Your message dated Mon, 28 Sep 2026 11:26:00 +0900
with message-id <[email protected]>
and subject line Re: r-bioc-delayedarray: FTBFS:
compress_atomic_vector.c:23:13: error: implicit declaration of function
'ATTRIB' [-Wimplicit-function-declaration]
has caused the Debian Bug report #1135461,
regarding r-bioc-delayedarray: FTBFS: compress_atomic_vector.c:23:13: error:
implicit declaration of function 'ATTRIB' [-Wimplicit-function-declaration]
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1135461: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1135461
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-bioc-delayedarray
Version: 0.32.0+dfsg-3
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202605/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:r-bioc-delayedarray, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules binary
dh binary --buildsystem R
dh_update_autotools_config -O--buildsystem=R
dh_autoreconf -O--buildsystem=R
dh_auto_configure -O--buildsystem=R
dh_auto_build -O--buildsystem=R
dh_auto_test -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=R
dh_prep -O--buildsystem=R
dh_auto_install --destdir=debian/r-bioc-delayedarray/ -O--buildsystem=R
I: R Package: DelayedArray Version: 0.32.0
I: Building using R version 4.6.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 13 Mar 2026 13:31:31 +0900
mkdir -p
/<<BUILDDIR>>/r-bioc-delayedarray-0.32.0\+dfsg/debian/r-bioc-delayedarray/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-delayedarray-0.32.0\+dfsg/debian/r-bioc-delayedarray/usr/lib/R/site-library
--clean . --built-timestamp="'Fri, 13 Mar 2026 13:31:31 +0900'"
* installing *source* package âDelayedArrayâ ...
** this is package âDelayedArrayâ version â0.32.0â
file âinst/doc/B-Implementing_a_backend.htmlâ is missing
** using staged installation
** libs
using C compiler: âx86_64-linux-gnu-gcc (Debian 15.2.0-17) 15.2.0â
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
R_init_DelayedArray.c -o R_init_DelayedArray.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
S4Vectors_stubs.c -o S4Vectors_stubs.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
compress_atomic_vector.c -o compress_atomic_vector.o
compress_atomic_vector.c: In function âsimple_object_sizeâ:
compress_atomic_vector.c:23:13: error: implicit declaration of function
âATTRIBâ [-Wimplicit-function-declaration]
23 | if (ATTRIB(x) != R_NilValue)
| ^~~~~~
compress_atomic_vector.c:23:23: warning: comparison between pointer and integer
23 | if (ATTRIB(x) != R_NilValue)
| ^~
make[1]: *** [/usr/lib/R/etc/Makeconf:190: compress_atomic_vector.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package âDelayedArrayâ
* removing
â/<<PKGBUILDDIR>>/debian/r-bioc-delayedarray/usr/lib/R/site-library/DelayedArrayâ
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-delayedarray-0.32.0\+dfsg/debian/r-bioc-delayedarray/usr/lib/R/site-library
--clean . --built-timestamp="'Fri, 13 Mar 2026 13:31:31 +0900'" returned exit
code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Version:0.38.2+dfsg-1
Latest version builds fine.
Cheers,
--
Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - [email protected]
Okinawa Institute of Science and Technology Graduate University
Senior staff scientist ~~ Luscombe Unit ~~ https://groups.oist.jp/grsu
Toots from work - ~~ ~~~~ ~~ - https://fediscience.org/@charles_plessy
--- End Message ---
