In [1]:
!date
Wed Apr  6 11:53:38 PDT 2016
In [2]:
%%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

In [3]:
%%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]

In [5]:
cp stacks-1.37.tar.gz /usr/local/bioinformatics/
cp: /usr/local/bioinformatics/stacks-1.37.tar.gz: Permission denied
In [6]:
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/
In [7]:
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
In [8]:
%%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
In [9]:
%%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]

In [12]:
%%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  
In [13]:
cd sparsehash-master/
/Users/Sam/sparsehash-master
In [14]:
%%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
In [15]:
%%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 '[email protected]^/usr/[email protected]${prefix}@'` >> "libsparsehash.pc".tmp
echo 'libdir='`echo '/usr/local/lib' | sed '[email protected]^/usr/[email protected]${exec_prefix}@'` >> "libsparsehash.pc".tmp
echo 'includedir='`echo '/usr/local/include' | sed '[email protected]^/usr/[email protected]${prefix}@'` >> "libsparsehash.pc".tmp
echo '' >> "libsparsehash.pc".tmp
echo 'Name: sparsehash' >> "libsparsehash.pc".tmp
echo 'Version: 2.0.2' >> "libsparsehash.pc".tmp
grep '^Summary:' ./packages/rpm/rpm.spec | sed s/^Summary:/Description:/ | head -n1 >> "libsparsehash.pc".tmp
grep '^URL: ' ./packages/rpm/rpm.spec >> "libsparsehash.pc".tmp
echo 'Requires:' >> "libsparsehash.pc".tmp
echo 'Libs:' >> "libsparsehash.pc".tmp
echo 'Cflags: -I${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.
In [16]:
%%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'
In [17]:
cd /usr/local/bioinformatics/
/usr/local/bioinformatics
In [19]:
%%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.
In [20]:
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/
In [21]:
%%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).
In [22]:
ls /Users/Sam/samtools-0.1.19.tar.bz2
/Users/Sam/samtools-0.1.19.tar.bz2
In [24]:
%%bash
bunzip2 /Users/Sam/samtools-0.1.19.tar.bz2
In [25]:
ls /Users/Sam/samtools-0.1.19*
/Users/Sam/samtools-0.1.19.tar
In [27]:
%%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.
In [28]:
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/
In [29]:
cd samtools-0.1.19/
[Errno 13] Permission denied: 'samtools-0.1.19/'
/usr/local/bioinformatics
In [30]:
cd samtools-0.1.19/
/usr/local/bioinformatics/samtools-0.1.19
In [31]:
%%bash
./configure
bash: line 1: ./configure: No such file or directory
In [32]:
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
In [33]:
%%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.
In [34]:
cd ../stacks-1.37/
/usr/local/bioinformatics/stacks-1.37
In [35]:
%%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
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In [36]:
%%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