Your message dated Thu, 3 May 2018 12:06:36 +0200
with message-id <20180503100636.z5ef757xcwjox...@an3as.eu>
and subject line Re: Bug#897484: r-bioc-iranges: FTBFS: NCList.c:1499:9: error:
too few arguments to function 'new_Hits'
has caused the Debian Bug report #897484,
regarding r-bioc-iranges: FTBFS: NCList.c:1499:9: error: too few arguments to
function 'new_Hits'
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
Bug report if necessary, and/or fix the problem forthwith.
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immediately.)
--
897484: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897484
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: r-bioc-iranges
Version: 2.12.0-2
Severity: serious
Tags: buster sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20180502 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
> -I"/usr/lib/R/site-library/S4Vectors/include" -fpic -g -O2
> -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c NCList.c -o
> NCList.o
> NCList.c: In function 'NCList_find_overlaps':
> NCList.c:1499:18: warning: passing argument 1 of 'new_Hits' from incompatible
> pointer type [-Wincompatible-pointer-types]
> return new_Hits(qh_buf->elts, sh_buf->elts, IntAE_get_nelt(qh_buf),
> ^~~~~~
> In file included from NCList.c:6:0:
> /usr/lib/R/site-library/S4Vectors/include/S4Vectors_interface.h:531:6: note:
> expected 'const char *' but argument is of type 'int *'
> SEXP new_Hits(
> ^~~~~~~~
> NCList.c:1499:46: warning: passing argument 3 of 'new_Hits' makes pointer
> from integer without a cast [-Wint-conversion]
> return new_Hits(qh_buf->elts, sh_buf->elts, IntAE_get_nelt(qh_buf),
> ^~~~~~~~~~~~~~
> In file included from NCList.c:6:0:
> /usr/lib/R/site-library/S4Vectors/include/S4Vectors_interface.h:531:6: note:
> expected 'const int *' but argument is of type 'size_t {aka long unsigned
> int}'
> SEXP new_Hits(
> ^~~~~~~~
> NCList.c:1499:9: error: too few arguments to function 'new_Hits'
> return new_Hits(qh_buf->elts, sh_buf->elts, IntAE_get_nelt(qh_buf),
> ^~~~~~~~
> In file included from NCList.c:6:0:
> /usr/lib/R/site-library/S4Vectors/include/S4Vectors_interface.h:531:6: note:
> declared here
> SEXP new_Hits(
> ^~~~~~~~
> NCList.c: In function 'NCList_find_overlaps_in_groups':
> NCList.c:1609:18: warning: passing argument 1 of 'new_Hits' from incompatible
> pointer type [-Wincompatible-pointer-types]
> return new_Hits(qh_buf->elts, sh_buf->elts, IntAE_get_nelt(qh_buf),
> ^~~~~~
> In file included from NCList.c:6:0:
> /usr/lib/R/site-library/S4Vectors/include/S4Vectors_interface.h:531:6: note:
> expected 'const char *' but argument is of type 'int *'
> SEXP new_Hits(
> ^~~~~~~~
> NCList.c:1609:46: warning: passing argument 3 of 'new_Hits' makes pointer
> from integer without a cast [-Wint-conversion]
> return new_Hits(qh_buf->elts, sh_buf->elts, IntAE_get_nelt(qh_buf),
> ^~~~~~~~~~~~~~
> In file included from NCList.c:6:0:
> /usr/lib/R/site-library/S4Vectors/include/S4Vectors_interface.h:531:6: note:
> expected 'const int *' but argument is of type 'size_t {aka long unsigned
> int}'
> SEXP new_Hits(
> ^~~~~~~~
> NCList.c:1609:9: error: too few arguments to function 'new_Hits'
> return new_Hits(qh_buf->elts, sh_buf->elts, IntAE_get_nelt(qh_buf),
> ^~~~~~~~
> In file included from NCList.c:6:0:
> /usr/lib/R/site-library/S4Vectors/include/S4Vectors_interface.h:531:6: note:
> declared here
> SEXP new_Hits(
> ^~~~~~~~
> make[1]: *** [/usr/lib/R/etc/Makeconf:159: NCList.o] Error 1
The full build log is available from:
http://aws-logs.debian.net/2018/05/02/r-bioc-iranges_2.12.0-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
On Wed, May 02, 2018 at 10:05:12PM +0200, Lucas Nussbaum wrote:
> Source: r-bioc-iranges
> Version: 2.12.0-2
Closed with new upstream version upload.
This error happened due to a transition of BioConductor packaged. We
are aware that we are not following the roles for transition by
upgrading r-bioc-* packages. However, since the transitions in the
past went well this way and due to the limited number of users that
might be affected that way it seems a reasonable approach to do the
transition this way.
Debian-r list readers: Please rise your voice if you disagree that we
are following this "sloppy transition" route without a formal transition
announcement.
Kind regards
Andreas.
--
http://fam-tille.de
--- End Message ---
