Package: src:cyvcf2
Version: 0.10.0+git20180727-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in sid but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-arch
dh build-arch --with python2,python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:217: python2.7 setup.py config
running config
I: pybuild base:217: python3.7 setup.py config
running config
I: pybuild base:217: python3.6 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python setup.py build
running build
[... snipped ...]
cyvcf2/cyvcf2.c: In function '__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record':
cyvcf2/cyvcf2.c:40497:60: warning: passing argument 1 of 'bcf_hdr_add_hrec'
discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
__pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) <
0) != 0);
~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from cyvcf2/helpers.h:1,
from cyvcf2/cyvcf2.c:571:
htslib/htslib/vcf.h:482:37: note: expected 'bcf_hdr_t *' {aka 'struct
<anonymous> *'} but argument is of type 'const bcf_hdr_t *' {aka 'const struct
<anonymous> *'}
int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
~~~~~~~~~~~^~~
cyvcf2/cyvcf2.c:40535:49: warning: passing argument 1 of 'bcf_hdr_sync'
discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
(void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from cyvcf2/helpers.h:1,
from cyvcf2/cyvcf2.c:571:
htslib/htslib/vcf.h:479:33: note: expected 'bcf_hdr_t *' {aka 'struct
<anonymous> *'} but argument is of type 'const bcf_hdr_t *' {aka 'const struct
<anonymous> *'}
int bcf_hdr_sync(bcf_hdr_t *h);
~~~~~~~~~~~^
cyvcf2/cyvcf2.c:40594:100: warning: passing argument 2 of 'bcf_write' discards
'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
__pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts,
__pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2))
__PYX_ERR(0, 2073, __pyx_L1_error)
~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from cyvcf2/helpers.h:1,
from cyvcf2/cyvcf2.c:571:
htslib/htslib/vcf.h:370:43: note: expected 'bcf_hdr_t *' {aka 'struct
<anonymous> *'} but argument is of type 'const bcf_hdr_t *' {aka 'const struct
<anonymous> *'}
int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v);
~~~~~~~~~~~^
At top level:
cyvcf2/cyvcf2.c:6771:18: warning: '__pyx_f_6cyvcf2_6cyvcf2_xstr' defined but
not used [-Wunused-function]
static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
-fno-strict-aliasing -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/cyvcf2-0.10.0+git20180727=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2
-I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7
-c htslib/hfile_s3.c -o build/temp.linux-amd64-2.7/htslib/hfile_s3.o
In file included from htslib/hfile_internal.h:32,
from htslib/hfile_s3.c:33:
htslib/textutils_internal.h:68:1: warning: function declaration isn't a
prototype [-Wstrict-prototypes]
hts_json_token * hts_json_alloc_token();
^~~~~~~~~~~~~~
In file included from htslib/htslib/hts.h:35,
from htslib/hfile_s3.c:37:
htslib/htslib/hts_log.h:52:6: warning: function declaration isn't a prototype
[-Wstrict-prototypes]
enum htsLogLevel hts_get_log_level();
^~~~~~~~~~~
htslib/hfile_s3.c:69:10: fatal error: openssl/hmac.h: No such file or directory
#include <openssl/hmac.h>
^~~~~~~~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
E: pybuild pybuild:338: build: plugin distutils failed with: exit code=1:
/usr/bin/python setup.py build
dh_auto_build: pybuild --build -i python{version} -p 2.7 returned exit code 13
make: *** [debian/rules:9: build-arch] Error 25
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit
status 2
--------------------------------------------------------------------------------
Seems like a missing build-depends somewhere.
There are also build failures here:
https://buildd.debian.org/status/package.php?p=cyvcf2
Thanks.
