[R-pkg-team] Bug#1135465: r-bioc-rsamtools: FTBFS: utilities.h:55:5: error: implicit declaration of function 'SET_TYPEOF'; did you mean 'TYPEOF'? [-Wimplicit-function-declaration]
Santiago Vila
sanvila at debian.org
Sat May 2 00:14:41 BST 2026
Package: src:r-bioc-rsamtools
Version: 2.22.0+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-rsamtools, 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-rsamtools/ -O--buildsystem=R
I: R Package: Rsamtools Version: 2.22.0
I: Building using R version 4.6.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 13 Mar 2026 19:36:37 +0900
mkdir -p /<<BUILDDIR>>/r-bioc-rsamtools-2.22.0\+dfsg/debian/r-bioc-rsamtools/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-rsamtools-2.22.0\+dfsg/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 19:36:37 +0900'"
* installing *source* package âRsamtoolsâ ...
** this is package âRsamtoolsâ version â2.22.0â
file âinst/doc/Rsamtools-Overview.htmlâ is missing
files âinst/unitTests/test_FaFile.Râ, âinst/unitTests/test_utilities.Râ have the wrong MD5 checksums
** using staged installation
** libs
using C compiler: âx86_64-linux-gnu-gcc (Debian 15.2.0-17) 15.2.0â
using C++ compiler: âx86_64-linux-gnu-g++ (Debian 15.2.0-17) 15.2.0â
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -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-g++ -std=gnu++20 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c PileupBuffer.cpp -o PileupBuffer.o
x86_64-linux-gnu-g++ -std=gnu++20 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c PosCacheColl.cpp -o PosCacheColl.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
x86_64-linux-gnu-g++ -std=gnu++20 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ResultManager.cpp -o ResultManager.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c XVector_stubs.c -o XVector_stubs.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c as_bam.c -o as_bam.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bam.c -o bam.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_data.c -o bam_data.o
x86_64-linux-gnu-g++ -std=gnu++20 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from Template.h:9,
from BamIterator.h:10,
from BamRangeIterator.h:7,
from bam_mate_iter.cpp:1:
BamRangeIterator.h: In member function âvirtual void BamRangeIterator::finalize_inprogress(bamFile)â:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of âint64_t bgzf_seek(BGZF*, int64_t, int)â declared with attribute âwarn_unused_resultâ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro âbam_seekâ
138 | (void) bam_seek(bfile, pos, SEEK_SET);
| ^~~~~~~~
BamIterator.h: In constructor âBamIterator::BamIterator(bamFile, const bam_index_t*)â:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of âint64_t bgzf_seek(BGZF*, int64_t, int)â declared with attribute âwarn_unused_resultâ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro âbam_seekâ
87 | (void) bam_seek(bfile, 0, 0);
| ^~~~~~~~
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_plbuf.c -o bam_plbuf.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_sort.c -o bam_sort.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bambuffer.c -o bambuffer.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bamfile.c -o bamfile.o
bamfile.c: In function âbamfile_isincompleteâ:
bamfile.c:168:20: warning: ignoring return value of âbgzf_seekâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
168 | (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bcffile.c -o bcffile.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c bedidx.c -o bedidx.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c encode.c -o encode.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c fafile.c -o fafile.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c idxstats.c -o idxstats.o
In file included from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function âidxstats_bamfileâ:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of âbgzf_seekâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro âbam_seekâ
20 | (void) bam_seek(fp, 0, 0);
| ^~~~~~~~
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c io_sam.c -o io_sam.o
In file included from io_sam.c:9:
io_sam.c: In function â_tmpl_PhredQualityâ:
utilities.h:55:5: error: implicit declaration of function âSET_TYPEOFâ; did you mean âTYPEOFâ? [-Wimplicit-function-declaration]
55 | SET_TYPEOF(T, LANGSXP); \
| ^~~~~~~~~~
io_sam.c:88:5: note: in expansion of macro âNEW_CALLâ
88 | NEW_CALL(s, t, "PhredQuality", nmspc, 2);
| ^~~~~~~~
In file included from io_sam.c:3:
io_sam.c: In function â_scan_bam_allâ:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of âbgzf_seekâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:302:12: note: in expansion of macro âbam_seekâ
302 | (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
| ^~~~~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:190: io_sam.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 âRsamtoolsâ
* removing â/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtoolsâ
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-rsamtools-2.22.0\+dfsg/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 19:36:37 +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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