[R-pkg-team] Bug#1114342: r-cran-markovchain: FTBFS: ctmcProbabilistic.cpp:3:10: fatal error: armadillo: No such file or directory

Santiago Vila sanvila at debian.org
Fri Sep 5 19:25:09 BST 2025 

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 ‘markovchain’ ...
** this is package ‘markovchain’ version ‘0.10.0’
file ‘src/Makevars’ has the wrong MD5 checksum
** using staged installation
** libs
using C++ compiler: ‘g++ (Debian 15.2.0-3) 15.2.0’
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: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
   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: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
   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 ‘markovchain’
* removing ‘/<<PKGBUILDDIR>>/debian/r-cran-markovchain/usr/lib/R/site-library/markovchain’
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
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