Your message dated Mon, 22 Sep 2025 13:52:15 +0100
with message-id <[email protected]>
and subject line Re: r-cran-markovchains FTBFS
has caused the Debian Bug report #1114342,
regarding r-cran-markovchain: FTBFS: ctmcProbabilistic.cpp:3:10: fatal error:
armadillo: No such file or directory
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.
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--
1114342: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114342
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-cran-markovchain
Version: 0.10.0-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
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 could not 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-cran-markovchain, 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-cran-markovchain/ -O--buildsystem=R
I: R packages needed for DEP8: knitr, testthat, msm, rsolnp, rmarkdown, ctmcd,
bookdown, diagram
I: R Package: markovchain Version: 0.10.0
I: Building using R version 4.5.1-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 03 Mar 2025 15:21:09 +0900
mkdir -p
/<<PKGBUILDDIR>>/debian/r-cran-markovchain/usr/lib/R/site-library
R CMD INSTALL -l
/<<PKGBUILDDIR>>/debian/r-cran-markovchain/usr/lib/R/site-library --clean .
"--built-timestamp='Mon, 03 Mar 2025 15:21:09 +0900'"
* installing *source* package âmarkovchainâ ...
** this is package âmarkovchainâ version â0.10.0â
file âsrc/Makevarsâ has the wrong MD5 checksum
** using staged installation
** libs
using C++ compiler: âg++ (Debian 15.2.0-3) 15.2.0â
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/RcppParallel/include'
-I'/usr/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.5.1=.
-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
/usr/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153:
note: â#pragma message: Using fallback compilation with Armadillo 14.6.3.
Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.â
71 | #pragma message("Using fallback compilation with Armadillo
14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for
more.")
|
^
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/RcppParallel/include'
-I'/usr/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.5.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
classesAndMethods.cpp -o classesAndMethods.o
In file included from
/usr/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from classesAndMethods.cpp:2:
/usr/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153:
note: â#pragma message: Using fallback compilation with Armadillo 14.6.3.
Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.â
71 | #pragma message("Using fallback compilation with Armadillo
14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for
more.")
|
^
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/RcppParallel/include'
-I'/usr/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.5.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
ctmcClassesAndMethods.cpp -o ctmcClassesAndMethods.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/RcppParallel/include'
-I'/usr/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.5.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
ctmcFittingFunctions.cpp -o ctmcFittingFunctions.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/RcppParallel/include'
-I'/usr/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.5.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
ctmcProbabilistic.cpp -o ctmcProbabilistic.o
ctmcProbabilistic.cpp:3:10: fatal error: armadillo: No such file or directory
3 | #include <armadillo>
| ^~~~~~~~~~~
compilation terminated.
make[1]: *** [/usr/lib/R/etc/Makeconf:211: ctmcProbabilistic.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 âmarkovchainâ
* removing
â/<<PKGBUILDDIR>>/debian/r-cran-markovchain/usr/lib/R/site-library/markovchainâ
dh_auto_install: error: R CMD INSTALL -l
/<<PKGBUILDDIR>>/debian/r-cran-markovchain/usr/lib/R/site-library --clean .
"--built-timestamp='Mon, 03 Mar 2025 15:21:09 +0900'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
This appears to have been fixed already, as this package has since built
successfully on reproducible-builds.
It was probably caused by r-cran-rcpparmadillo 15.0.1 and fixed in 15.0.2:
https://github.com/RcppCore/RcppArmadillo/pull/480
--- End Message ---
