Your message dated Wed, 12 Aug 2026 04:22:33 +0000
with message-id <[email protected]>
and subject line Bug#1144177: fixed in r-bioc-alabaster.base 1.12.1+dfsg-1
has caused the Debian Bug report #1144177,
regarding r-bioc-alabaster.base: FTBFS: collect2: error: ld returned 1 exit
status
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.)
--
1144177: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1144177
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-bioc-alabaster.base
Version: 1.6.1+ds-2
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-alabaster.base, 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-alabaster.base/ -O--buildsystem=R
I: R Package: alabaster.base Version: 1.6.1
I: Building using R version 4.6.1-4
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Sun, 12 Jan 2025 11:19:49 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library
--clean . --built-timestamp="'Sun, 12 Jan 2025 11:19:49 +0100'"
* installing *source* package âalabaster.baseâ ...
** this is package âalabaster.baseâ version â1.6.1â
** using staged installation
** libs
specified C++17
using C++ compiler: âx86_64-linux-gnu-g++ (Debian 16.2.0-1) 16.2.0â
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/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I/usr/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
check_csv.cpp -o check_csv.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I/usr/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
check_list.cpp -o check_list.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I/usr/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I/usr/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
is_rfc3339.cpp -o is_rfc3339.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I/usr/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
load_csv.cpp -o load_csv.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I/usr/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
load_list.cpp -o load_list.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I../inst/include -I/usr/include/hdf5/serial/
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/Rhdf5lib/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
validate.cpp -o validate.o
x86_64-linux-gnu-g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o
alabaster.base.so RcppExports.o check_csv.o check_list.o
choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o
validate.o -fPIC /usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so
-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lhdf5_cpp -lcrypto -lcurl
-lpthread -lsz -lz -L/usr/lib/R/lib -lR
/usr/bin/x86_64-linux-gnu-ld.bfd: cannot find
/usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so: No such file or directory
collect2: error: ld returned 1 exit status
make[1]: *** [/usr/share/R/share/make/shlib.mk:10: alabaster.base.so] 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 âalabaster.baseâ
* removing
â/<<PKGBUILDDIR>>/debian/r-bioc-alabaster.base/usr/lib/R/site-library/alabaster.baseâ
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library
--clean . --built-timestamp="'Sun, 12 Jan 2025 11:19:49 +0100'" 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-alabaster.base
Source-Version: 1.12.1+dfsg-1
Done: Charles Plessy <[email protected]>
We believe that the bug you reported is fixed in the latest version of
r-bioc-alabaster.base, 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-alabaster.base
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: Wed, 12 Aug 2026 11:03:42 +0900
Source: r-bioc-alabaster.base
Architecture: source
Version: 1.12.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Charles Plessy <[email protected]>
Closes: 1144177
Changes:
r-bioc-alabaster.base (1.12.1+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version. Closes: #1144177
* Use uscan v5 $template template. (routine-update)
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Restrict to R packages team core architectures (routine-update)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Refresh patch.
* Drop hdf5lib patch as unvendoring system changed.
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