Your message dated Thu, 3 May 2018 12:06:36 +0200 with message-id <[email protected]> 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.
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--- Begin Message ---Source: r-bioc-iranges Version: 2.12.0-2 Severity: serious Tags: buster sid User: [email protected] 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.
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--- 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
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