 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' x stacks-1.37/php/tag.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/tag.php' x stacks-1.37/php/tags.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/tags.php' x stacks-1.37/php/version.php: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/php/version.php' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' x stacks-1.37/config/compile: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/compile' x stacks-1.37/config/depcomp: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/depcomp' x stacks-1.37/config/install-sh: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/install-sh' x stacks-1.37/config/missing: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/missing' x stacks-1.37/config/test-driver: Failed to create dir 'stacks-1.37'Can't create 'stacks-1.37/config/test-driver' tar: Error exit delayed from previous errors.
ls stack*
stacks@ stacks-1.37.tar.gz stacks-1.13: bin/ share/ stacks-1.37: ChangeLog LICENSE Makefile.in acinclude.m4 autogen.sh* config.h.in configure.ac scripts/ src/ INSTALL Makefile.am README aclocal.m4 config/ configure* php/ sql/ tests/
%%bash
wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2
--2016-04-06 12:19:29-- https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2 Resolving sourceforge.net... 216.34.181.60 Connecting to sourceforge.net|216.34.181.60|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download [following] --2016-04-06 12:19:29-- https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download Connecting to sourceforge.net|216.34.181.60|:443... connected. HTTP request sent, awaiting response... 302 Found Location: http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2?r=&ts=1459970470&use_mirror=iweb [following] --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 Resolving downloads.sourceforge.net... 216.34.181.59 Connecting to downloads.sourceforge.net|216.34.181.59|:80... connected. HTTP request sent, awaiting response... 302 Found Location: http://iweb.dl.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 [following] --2016-04-06 12:19:30-- http://iweb.dl.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 Resolving iweb.dl.sourceforge.net... 70.38.0.134, 2607:f748:10:12::5f:2 Connecting to iweb.dl.sourceforge.net|70.38.0.134|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 514507 (502K) [application/octet-stream] samtools-0.1.19.tar.bz2: Permission denied Cannot write to 'samtools-0.1.19.tar.bz2' (Success).
ls /Users/Sam/samtools-0.1.19.tar.bz2
/Users/Sam/samtools-0.1.19.tar.bz2
%%bash
bunzip2 /Users/Sam/samtools-0.1.19.tar.bz2
ls /Users/Sam/samtools-0.1.19*
/Users/Sam/samtools-0.1.19.tar
%%bash
tar -xjf /Users/Sam/samtools-0.1.19.tar
samtools-0.1.19/: Can't create 'samtools-0.1.19' samtools-0.1.19/.gitignore: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/.gitignore' samtools-0.1.19/AUTHORS: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/AUTHORS' samtools-0.1.19/COPYING: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/COPYING' samtools-0.1.19/ChangeLog.old: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/ChangeLog.old' samtools-0.1.19/INSTALL: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/INSTALL' samtools-0.1.19/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/Makefile' samtools-0.1.19/Makefile.mingw: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/Makefile.mingw' samtools-0.1.19/NEWS: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/NEWS' samtools-0.1.19/bam.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam.c' samtools-0.1.19/bam.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam.h' samtools-0.1.19/bam2bcf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam2bcf.c' samtools-0.1.19/bam2bcf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam2bcf.h' 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' samtools-0.1.19/bam2depth.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam2depth.c' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' samtools-0.1.19/bamshuf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bamshuf.c' samtools-0.1.19/bamtk.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bamtk.c' samtools-0.1.19/bcftools/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools' samtools-0.1.19/bcftools/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/Makefile' samtools-0.1.19/bcftools/README: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bcftools/README' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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~' samtools-0.1.19/bedcov.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bedcov.c' samtools-0.1.19/bedidx.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bedidx.c' samtools-0.1.19/bgzf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bgzf.c' samtools-0.1.19/bgzf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bgzf.h' samtools-0.1.19/bgzip.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bgzip.c' 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' samtools-0.1.19/errmod.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/errmod.c' samtools-0.1.19/errmod.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/errmod.h' samtools-0.1.19/examples/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples' 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' samtools-0.1.19/examples/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/examples/Makefile' 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' 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' 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' 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' 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' 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' 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' samtools-0.1.19/faidx.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/faidx.c' samtools-0.1.19/faidx.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/faidx.h' samtools-0.1.19/kaln.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kaln.c' samtools-0.1.19/kaln.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kaln.h' samtools-0.1.19/khash.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/khash.h' samtools-0.1.19/klist.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/klist.h' samtools-0.1.19/knetfile.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/knetfile.c' samtools-0.1.19/knetfile.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/knetfile.h' samtools-0.1.19/kprobaln.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kprobaln.c' samtools-0.1.19/kprobaln.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kprobaln.h' samtools-0.1.19/kseq.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kseq.h' samtools-0.1.19/ksort.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/ksort.h' samtools-0.1.19/kstring.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kstring.c' samtools-0.1.19/kstring.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/kstring.h' samtools-0.1.19/misc/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc' 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' samtools-0.1.19/misc/Makefile: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/misc/Makefile' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' samtools-0.1.19/padding.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/padding.c' samtools-0.1.19/phase.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/phase.c' samtools-0.1.19/razf.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/razf.c' samtools-0.1.19/razf.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/razf.h' samtools-0.1.19/razip.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/razip.c' samtools-0.1.19/sam.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sam.c' samtools-0.1.19/sam.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sam.h' 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' 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' 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' samtools-0.1.19/sample.c: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sample.c' samtools-0.1.19/sample.h: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/sample.h' samtools-0.1.19/samtools.1: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/samtools.1' samtools-0.1.19/win32/: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/win32' 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' 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' 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' 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' 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' samtools-0.1.19/bam.h~: Failed to create dir 'samtools-0.1.19'Can't create 'samtools-0.1.19/bam.h~' tar: Error exit delayed from previous errors.
ls
FastQC/ bismark_v0.14.2/ fastx_toolkit@ ngsplot@ stacks@ Trimmomatic@ bowtie@ fastx_toolkit-0.0.13.2/ ngsplot-2.08/ stacks-1.13/ Trimmomatic-0.30/ bowtie-1.0.0/ hmmer@ rsem@ stacks-1.37/ Trinotate@ bowtie2@ hmmer-3.1b1/ rsem-1.2.10/ stacks-1.37.tar.gz Trinotate_r20140708/ bowtie2-2.1.0/ libgtextutils-0.6.1/ samtools-0.1.19/ tophat-2.0.13.OSX_x86_64/ anaconda/ cufflinks-2.2.1.OSX_x86_64/ ncbi-blast@ signalp-4.1/ trinity@ bedtools-2.22.1/ dbs/ ncbi-blast-2.2.29+/ source.sh trinityrnaseq_r20131110/
cd samtools-0.1.19/
[Errno 13] Permission denied: 'samtools-0.1.19/' /usr/local/bioinformatics
cd samtools-0.1.19/
/usr/local/bioinformatics/samtools-0.1.19
%%bash
./configure
bash: line 1: ./configure: No such file or directory
ls
AUTHORS bam2bcf.h bam_md.c bam_tview_html.c errmod.h kprobaln.h sam.c COPYING bam2bcf_indel.c bam_pileup.c bamshuf.c examples/ kseq.h sam.h ChangeLog.old bam2depth.c bam_plcmd.c bamtk.c faidx.c ksort.h sam_header.c INSTALL bam_aux.c bam_reheader.c bcftools/ faidx.h kstring.c sam_header.h Makefile bam_cat.c bam_rmdup.c bedcov.c kaln.c kstring.h sam_view.c Makefile.mingw bam_color.c bam_rmdupse.c bedidx.c kaln.h misc/ sample.c NEWS bam_endian.h bam_sort.c bgzf.c khash.h padding.c sample.h bam.c bam_import.c bam_stat.c bgzf.h klist.h phase.c samtools.1 bam.h bam_index.c bam_tview.c bgzip.c knetfile.c razf.c win32/ bam.h~ bam_lpileup.c bam_tview.h cut_target.c knetfile.h razf.h bam2bcf.c bam_mate.c bam_tview_curses.c errmod.c kprobaln.c razip.c
%%bash
make
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 make[2]: Nothing to be done for `lib'. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -g -Wall -O2 -o md5sum-lite md5sum-lite.o 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 gcc -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
bgzf.c:82:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:98:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:200:1: note: expanded from here
kh_clear_s
^
bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:214:1: note: expanded from here
kh_del_s
^
bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
KHASH_MAP_INIT_STR(r2l, str_p)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() { \
^
<scratch space>:221:1: note: expanded from here
kh_init_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h) \
^
<scratch space>:226:1: note: expanded from here
kh_destroy_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:229:1: note: expanded from here
kh_clear_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:232:1: note: expanded from here
kh_get_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:238:1: note: expanded from here
kh_put_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:243:1: note: expanded from here
kh_del_r2l
^
8 warnings generated.
bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function]
KHASH_MAP_INIT_STR(ref, uint64_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:200:1: note: expanded from here
kh_clear_ref
^
bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:203:1: note: expanded from here
kh_get_ref
^
bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:214:1: note: expanded from here
kh_del_ref
^
3 warnings generated.
bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:218:1: note: expanded from here
kh_clear_i
^
bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:232:1: note: expanded from here
kh_del_i
^
2 warnings generated.
faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:154:1: note: expanded from here
kh_clear_s
^
faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:168:1: note: expanded from here
kh_del_s
^
2 warnings generated.
bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:214:1: note: expanded from here
kh_clear_reg
^
bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:228:1: note: expanded from here
kh_del_reg
^
2 warnings generated.
sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, const char *)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:154:1: note: expanded from here
kh_clear_str
^
sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:168:1: note: expanded from here
kh_del_str
^
2 warnings generated.
vcf.c:243:15: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
endblock: i = i;
~ ^ ~
vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 4096)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
2 warnings generated.
bcfutils.c:7:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]
KHASH_MAP_INIT_STR(str2id, int)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:51:1: note: expanded from here
kh_clear_str2id
^
bcfutils.c:7:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:65:1: note: expanded from here
kh_del_str2id
^
2 warnings generated.
prob1.c:13:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
1 warning generated.
sam_view.c:12:1: warning: unused function 'kh_clear_rg' [-Wunused-function]
KHASH_SET_INIT_STR(rg)
^
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:41:1: note: expanded from here
kh_clear_rg
^
sam_view.c:12:1: warning: unused function 'kh_del_rg' [-Wunused-function]
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:55:1: note: expanded from here
kh_del_rg
^
2 warnings generated.
bam_rmdup.c:12:1: warning: unused function 'kh_get_pos' [-Wunused-function]
KHASH_MAP_INIT_INT64(pos, bam1_p)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:232:1: note: expanded from here
kh_get_pos
^
bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function]
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:243:1: note: expanded from here
kh_del_pos
^
bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
KHASH_MAP_INIT_STR(lib, lib_aux_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:260:1: note: expanded from here
kh_clear_lib
^
bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:274:1: note: expanded from here
kh_del_lib
^
4 warnings generated.
bam_rmdupse.c:18:1: warning: unused function 'kh_clear_best' [-Wunused-function]
KHASH_MAP_INIT_INT(best, elem_p)
^
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:103:1: note: expanded from here
kh_clear_best
^
bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function]
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:106:1: note: expanded from here
kh_get_best
^
bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
KHASH_MAP_INIT_STR(lib, lib_aux_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:134:1: note: expanded from here
kh_clear_lib
^
bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:148:1: note: expanded from here
kh_del_lib
^
4 warnings generated.
bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body]
for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
^
bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence this warning
bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body]
for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
^
bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence this warning
bam2bcf_indel.c:9:1: warning: unused function 'kh_clear_rg' [-Wunused-function]
KHASH_SET_INIT_STR(rg)
^
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:200:1: note: expanded from here
kh_clear_rg
^
bam2bcf_indel.c:9:1: warning: unused function 'kh_del_rg' [-Wunused-function]
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:214:1: note: expanded from here
kh_del_rg
^
4 warnings generated.
errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (m > m) return -1;
^
1 warning generated.
sample.c:5:1: warning: unused function 'kh_clear_sm' [-Wunused-function]
KHASH_MAP_INIT_STR(sm, int)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:136:1: note: expanded from here
kh_clear_sm
^
sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:150:1: note: expanded from here
kh_del_sm
^
2 warnings generated.
phase.c:45:1: warning: unused function 'kh_clear_set64' [-Wunused-function]
KHASH_SET_INIT_INT64(set64)
^
./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:49:1: note: expanded from here
kh_clear_set64
^
phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function]
./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:63:1: note: expanded from here
kh_del_set64
^
phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function]
KHASH_MAP_INIT_INT64(64, frag_t)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:78:1: note: expanded from here
kh_clear_64
^
3 warnings generated.
bedcov.c:12:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
./kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
1 warning generated.
call1.c:17:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
1 warning generated.
main.c:9:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 0x10000)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
1 warning generated.
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]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
~~~ ^~~
md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)?
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^~~
1 warning generated.
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]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
~~~ ^~~
md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)?
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^~~
1 warning generated.
ace2sam.c:33:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
1 warning generated.
bamcheck.c:52:1: warning: unused function 'kh_init_kh_faidx' [-Wunused-function]
KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() { \
^
<scratch space>:42:1: note: expanded from here
kh_init_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_destroy_kh_faidx' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h) \
^
<scratch space>:47:1: note: expanded from here
kh_destroy_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_clear_kh_faidx' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:50:1: note: expanded from here
kh_clear_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_put_kh_faidx' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:59:1: note: expanded from here
kh_put_kh_faidx
^
bamcheck.c:52:1: warning: unused function 'kh_del_kh_faidx' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:64:1: note: expanded from here
kh_del_kh_faidx
^
bamcheck.c:53:1: warning: unused function 'kh_init_kh_bam_tid' [-Wunused-function]
KHASH_MAP_INIT_STR(kh_bam_tid, int)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() { \
^
<scratch space>:71:1: note: expanded from here
kh_init_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_destroy_kh_bam_tid' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h) \
^
<scratch space>:76:1: note: expanded from here
kh_destroy_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_clear_kh_bam_tid' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:79:1: note: expanded from here
kh_clear_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_put_kh_bam_tid' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:88:1: note: expanded from here
kh_put_kh_bam_tid
^
bamcheck.c:53:1: warning: unused function 'kh_del_kh_bam_tid' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:93:1: note: expanded from here
kh_del_kh_bam_tid
^
bamcheck.c:54:1: warning: unused function 'kh_clear_kh_rg' [-Wunused-function]
KHASH_MAP_INIT_STR(kh_rg, const char *)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:108:1: note: expanded from here
kh_clear_kh_rg
^
bamcheck.c:54:1: warning: unused function 'kh_del_kh_rg' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:122:1: note: expanded from here
kh_del_kh_rg
^
12 warnings generated.
cd ../stacks-1.37/
/usr/local/bioinformatics/stacks-1.37
%%bash
./configure --disable-openmp --enable-sparsehash --enable-bam
checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... config/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking whether g++ supports C++11 features by default... no checking whether g++ supports C++11 features with -std=gnu++11... yes checking for omp_set_num_threads in -lgomp... no checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for gawk... (cached) awk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands
configure: WARNING: Unable to locate OpenMP library, you should probably specify '--disable-openmp'. mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/clone_filter-clean.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/clone_filter-clone_filter.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/clone_filter-file_io.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/clone_filter-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/clone_filter-kmers.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/clone_filter-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/clone_filter-write.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-cstacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-kmers.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-locus.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/cstacks-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-estacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-models.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-mstack.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/estacks-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-catalog_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-genotypes.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-locus.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-log_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/genotypes-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-hstacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-kmers.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-locus.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/hstacks-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/kmer_filter-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/kmer_filter-kmer_filter.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/kmer_filter-kmers.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/kmer_filter-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/kmer_filter-write.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/phasedstacks-catalog_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/phasedstacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/phasedstacks-locus.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/phasedstacks-log_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/phasedstacks-phasedstacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/phasedstacks-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-catalog_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-locus.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-log_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-populations.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/populations-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_radtags-clean.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_radtags-file_io.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_radtags-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_radtags-log_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_radtags-process_radtags.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_radtags-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_radtags-write.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-clean.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-file_io.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-kmers.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-log_utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-process_shortreads.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/process_shortreads-write.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-models.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-mstack.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-pstacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/pstacks-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-locus.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-models.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-mst.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-rxstacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/rxstacks-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/sstacks-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/sstacks-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/sstacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/sstacks-locus.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/sstacks-sstacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/sstacks-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/sstacks-utils.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-DNANSeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-DNASeq.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-cmb.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-input.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-kmers.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-models.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-mst.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-mstack.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-stacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-ustacks.Po: No such file or directory mkdir: ./src/.deps: Permission denied mkdir: ./src/.deps: Permission denied ./config.status: line 1206: ./src/.deps/ustacks-utils.Po: No such file or directory
%%bash
make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
/bin/sh: src/.dirstamp: Permission denied make[1]: *** [src/.dirstamp] Error 1 make: *** [all] Error 2
./configure --with-bam-include-path=/usr/local/bionformatics/samtools-0.1.19