[R-pkg-team] Bug#1134312: r-bioc-biostrings: FTBFS: MIndex_class.c:186:27: error: implicit declaration of function 'R_lsInternal'; did you mean 'R_lsInternal3'? [-Wimplicit-function-declaration]
Santiago Vila
sanvila at debian.org
Sat Apr 18 18:32:37 BST 2026
Package: src:r-bioc-biostrings
Version: 2.74.1+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/202604/
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-biostrings, so that this is still
visible in the BTS web page for this package.
Thanks.
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[...]
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-biostrings/ -O--buildsystem=R
I: R Package: Biostrings Version: 2.74.1
I: Building using R version 4.5.3.20260417-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 13 Mar 2026 12:41:32 +0900
mkdir -p /<<BUILDDIR>>/r-bioc-biostrings-2.74.1\+dfsg/debian/r-bioc-biostrings/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-biostrings-2.74.1\+dfsg/debian/r-bioc-biostrings/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 12:41:32 +0900'"
* installing *source* package ‘Biostrings’ ...
** this is package ‘Biostrings’ version ‘2.74.1’
files ‘inst/doc/MultipleAlignments.html’, ‘inst/doc/matchprobes.html’ are missing
** using staged installation
** libs
using C compiler: ‘x86_64-linux-gnu-gcc (Debian 15.2.0-16) 15.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.3.20260417=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c BAB_class.c -o BAB_class.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.3.20260417=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c BitMatrix.c -o BitMatrix.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.3.20260417=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.3.20260417=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c MIndex_class.c -o MIndex_class.o
In file included from /usr/share/R/include/Rdefines.h:41,
from /usr/lib/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /usr/lib/R/site-library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from MIndex_class.c:5:
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:186:27: error: implicit declaration of function ‘R_lsInternal’; did you mean ‘R_lsInternal3’? [-Wimplicit-function-declaration]
186 | PROTECT(symbols = R_lsInternal(x_ends_envir, 1));
| ^~~~~~~~~~~~
/usr/share/R/include/Rinternals.h:357:36: note: in definition of macro ‘PROTECT’
357 | #define PROTECT(s) Rf_protect(s)
| ^
MIndex_class.c:186:25: error: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
186 | PROTECT(symbols = R_lsInternal(x_ends_envir, 1));
| ^
/usr/share/R/include/Rinternals.h:357:36: note: in definition of macro ‘PROTECT’
357 | #define PROTECT(s) Rf_protect(s)
| ^
make[1]: *** [/usr/lib/R/etc/Makeconf:190: MIndex_class.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 ‘Biostrings’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-biostrings/usr/lib/R/site-library/Biostrings’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-biostrings-2.74.1\+dfsg/debian/r-bioc-biostrings/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 12:41:32 +0900'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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