Your message dated Sat, 15 Dec 2018 08:28:09 +0100
with message-id <20181215072809.kdqmfqerhpzh6...@an3as.eu>
and subject line Issue was solved in 0.10.0+git20180727-2
has caused the Debian Bug report #904836,
regarding cyvcf2: FTBFS in sid
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
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--
904836: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=904836
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Hi,
the problem was solved in 0.10.0+git20180727-2 but the bug was
not closed in changelog.
Kind regards
Andreas.
--
http://fam-tille.de
--- End Message ---
