Error Building Playpus‏

[Bob May]

On my  C drive I have Python34 and Cygwin64
Cygwin has has in /usr/local/bin
bcftools-1.3
bedtools-2.25.0
bwa-0.7.12
htslib-1.3
Platypus_0.8.1
Samtools-1.3
Stampy-a.0.28

cd c:/cygwin64/usr/local/bin/Platypus_0.8.1

Robert@DESKTOP-14EL82S /cygdrive/c/cygwin64/usr/local/bin/Platypus_0.8.1
$ ./buildPlatypus.sh
Building Platypus
running build
running build_py
creating build
creating build/lib
copying vcf.py -> build/lib
running build
running build_py
copying extendedoptparse.py -> build/lib
running build
running build_py
copying window.py -> build/lib
running build
running build_py
copying variantutils.py -> build/lib
running build
running build_py
copying platypusexceptions.py -> build/lib
running build
running build_py
running build
running build_py
copying filez.py -> build/lib
running build
running build_py
copying runner.py -> build/lib
running build
running build_ext
building 'ctabix' extension
creating build/temp.cygwin-2.4.0-x86_64-2.7
creating build/temp.cygwin-2.4.0-x86_64-2.7/tabix

build/t                                                                                                                                                                                  emp.cygwin-2.4.0-x86_64-2.7/ctabix.o
ctabix.c: In function ‘__pyx_pf_6ctabix_9Tabixfile_7contigs___get__’:
ctabix.c:3304:21: warning: assignment from incompatible pointer type
   __pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nseque                                                                                                                                                                                  nces));

ctabix.c: In function ‘__pyx_pf_6ctabix_13TabixIterator_4__next__’:
ctabix.c:3858:15: warning: assignment discards ‘const’ qualifier from pointer ta                                                                                                                                                                                  rget type
     __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__py                                                                                                                                                                                  x_v_len));

ctabix.c:4239:13: warning: assignment discards ‘const’ qualifier from pointer ta                                                                                                                                                                                  rget type
   __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_                                                                                                                                                                                  v_len));

ctabix.c: In function ‘__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__’:
ctabix.c:5249:15: warning: assignment discards ‘const’ qualifier from pointer ta                                                                                                                                                                                  rget type
     __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__py                                                                                                                                                                                  x_v_len));

tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-                                                                                                                                                                                  prototypes]
  static inline kh_##name##_t *kh_init_##name() {      \

tabix/khash.h:484:2: note: in expansion of macro ‘KHASH_INIT’
  KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
  ^
tabix/bedidx.c.pysam.c:22:1: note: in expansion of macro ‘KHASH_MAP_INIT_STR’
 KHASH_MAP_INIT_STR(reg, bed_reglist_t)

tabix/bedidx.c.pysam.c: In function ‘bed_read’:
tabix/bedidx.c.pysam.c:121:4: warning: array subscript has type ‘char’ [-Wchar-s                                                                                                                                                                                  ubscripts]

tabix/bedidx.c.pysam.c:124:6: warning: array subscript has type ‘char’ [-Wchar-s                                                                                                                                                                                  ubscripts]
      if (ks_getuntil(ks, 0,

In file included from tabix/bgzf.c.pysam.c:40:0:
tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-                                                                                                                                                                                  prototypes]
  static inline kh_##name##_t *kh_init_##name() {      \
                               ^
tabix/khash.h:468:2: note: in expansion of macro ‘KHASH_INIT’
  KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal                                                                                                                                                                                  )
  ^

tabix/bgzf.c.pysam.c:46:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT64’
 KHASH_MAP_INIT_INT64(cache, cache_t)
 ^
tabix/bgzf.c.pysam.c:142:14: warning: function declaration isn’t a prototype [-W                                                                                                                                                                                  strict-prototypes]
 static BGZF *bgzf_read_init()
              ^

In function ‘bgzf_close’:
tabix/bgzf.c.pysam.c:632:8: warning: variable ‘count’ set but not used [-Wunused                                                                                                                                                                                  -but-set-variable]
    int count, block_length = deflate_block(fp, 0);

tabix/bgzip.c.pysam.c:38:12: warning: function declaration isn’t a prototype [-W                                                                                                                                                                                  strict-prototypes]

tabix/bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstri                                                                                                                                                                                  ct-prototypes]

In file included from tabix/index.c.pysam.c:6:0:
tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-                                                                                                                                                                                  prototypes]
  static inline kh_##name##_t *kh_init_##name() {      \
                               ^
tabix/khash.h:453:2: note: in expansion of macro ‘KHASH_INIT’
  KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
  ^
tabix/index.c.pysam.c:36:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT’
 KHASH_MAP_INIT_INT(i, ti_binlist_t)
 ^
tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-                                                                                                                                                                                  prototypes]
  static inline kh_##name##_t *kh_init_##name() {      \
                               ^
tabix/khash.h:484:2: note: in expansion of macro ‘KHASH_INIT’
  KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
  ^
tabix/index.c.pysam.c:37:1: note: in expansion of macro ‘KHASH_MAP_INIT_STR’
 KHASH_MAP_INIT_STR(s, int)
 ^
tabix/index.c.pysam.c: In function ‘ti_get_intv’:
tabix/index.c.pysam.c:187:8: warning: array subscript has type ‘char’ [-Wchar-su                                                                                                                                                                                  bscripts]
        op = toupper(*t);
        ^
tabix/index.c.pysam.c: In function ‘ti_parse_region’:
tabix/index.c.pysam.c:746:3: warning: array subscript has type ‘char’ [-Wchar-su                                                                                                                                                                                  bscripts]
   if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
   ^

 In function ‘kftp_get_response’:
tabix/knetfile.c.pysam.c:227:4: warning: array subscript has type ‘char’ [-Wchar                                                                                                                                                                                  -subscripts]

tabix/knetfile.c.pysam.c:227:4: warning: array subscript has type ‘char’ [-Wchar                                                                                                                                                                                  -subscripts]
tabix/knetfile.c.pysam.c:227:4: warning: array subscript has type ‘char’ [-Wchar                                                                                                                                                                                  -subscripts]

tabix/kstring.c.pysam.c: In function ‘ksplit_core’:
tabix/kstring.c.pysam.c:49:4: warning: array subscript has type ‘char’ [-Wchar-s                                                                                                                                                                                  ubscripts]

htslibWrapper.c:1:0: warning: -fPIC ignored for target (all code is position ind                                                                                                                                                                                  ependent)
 /* Generated by Cython 0.21.1 */
 ^
gcc -shared -Wl,--enable-auto-image-base -L. build/temp.cygwin-2.4.0-x86_64-2.7/                                                                                                                                                                                  htslibWrapper.o -L/usr/lib/python2.7/config -L/usr/lib -lhts -lpython2.7 -o buil                                                                                                                                                                                  d/lib.cygwin-2.4.0-x86_64-2.7/htslibWrapper.dll
/usr/lib/gcc/x86_64-pc-cygwin/4.9.3/../../../../x86_64-pc-cygwin/bin/ld: cannot                                                                                                                                                                                   find -lhts
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

Setup failed. Check previous lines for errors


I am new at this stuff and one question that comes to mind is should I be running Platypus inside cygwin?

 Bob May

[Daniel Cooke]

Hi Bob,

I don’t have any experience with Cygwin, but it looks like the problem is htslib isn’t found. I’m not sure just having the binaries is sufficient. There are instructions on the Github page on how to set up htslib properly for unix based systems.

Best

Dan

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[Robert May]

Daniel
Right here goes, this is what I did

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1
$ dir
align.c      build             cerrormodel.c  cpopulation.c  extendedoptparse.py  htslib-1.3       Platypus.py            pysam_util.c  runner.py  tabix         tandem.c   variantcaller.c  vcf.py
align.h      buildPlatypus.sh  cgenotype.c    ctabix.c       fastafile.c          htslibWrapper.c  platypusexceptions.py  pysam_util.h  setup.py   tabix_util.c  tandem.h   variantFilter.c  vcfutils.c
assembler.c  calign.c          chaplotype.c   cwindow.c      filez.py             LICENSE          platypusutils.c        README.txt    src        TabProxies.c  variant.c  variantutils.py  window.py

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1
$ export C_INCLUDE_PATH=HTSLIB-1.3/include

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1
$ export library_PATH=HTSLIB-1.3/lib

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1
$ export ld_library_PATH=HTSLIB-1.3/lib

ARE these two supposed to be files or folders? If folders should read htslib,
files are libhts.a, libhts.so, libhts.so.1

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1
$ cd htslib-1.3

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1/htslib-1.3
$ ./configure
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1/htslib-1.3
$ make
make: Nothing to be done for 'all'.

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1/htslib-1.3
$ make install
mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig
if test -n ""; then mkdir -p -m 755 ; fi
install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.3
ln -sf libhts.so.1.3 /usr/local/lib/libhts.so
ln -sf libhts.so.1.3 /usr/local/lib/libhts.so.1
sed -e 's#@includedir@#/usr/local/include#g;s#@libdir@#/usr/local/lib#g;s#@PACKAGE_VERSION@#1.3#g' htslib.pc.in > /usr/local/lib/pkgconfig/htslib.pc
chmod 644 /usr/local/lib/pkgconfig/htslib.pc
install -p bgzip htsfile tabix /usr/local/bin
if test -n ""; then install -p  ; fi
install -p -m 644 htslib/*.h /usr/local/include/htslib
install -p -m 644 libhts.a /usr/local/lib/libhts.a
install -p -m 644 htsfile.1 tabix.1 /usr/local/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/man5

Robert@DESKTOP-14EL82S ~
$ cd c:/cygwin64/usr/local/bin/Platypus_0.8.1

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1

$ ./buildPlatypus.sh
Building Platypus
running build
running build_py

running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build

running build_ext
building 'htslibWrapper' extension
gcc -fno-strict-aliasing -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python/python-2.7.10-1.x86_64/build=/usr/src/debug/python-2.7.10-1 -fdebug-prefix-map=/usr/src/ports/python/python-2.7.10-1.x86_64/src/Python-2.7.10=/usr/src/debug/python-2.7.10-1 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.cygwin-2.4.1-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC

htslibWrapper.c:1:0: warning: -fPIC ignored for target (all code is position independent)
 /* Generated by Cython 0.21.1 */
 ^

gcc -shared -Wl,--enable-auto-image-base -L. build/temp.cygwin-2.4.1-x86_64-2.7/htslibWrapper.o -L/usr/lib/python2.7/config -L/usr/lib -lhts -lpython2.7 -o build/lib.cygwin-2.4.1-x86_64-2.7/htslibWrapper.dll

/usr/lib/gcc/x86_64-pc-cygwin/4.9.3/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lhts
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

Setup failed. Check previous lines for errors

The reason I inserted htslib-1.3 into the folder Platypus_0.8.1 was to follow the convention in samtools-1.3 and bcftools-1.3
in there makefile I think the code is included to install htslib


bob







 Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree

---

From: dco...@well.ox.ac.uk
To: tpi...@gmail.com
CC: platypu...@googlegroups.com
Subject: Re: [Platypus] Error Building Playpus‏
Date: Wed, 27 Jan 2016 14:08:34 +0000

[Sven Klages]

Hi,

usually I compile htslib/platypus this way (as stated ini READM.md):

git clone https://github.com/andyrimmer/Platypus.git
cd Platypus/
git clone https://github.com/samtools/htslib.git
cd htslib/
make install prefix=$(pwd)
cd ..

export C_INCLUDE_PATH=/path/to/Platypus/htslib/include
export LIBRARY_PATH=/path/to/Platypus/htslib/lib
export LD_LIBRARY_PATH=/path/to/Platypus/htslib/lib

make

One problem I see is the naming of your env variables:

export library_PATH=HTSLIB-1.3/lib
export ld_library_PATH=HTSLIB-1.3/lib

naming is case-sensitive, path does not exist. It should better read:

export C_INCLUDE_PATH=/path/to/Platypus/htslib/include
export LIBRARY_PATH=/path/to/Platypus/htslib/lib
export LD_LIBRARY_PATH=/path/to/Platypus/htslib/lib

But that is probably not the problem that makes make fail ..

You have installed htslib in /usr/local and it seems that this directory is not used, so set the vars explicitly before compiling platypus:

export C_INCLUDE_PATH=/usr/local/include
export LIBRARY_PATH=/usr/local/lib
export LD_LIBRARY_PATH=/usr/local/lib

Check that these directories exist in /usr/local. Then type 'make' ...

hth,
Sven

[Bob May]

Sven
In the local dir there are 5 folders bin, etc (empty), include, lib and share

share > man > man1, man1##, man1install and man5

lib > folder pkgconfig and these files
libhts.a, libhts.so, libhts.so.1, libhts.so.1.1, libhts.so.1.2.1 and libhts.so.

include> htslib > 22 files

bin > goes to wherre packages  are

bob

[Sven Klages]

Have you tried compiling with

export C_INCLUDE_PATH=/usr/local/include
export LIBRARY_PATH=/usr/local/lib
export LD_LIBRARY_PATH=

/usr/local/lib

best,
Sven


[Bob May]

Sven have now but build still fails

/usr/local/lib/../lib/libhts.a(hts.o): In function `decompress_peek':
/usr/local/bin/bcftools-1.3/htslib-1.3/hts.c:142: undefined reference to `inflateInit2_'

this could be the problem as bcftools also has a problem

/usr/local/lib/../lib/libhts.a(cram_io.o): In function `zlib_mem_deflate':
/usr/local/bin/bcftools-1.3/htslib-1.3/cram/cram_io.c:782: undefined reference to `deflateInit2_'
the two highlighted are the probable problems
bcftools is still not installed

building 'htslibWrapper' extension
gcc -fno-strict-aliasing -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python/python-2.7.10-1.x86_64/build=/usr/src/debug/python-2.7.10-1 -fdebug-prefix-map=/usr/src/ports/python/python-2.7.10-1.x86_64/src/Python-2.7.10=/usr/src/debug/python-2.7.10-1 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.cygwin-2.4.1-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC
htslibWrapper.c:1:0: warning: -fPIC ignored for target (all code is position independent)
 /* Generated by Cython 0.2

so there is still a mess

[Sven Klages]

Please check if "zlib" is installed on your system, including "development" files (dev, header).
This error is related to zlib.

And think about using a "genuine" linux :-)

best,
Sven

[calima...@gmail.com]

Hi,

I'm also struggling with Platypus installation.
I tried to follow Sven's suggestions, but the htslib installation stopped with in an error:

cassia@cassia-pc:~/Área de Trabalho/SNPS/Platypus/htslib$ make install prefix=$(pwd)
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
gcc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.5-10-gcc55632"' > version.h
gcc -g -Wall -O2 -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
gcc -g -Wall -O2 -I.  -c -o bgzip.o bgzip.c
gcc  -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o htsfile.o htsfile.c
gcc  -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o tabix.o tabix.c
gcc  -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread
mkdir -p -m 755 /home/cassia/Área/bin /home/cassia/Área/include /home/cassia/Área/include/htslib /home/cassia/Área/lib /home/cassia/Área/share/man/man1 /home/cassia/Área/share/man/man5 /home/cassia/Área/lib/pkgconfig

if test -n ""; then mkdir -p -m 755 ; fi

gcc -g -Wall -O2 -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -I.  -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -I.  -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -Wall -O2 -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -I.  -fpic -c -o errmod.pico errmod.c
gcc -g -Wall -O2 -I.  -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -I.  -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -I.  -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -I.  -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -I.  -fpic -c -o hts_os.pico hts_os.c
gcc -g -Wall -O2 -I.  -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -I.  -fpic -c -o multipart.pico multipart.c
gcc -g -Wall -O2 -I.  -fpic -c -o probaln.pico probaln.c
gcc -g -Wall -O2 -I.  -fpic -c -o realn.pico realn.c
gcc -g -Wall -O2 -I.  -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -I.  -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -I.  -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -I.  -fpic -c -o textutils.pico textutils.c
gcc -g -Wall -O2 -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/files.pico cram/files.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -shared -Wl,-soname,libhts.so.2  -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread
ln -sf libhts.so libhts.so.2
install -p -m 644 libhts.so /home/cassia/Área/lib/libhts.so.1.5-10-gcc55632
ln -sf libhts.so.1.5-10-gcc55632 /home/cassia/Área/lib/libhts.so
ln -sf libhts.so.1.5-10-gcc55632 /home/cassia/Área/lib/libhts.so.2
sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp
sed -e 's#@-includedir@#/home/cassia/Área/include#g;s#@-libdir@#/home/cassia/Área/lib#g;s#@-PACKAGE_VERSION@#1.5-10-gcc55632#g' htslib.pc.tmp > /home/cassia/Área/lib/pkgconfig/htslib.pc
chmod 644 /home/cassia/Área/lib/pkgconfig/htslib.pc
install -p bgzip htsfile tabix /home/cassia/Área/bin

if test -n ""; then install -p  ; fi

install -p -m 644 htslib/*.h /home/cassia/Área/include/htslib
install -p -m 644 libhts.a /home/cassia/Área/lib/libhts.a
install -p -m 644 htsfile.1 tabix.1 /home/cassia/Área/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /home/cassia/Área/share/man/man5
make: *** No rule to make target 'de'.  Pare.


Can anyone help me to fix this error?

Cássia