Many warnings when running setup.py

[pieterlukasse]

I get these warnings when installing the tool. Not sure if this is a known issue (or maybe not a real issue at all?):

config.status: creating config.h
make: ./version.sh: Command not found
make: ./version.sh: Command not found
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
In function ‘full_path’,
    inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17:
htslib/cram/cram_io.c:3748:13: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
             strncpy(out, in, PATH_MAX);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.c:3740:9: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
         strncpy(out, in, PATH_MAX);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/bam_sort.c.pysam.c: In function ‘bam_sort_core_ext’:
samtools/bam_sort.c.pysam.c:2144:9: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
         strncpy(g_sort_tag, sort_by_tag, 2);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:511:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5877:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29358:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
In file included from pysam/htslib_util.h:4,
                 from pysam/libcalignmentfile.c:604:
/tmp/easy_install-vxtp94dd/pysam-0.15.3/htslib/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~

pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
In file included from pysam/libctabix.c:611:
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
/tmp/easy_install-vxtp94dd/pysam-0.15.3/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^~~~~~~
pysam/libctabix.c:13709:39: note: in expansion of macro ‘TBX_UCSC’
   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
                                       ^~~~~~~~
/tmp/easy_install-vxtp94dd/pysam-0.15.3/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^~~~~~~
pysam/libctabix.c:13741:39: note: in expansion of macro ‘TBX_UCSC’
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
                                       ^~~~~~~~
/tmp/easy_install-vxtp94dd/pysam-0.15.3/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^~~~~~~
pysam/libctabix.c:14111:43: note: in expansion of macro ‘TBX_UCSC’
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
                                           ^~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:32790:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5,
                 from pysam/libcbcf.c:603:
/tmp/easy_install-vxtp94dd/pysam-0.15.3/htslib/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~

pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.81’:
pysam/libcvcf.c:24840:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# pysam: htslib configure options: --enable-libcurl
# pysam: htslib_config LDFLAGS=

[alliemclean]

If they are just warning and the install was successful I don't think it is an issue.

[pieterlukasse]

just an example...why leave in warnings like:

warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'

? Might seem picky, but the point is: if one leaves in too many unnecessary warnings, the really important warnings will often be missed by the user/admin.

But perhaps this is not coming from your scripts but is part of pysam or some other library? Please let me know if this needs to be logged in some other repo. Thanks!

[alliemclean]

These warnings are definitely coming from another library.