Package: src:r-bioc-rsamtools
Version: 2.18.0+dfsg-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
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: 2.18.0
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Thu, 30 Nov 2023 11:30:31 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-rsamtools-2.18.0\+dfsg/debian/r-bioc-rsamtools/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-rsamtools-2.18.0\+dfsg/debian/r-bioc-rsamtools/usr/lib/R/site-library
--clean . "--built-timestamp='Thu, 30 Nov 2023 11:30:31 +0100'"
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++ (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
g++ -std=gnu++17 -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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c PileupBuffer.cpp -o PileupBuffer.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c PosCacheColl.cpp -o PosCacheColl.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
g++ -std=gnu++17 -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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c ResultManager.cpp -o ResultManager.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
g++ -std=gnu++17 -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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
In file included from Template.h:9,
from BamIterator.h:10,
from BamRangeIterator.h:7,
from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function ‘virtual void
BamRangeIterator::finalize_inprogress(bamFile)’:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning:
ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
138 | (void) bam_seek(bfile, pos, SEEK_SET);
| ^~~~~~~~
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const
bam_index_t*)’:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning:
ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
87 | (void) bam_seek(bfile, 0, 0);
| ^~~~~~~~
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c bambuffer.c -o bambuffer.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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 ‘bamfile_isincomplete’:
bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
168 | (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c bcffile.c -o bcffile.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c bedidx.c -o bedidx.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c encode.c -o encode.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c fafile.c -o fafile.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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 ‘idxstats_bamfile’:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning:
ignoring return value of ‘bgzf_seek’ declared with attribute
‘warn_unused_result’ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
20 | (void) bam_seek(fp, 0, 0);
| ^~~~~~~~
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -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:2:
io_sam.c: In function ‘_scan_bam_all’:
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning:
ignoring return value of ‘bgzf_seek’ declared with attribute
‘warn_unused_result’ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:307:12: note: in expansion of macro ‘bam_seek’
307 | (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
| ^~~~~~~~
g++ -std=gnu++17 -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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c pileup.cpp -o pileup.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c pileupbam.c -o pileupbam.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c sam_opts.c -o sam_opts.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c sam_utils.c -o sam_utils.o
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
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c samtools_patch.c -o samtools_patch.o
samtools_patch.c: In function ‘_samtools_fprintf’:
samtools_patch.c:37:13: error: format not a string literal and no format
arguments [-Werror=format-security]
37 | Rf_error(buf);
| ^~~~~~~~
samtools_patch.c:38:9: error: format not a string literal and no format
arguments [-Werror=format-security]
38 | Rf_warning(buf);
| ^~~~~~~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: samtools_patch.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 ‘Rsamtools’
* removing
‘/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools’
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-rsamtools-2.18.0\+dfsg/debian/r-bioc-rsamtools/usr/lib/R/site-library
--clean . "--built-timestamp='Thu, 30 Nov 2023 11:30:31 +0100'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
