Your message dated Mon, 28 Sep 2026 11:18:09 +0900
with message-id <[email protected]>
and subject line Re: r-bioc-ioniser: FTBFS: Detected bibliography in YAML
(IONiseR.md) but the rbibutils package is unavailable.
has caused the Debian Bug report #1136926,
regarding r-bioc-ioniser: FTBFS: Detected bibliography in YAML (IONiseR.md) but
the rbibutils package is unavailable.
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
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1136926: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1136926
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-bioc-ioniser
Version: 2.30.0+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-ioniser, 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
debian/rules execute_after_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd inst/doc && Rscript -e "require(knitr); require(markdown);
knit('IONiseR.Rmd', 'IONiseR.md'); markdownToHTML('IONiseR.md', 'IONiseR.html',
options=c('use_xhtml', 'base64_images'));" && rm -f IONiseR.md
Loading required package: knitr
Loading required package: markdown
processing file: IONiseR.Rmd
1/37
2/37 [style]
3/37
4/37 [loadLibs]
5/37
6/37 [readData]
7/37
8/37 [loadData]
9/37
10/37 [exampleData]
11/37
12/37 [extractData1]
13/37
14/37 [extractData2]
15/37
16/37 [summaryPlots1]
17/37
18/37 [readCategories]
19/37
20/37 [summaryPlots2]
21/37
22/37 [numReads]
23/37
24/37 [heatmapExample]
25/37
26/37 [channelActivity]
27/37
28/37 [pentamerCorrelation]
29/37
30/37 [combinedplots]
31/37
32/37 [writefastq]
33/37
34/37 [writefastq2]
35/37
36/37 [fast5toFastq]
37/37
output file: IONiseR.md
[1] "IONiseR.md"
Error in mark(..., format = "html", template = template) :
Detected bibliography in YAML (IONiseR.md) but the rbibutils package is
unavailable. Please make sure it is installed (and declared in Suggests if
bibliography is used in package vignettes).
Calls: markdownToHTML -> mark_html -> mark
Execution halted
make[1]: *** [debian/rules:7: execute_after_dh_auto_build] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Version: 2.35.0+dfsg-2
Hi Santiago,
Last source upload built find on Debian's buildds therefore closing this
bug.
Thanks for your screen,
Charles
On Sun, 17 May 2026 10:48:37 +0000 Santiago Vila <[email protected]> wrote:
Package: src:r-bioc-ioniser
Version: 2.30.0+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-ioniser, 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
debian/rules execute_after_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd inst/doc && Rscript -e "require(knitr); require(markdown); knit('IONiseR.Rmd',
'IONiseR.md'); markdownToHTML('IONiseR.md', 'IONiseR.html', options=c('use_xhtml',
'base64_images'));" && rm -f IONiseR.md
Loading required package: knitr
Loading required package: markdown
processing file: IONiseR.Rmd
1/37
2/37 [style]
3/37
4/37 [loadLibs]
5/37
6/37 [readData]
7/37
8/37 [loadData]
9/37
10/37 [exampleData]
11/37
--
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 ---
