Your message dated Mon, 03 Aug 2026 00:50:17 +0000
with message-id <[email protected]>
and subject line Bug#1143377: fixed in r-bioc-biocneighbors 2.6.0+dfsg-1
has caused the Debian Bug report #1143377,
regarding r-bioc-biocneighbors: FTBFS: ../inst/include/BiocNeighbors.h:23:48:
error: wrong number of template arguments (3, should be 2)
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.)
--
1143377: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1143377
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-bioc-biocneighbors
Version: 2.0.1+ds-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/202608/
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-biocneighbors, 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-biocneighbors/ -O--buildsystem=R
I: R Package: BiocNeighbors Version: 2.0.1
I: Building using R version 4.6.1-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 13 Mar 2026 12:17:11 +0900
mkdir -p
/<<BUILDDIR>>/r-bioc-biocneighbors-2.0.1\+ds/debian/r-bioc-biocneighbors/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-biocneighbors-2.0.1\+ds/debian/r-bioc-biocneighbors/usr/lib/R/site-library
--clean . --built-timestamp="'Fri, 13 Mar 2026 12:17:11 +0900'"
* installing *source* package âBiocNeighborsâ ...
** this is package âBiocNeighborsâ version â2.0.1â
file âinst/doc/userguide.htmlâ is missing
** using staged installation
** libs
specified C++17
using C++ compiler: âx86_64-linux-gnu-g++ (Debian 16.1.0-3) 16.1.0â
using C++17
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/assorthead/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
../inst/include/BiocNeighbors.h:23:48: error: wrong number of template
arguments (3, should be 2)
23 | typedef knncolle::SimpleMatrix<int, int, double> SimpleMatrix;
| ^
In file included from
/usr/lib/R/site-library/assorthead/include/knncolle/Builder.hpp:5,
from
/usr/lib/R/site-library/assorthead/include/knncolle/knncolle.hpp:4,
from ../inst/include/BiocNeighbors.h:6:
/usr/lib/R/site-library/assorthead/include/knncolle/Matrix.hpp:135:20: note:
provided for âtemplate<class Index_, class Data_> class
knncolle::SimpleMatrixâ
135 | class SimpleMatrix final : public Matrix<Index_, Data_> {
| ^~~~~
../inst/include/BiocNeighbors.h:28:47: error: wrong number of template
arguments (2, should be at least 3)
28 | typedef knncolle::Builder<SimpleMatrix, double> Builder;
| ^
/usr/lib/R/site-library/assorthead/include/knncolle/Builder.hpp:28:7: note:
provided for âtemplate<class Index_, class Data_, class Distance_, class
Matrix_> class knncolle::Builderâ
28 | class Builder {
| ^~~~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:199: RcppExports.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 âBiocNeighborsâ
* removing
â/<<PKGBUILDDIR>>/debian/r-bioc-biocneighbors/usr/lib/R/site-library/BiocNeighborsâ
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-biocneighbors-2.0.1\+ds/debian/r-bioc-biocneighbors/usr/lib/R/site-library
--clean . --built-timestamp="'Fri, 13 Mar 2026 12:17:11 +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 ---
Source: r-bioc-biocneighbors
Source-Version: 2.6.0+dfsg-1
Done: Charles Plessy <[email protected]>
We believe that the bug you reported is fixed in the latest version of
r-bioc-biocneighbors, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <[email protected]> (supplier of updated r-bioc-biocneighbors
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 03 Aug 2026 08:06:18 +0900
Source: r-bioc-biocneighbors
Architecture: source
Version: 2.6.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Charles Plessy <[email protected]>
Closes: 1143377
Changes:
r-bioc-biocneighbors (2.6.0+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version. Closes: #1143377.
* Use uscan v5 $template template. (routine-update)
* Standards-Version: 4.7.4 (routine-update)
* Restrict to R packages team core architectures (routine-update)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* lintian-brush: add d/u/metadata (routine-update)
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