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higlass / clodius

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
MIT License
38 stars 21 forks source link

error installation #136

Open Nico-FR opened 3 years ago

Nico-FR commented 3 years ago

I am using conda version 4.9.2 with python version 3.7.9

I am getting this error while trying to install clodius. pip install clodius

Defaulting to user installation because normal site-packages is not writeable
Collecting clodius
  Using cached clodius-0.15.4-py2.py3-none-any.whl
Requirement already satisfied: pandas in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.1.5)
Requirement already satisfied: pybbi>=0.2.0 in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (0.3.0)
Requirement already satisfied: dask in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (2.30.0)
Requirement already satisfied: nose in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.3.7)
Requirement already satisfied: numpy in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.19.4)
Requirement already satisfied: pysam in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (0.16.0.1)
Requirement already satisfied: h5py>=3.0.0 in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (3.1.0)
Requirement already satisfied: requests in /usr/lib/python3/dist-packages (from clodius) (2.9.1)
Requirement already satisfied: slugid in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (2.0.0)
Requirement already satisfied: sortedcontainers in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (2.3.0)
Requirement already satisfied: negspy in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (0.2.24)
Requirement already satisfied: Click>=7 in /home/nmary/.local/lib/python3.6/site-packages (fromclodius) (7.1.2)
Collecting cooler>=0.8.5
  Using cached cooler-0.8.10-py2.py3-none-any.whl (100 kB)
Requirement already satisfied: pyfaidx in /home/nmary/.local/lib/python3.6/site-packages (from cooler>=0.8.5->clodius) (0.5.9.2)
Requirement already satisfied: pandas in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.1.5)
Requirement already satisfied: scipy>=0.16 in /usr/lib/python3/dist-packages (from cooler>=0.8.5->clodius) (0.17.0)
Requirement already satisfied: pyyaml in /home/nmary/.local/lib/python3.6/site-packages (from cooler>=0.8.5->clodius) (5.3.1)
Requirement already satisfied: simplejson in /home/nmary/.local/lib/python3.6/site-packages (from cooler>=0.8.5->clodius) (3.17.2)
Requirement already satisfied: numpy in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.19.4)
Requirement already satisfied: asciitree in /home/nmary/.local/lib/python3.6/site-packages (from cooler>=0.8.5->clodius) (0.3.3)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from cooler>=0.8.5->clodius) (1.10.0)
Requirement already satisfied: multiprocess in /home/nmary/.local/lib/python3.6/site-packages (from cooler>=0.8.5->clodius) (0.70.11.1)
Requirement already satisfied: Click>=7 in /home/nmary/.local/lib/python3.6/site-packages (fromclodius) (7.1.2)
Requirement already satisfied: h5py>=3.0.0 in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (3.1.0)
Collecting cytoolz<0.11
  Using cached cytoolz-0.10.1.tar.gz (475 kB)
Requirement already satisfied: toolz>=0.8.0 in /home/nmary/.local/lib/python3.6/site-packages (from cytoolz<0.11->cooler>=0.8.5->clodius) (0.11.1)
Requirement already satisfied: pyyaml in /home/nmary/.local/lib/python3.6/site-packages (from cooler>=0.8.5->clodius) (5.3.1)
Requirement already satisfied: cached-property in /home/nmary/.local/lib/python3.6/site-packages (from h5py>=3.0.0->clodius) (1.5.2)
Requirement already satisfied: numpy in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.19.4)
Requirement already satisfied: dill>=0.3.3 in /home/nmary/.local/lib/python3.6/site-packages (from multiprocess->cooler>=0.8.5->clodius) (0.3.3)
Requirement already satisfied: numpy in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.19.4)
Requirement already satisfied: python-dateutil>=2.7.3 in /home/nmary/.local/lib/python3.6/site-packages (from pandas->clodius) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in /home/nmary/.local/lib/python3.6/site-packages (from pandas->clodius) (2020.4)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from cooler>=0.8.5->clodius) (1.10.0)
Requirement already satisfied: numpy in /home/nmary/.local/lib/python3.6/site-packages (from clodius) (1.19.4)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from cooler>=0.8.5->clodius) (1.10.0)
Requirement already satisfied: setuptools>=0.7 in /usr/lib/python3/dist-packages (from pyfaidx->cooler>=0.8.5->clodius) (20.7.0)
Collecting pypairix
  Using cached pypairix-0.3.7.tar.gz (65 kB)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from cooler>=0.8.5->clodius) (1.10.0)
Building wheels for collected packages: cytoolz, pypairix
  Building wheel for cytoolz (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u3134huj/cytoolz_2d7c79c3493f4977b45a100f52449866/setup.py'"'"'; __file__='"'"'/tmp/pip-install-u3134huj/cytoolz_2d7c79c3493f4977b45a100f52449866/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-_x8kzcl4
       cwd: /tmp/pip-install-u3134huj/cytoolz_2d7c79c3493f4977b45a100f52449866/
  Complete output (55 lines):
  ALERT: Cython not installed.  Building without Cython.
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/_signatures.py -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/__init__.py -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/utils_test.py -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/_version.py -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/compatibility.py -> build/lib.linux-x86_64-3.6/cytoolz
  creating build/lib.linux-x86_64-3.6/cytoolz/curried
  copying cytoolz/curried/operator.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
  copying cytoolz/curried/__init__.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
  copying cytoolz/curried/exceptions.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
  copying cytoolz/utils.pyx -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/dicttoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/functoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/recipes.pyx -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/itertoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/itertoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/utils.pxd -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/cpython.pxd -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/functoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/__init__.pxd -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/recipes.pxd -> build/lib.linux-x86_64-3.6/cytoolz
  copying cytoolz/dicttoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
  creating build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_serialization.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_tlz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_doctests.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_dicttoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_functoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_embedded_sigs.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_none_safe.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_itertoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_curried.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_recipes.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_docstrings.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_compatibility.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_signatures.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_utils.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_inspect_args.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/dev_skip_test.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_curried_toolzlike.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  copying cytoolz/tests/test_dev_skip_test.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
  running build_ext
  building 'cytoolz.dicttoolz' extension
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/cytoolz
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c cytoolz/dicttoolz.c -o build/temp.linux-x86_64-3.6/cytoolz/dicttoolz.o
  cytoolz/dicttoolz.c:17:20: fatal error: Python.h: No such file or directory
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for cytoolz
  Running setup.py clean for cytoolz
  Building wheel for pypairix (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/setup.py'"'"'; __file__='"'"'/tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-orgo01oy
       cwd: /tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/
  Complete output (146 lines):
  running bdist_wheel
  running build
  running build_ext
  building 'pypairix' extension
  creating build
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/src
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/bgzf.c -o build/temp.linux-x86_64-3.6/src/bgzf.o
  src/bgzf.c: In function ‘bgzf_block_length’:
  src/bgzf.c:331:27: warning: unused variable ‘remaining’ [-Wunused-variable]
    int count, block_length, remaining;
                             ^
  src/bgzf.c:330:40: warning: unused variable ‘compressed_block’ [-Wunused-variable]
    uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
                                          ^
  src/bgzf.c: In function ‘bgzf_close’:
  src/bgzf.c:456:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
    int ret, count, block_length;
             ^
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/bgzip.c -o build/temp.linux-x86_64-3.6/src/bgzip.o
  src/bgzip.c: In function ‘main’:
  src/bgzip.c:198:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
      write(f_dst, buffer, c);
      ^
  src/bgzip.c: In function ‘write_open’:
  src/bgzip.c:57:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
      scanf("%c", &c);
      ^
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/index.c -o build/temp.linux-x86_64-3.6/src/index.o
  src/index.c: In function ‘ti_parse_region2d’:
  src/index.c:864:69: warning: passing argument 1 of ‘ti_get_region_split_character’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           char region_split_character = ti_get_region_split_character(idx);
                                                                       ^
  In file included from src/index.c:11:0:
  src/pairix.h:218:14: note: expected ‘ti_index_t * {aka struct __ti_index_t *}’ but argument is of type ‘const ti_index_t * {aka const struct __ti_index_t *}’
           char ti_get_region_split_character(ti_index_t *idx);
                ^
  src/index.c:878:30: warning: passing argument 1 of ‘ti_get_sc2’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           int dim = ti_get_sc2(idx)+1==0?1:2;
                                ^
  In file included from src/index.c:11:0:
  src/pairix.h:209:13: note: expected ‘ti_index_t * {aka struct __ti_index_t *}’ but argument is of type ‘const ti_index_t * {aka const struct __ti_index_t *}’
           int ti_get_sc2(ti_index_t *idx);
               ^
  src/index.c: In function ‘ti_querys_2d_general’:
  src/index.c:1219:31: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
            char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
                                 ^
  src/index.c:1236:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types]
            sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list);
                                                             ^
  In file included from src/index.c:11:0:
  src/pairix.h:131:28: note: expected ‘const char **’ but argument is of type ‘char **’
           sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs);
                              ^
  src/index.c:1242:30: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
            *sp=0; char *chr1 = reg;
                                ^
  src/index.c:1246:31: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
            char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
                                 ^
  src/index.c:1263:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types]
            sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list);
                                                             ^
  In file included from src/index.c:11:0:
  src/pairix.h:131:28: note: expected ‘const char **’ but argument is of type ‘char **’
           sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs);
                              ^
  src/index.c: In function ‘ti_query_2d_tid’:
  src/index.c:1417:24: warning: return makes integer from pointer without a cast [-Wint-conversion]
    if (name == 0) return ti_iter_first();
                          ^
  src/index.c: In function ‘create_merged_iter’:
  src/index.c:1469:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
        if( miter->iu = calloc(n,sizeof(iter_unit*))) {
        ^
  src/index.c: In function ‘merged_ti_read’:
  src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly);
                     ^
  src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
         miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter
                   ^
  src/index.c: In function ‘sequential_ti_read’:
  src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
       char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
                 ^
  src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
         s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
           ^
  src/index.c: In function ‘get_unique_merged_seqname’:
  src/index.c:1643:22: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
               seqnames = ti_seqname(tbs[i]->idx,&len);
                        ^
  src/index.c: In function ‘flip_region’:
  src/index.c:1744:19: warning: variable ‘split_pos’ set but not used [-Wunused-but-set-variable]
       int l, i, l2, split_pos;
                     ^
  src/index.c: In function ‘querys_2D_wrapper’:
  src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           char *reg2 = flip_region(reg, get_region_split_character(tb));
                                    ^
  src/index.c:1743:7: note: expected ‘char *’ but argument is of type ‘const char *’
   char *flip_region ( char* s, char region_split_character) {
         ^
  src/index.c: In function ‘check_triangle’:
  src/index.c:1971:23: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
       char **seqnames = ti_seqname(idx,&len);
                         ^
  src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); }  // not atriangle
                                                                  ^
  In file included from src/khash.h:94:0,
                   from src/index.c:4:
  /usr/include/stdlib.h:483:13: note: expected ‘void *’ but argument is of type ‘const char *’
   extern void free (void *__ptr) __THROW;
               ^
  src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           free(reg2);
                ^
  In file included from src/khash.h:94:0,
                   from src/index.c:4:
  /usr/include/stdlib.h:483:13: note: expected ‘void *’ but argument is of type ‘const char *’
   extern void free (void *__ptr) __THROW;
               ^
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/knetfile.c -o build/temp.linux-x86_64-3.6/src/knetfile.o
  In file included from src/knetfile.c:49:0:
  src/knetfile.c: In function ‘kftp_send_cmd’:
  src/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                  ^
  src/knetfile.c:239:2: note: in expansion of macro ‘netwrite’
    netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
    ^
  src/knetfile.c: In function ‘khttp_connect_file’:
  src/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                  ^
  src/knetfile.c:418:2: note: in expansion of macro ‘netwrite’
    netwrite(fp->fd, buf, l);
    ^
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/kstring.c -o build/temp.linux-x86_64-3.6/src/kstring.o
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/pairixmodule.c -o build/temp.linux-x86_64-3.6/src/pairixmodule.o
  src/pairixmodule.c:33:20: fatal error: Python.h: No such file or directory
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pypairix
  Running setup.py clean for pypairix
Failed to build cytoolz pypairix
Installing collected packages: pypairix, cytoolz, cooler, clodius
    Running setup.py install for pypairix ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/setup.py'"'"'; __file__='"'"'/tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vvw_kum4/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/nmary/.local/include/python3.6m/pypairix
         cwd: /tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/
    Complete output (146 lines):
    running install
    running build
    running build_ext
    building 'pypairix' extension
    creating build
    creating build/temp.linux-x86_64-3.6
    creating build/temp.linux-x86_64-3.6/src
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/bgzf.c -o build/temp.linux-x86_64-3.6/src/bgzf.o
    src/bgzf.c: In function ‘bgzf_block_length’:
    src/bgzf.c:331:27: warning: unused variable ‘remaining’ [-Wunused-variable]
      int count, block_length, remaining;
                               ^
    src/bgzf.c:330:40: warning: unused variable ‘compressed_block’ [-Wunused-variable]
      uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
                                            ^
    src/bgzf.c: In function ‘bgzf_close’:
    src/bgzf.c:456:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
      int ret, count, block_length;
               ^
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/bgzip.c -o build/temp.linux-x86_64-3.6/src/bgzip.o
    src/bgzip.c: In function ‘main’:
    src/bgzip.c:198:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
        write(f_dst, buffer, c);
        ^
    src/bgzip.c: In function ‘write_open’:
    src/bgzip.c:57:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
        scanf("%c", &c);
        ^
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/index.c -o build/temp.linux-x86_64-3.6/src/index.o
    src/index.c: In function ‘ti_parse_region2d’:
    src/index.c:864:69: warning: passing argument 1 of ‘ti_get_region_split_character’ discards‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             char region_split_character = ti_get_region_split_character(idx);
                                                                         ^
    In file included from src/index.c:11:0:
    src/pairix.h:218:14: note: expected ‘ti_index_t * {aka struct __ti_index_t *}’ but argumentis of type ‘const ti_index_t * {aka const struct __ti_index_t *}’
             char ti_get_region_split_character(ti_index_t *idx);
                  ^
    src/index.c:878:30: warning: passing argument 1 of ‘ti_get_sc2’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             int dim = ti_get_sc2(idx)+1==0?1:2;
                                  ^
    In file included from src/index.c:11:0:
    src/pairix.h:209:13: note: expected ‘ti_index_t * {aka struct __ti_index_t *}’ but argumentis of type ‘const ti_index_t * {aka const struct __ti_index_t *}’
             int ti_get_sc2(ti_index_t *idx);
                 ^
    src/index.c: In function ‘ti_querys_2d_general’:
    src/index.c:1219:31: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
              char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
                                   ^
    src/index.c:1236:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types]
              sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list);
                                                               ^
    In file included from src/index.c:11:0:
    src/pairix.h:131:28: note: expected ‘const char **’ but argument is of type ‘char **’
             sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs);
                                ^
    src/index.c:1242:30: warning: initialization discards ‘const’ qualifier from pointer targettype [-Wdiscarded-qualifiers]
              *sp=0; char *chr1 = reg;
                                  ^
    src/index.c:1246:31: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
              char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
                                   ^
    src/index.c:1263:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types]
              sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list);
                                                               ^
    In file included from src/index.c:11:0:
    src/pairix.h:131:28: note: expected ‘const char **’ but argument is of type ‘char **’
             sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs);
                                ^
    src/index.c: In function ‘ti_query_2d_tid’:
    src/index.c:1417:24: warning: return makes integer from pointer without a cast [-Wint-conversion]
      if (name == 0) return ti_iter_first();
                            ^
    src/index.c: In function ‘create_merged_iter’:
    src/index.c:1469:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
          if( miter->iu = calloc(n,sizeof(iter_unit*))) {
          ^
    src/index.c: In function ‘merged_ti_read’:
    src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly);
                       ^
    src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter
                     ^
    src/index.c: In function ‘sequential_ti_read’:
    src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from pointer targettype [-Wdiscarded-qualifiers]
         char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
                   ^
    src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer target type[-Wdiscarded-qualifiers]
           s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
             ^
    src/index.c: In function ‘get_unique_merged_seqname’:
    src/index.c:1643:22: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                 seqnames = ti_seqname(tbs[i]->idx,&len);
                          ^
    src/index.c: In function ‘flip_region’:
    src/index.c:1744:19: warning: variable ‘split_pos’ set but not used [-Wunused-but-set-variable]
         int l, i, l2, split_pos;
                       ^
    src/index.c: In function ‘querys_2D_wrapper’:
    src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             char *reg2 = flip_region(reg, get_region_split_character(tb));
                                      ^
    src/index.c:1743:7: note: expected ‘char *’ but argument is of type ‘const char *’
     char *flip_region ( char* s, char region_split_character) {
           ^
    src/index.c: In function ‘check_triangle’:
    src/index.c:1971:23: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
         char **seqnames = ti_seqname(idx,&len);
                           ^
    src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
               if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); }  // nota triangle
                                                                    ^
    In file included from src/khash.h:94:0,
                     from src/index.c:4:
    /usr/include/stdlib.h:483:13: note: expected ‘void *’ but argument is of type ‘const char *’
     extern void free (void *__ptr) __THROW;
                 ^
    src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             free(reg2);
                  ^
    In file included from src/khash.h:94:0,
                     from src/index.c:4:
    /usr/include/stdlib.h:483:13: note: expected ‘void *’ but argument is of type ‘const char *’
     extern void free (void *__ptr) __THROW;
                 ^
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/knetfile.c -o build/temp.linux-x86_64-3.6/src/knetfile.o
    In file included from src/knetfile.c:49:0:
    src/knetfile.c: In function ‘kftp_send_cmd’:
    src/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
     #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                    ^
    src/knetfile.c:239:2: note: in expansion of macro ‘netwrite’
      netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
      ^
    src/knetfile.c: In function ‘khttp_connect_file’:
    src/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
     #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                    ^
    src/knetfile.c:418:2: note: in expansion of macro ‘netwrite’
      netwrite(fp->fd, buf, l);
      ^
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/kstring.c -o build/temp.linux-x86_64-3.6/src/kstring.o
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.6m -c src/pairixmodule.c -o build/temp.linux-x86_64-3.6/src/pairixmodule.o
    src/pairixmodule.c:33:20: fatal error: Python.h: No such file or directory
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/setup.py'"'"'; __file__='"'"'/tmp/pip-install-u3134huj/pypairix_718f50138e644c16bc5e5e7ed36493a6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record/tmp/pip-record-vvw_kum4/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/nmary/.local/include/python3.6m/pypairix Check the logs for full command output.

I aslo had many issues to install Higlass (see https://github.com/higlass/higlass-manage/issues/69).

Thank you for your help.

Nico-FR commented 3 years ago

I managed to install it with python3.7 -m pip install clodius But when I tried clodius aggregate bedfile /tmp/sample.short.bed:

Traceback (most recent call last):
  File "/home/nmary/.local/bin/clodius", line 5, in <module>
    from clodius.cli.aggregate import cli
ModuleNotFoundError: No module named 'clodius'
pkerpedjiev commented 3 years ago

Looks like this is the important part:

  src/pairixmodule.c:33:20: fatal error: Python.h: No such file or directory

Could you see if this helps: https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory?

Nico-FR commented 3 years ago

Indeed kg-config --cflags --libs python3 return python3.5m:

-I/usr/include/python3.5m -I/usr/include/x86_64-linux-gnu/python3.5m -lpython3.5m

while the installation procedure is looking for -fPIC -I/usr/include/python3.6m

I have python.h in python3.5m: ls -lh /usr/include/python3.5/Python.h

-rw-r--r-- 1 root root 2.9K Oct  9 18:52 /usr/include/python3.5/Python.h

But /usr/include/python3.6m doesn't exist. I will try to find a solution tomorrow.

Nico-FR commented 3 years ago

Hi, I solve the problem just by installing the needed version of python dev sudo apt-get install python3.6-dev.

I had another problem that I solved (I give my solution just in case):

curl https://raw.githubusercontent.com/hms-dbmi/clodius/develop/test/sample_data/geneAnnotationsExonsUnions.short.bed \
> ./sample.short.bed
clodius aggregate bedfile ./sample.short.bed

return:

Traceback (most recent call last):
  File "/home/nmary/.local/bin/clodius", line 5, in <module>
    from clodius.cli.aggregate import cli
  File "/home/nmary/.local/lib/python3.6/site-packages/clodius/cli/__init__.py", line 18, in <module>
    from . import (  # noqa: F401
  File "/home/nmary/.local/lib/python3.6/site-packages/clodius/cli/aggregate.py", line 23, in <module>
    import scipy.misc as sm
  File "/usr/lib/python3/dist-packages/scipy/misc/__init__.py", line 51, in <module>
    from scipy.special import comb, factorial, factorial2, factorialk
  File "/usr/lib/python3/dist-packages/scipy/special/__init__.py", line 627, in <module>
    from ._ufuncs import *
ModuleNotFoundError: No module named 'scipy.special._ufuncs'

So I removed the scipy version 0.17.0 installed by ubuntu sudo apt-get purge python3-scipy and installed the last one 1.5.4 pip3 install scipy and the aggregate command works!

pkerpedjiev commented 3 years ago

Glad you got it set up and thank you so much for posting the solutions!