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Groups > linux.debian.bugs.rc > #363806 > unrolled thread
| Started by | Santiago Vila <sanvila@debian.org> |
|---|---|
| First post | 2024-05-17 22:50 +0200 |
| Last post | 2024-07-14 20:40 +0200 |
| Articles | 4 — 3 participants |
Back to article view | Back to linux.debian.bugs.rc
Bug#1071346: r-bioc-rsamtools: FTBFS: samtools_patch.c:37:13: error: format not a string literal and no format arguments Santiago Vila <sanvila@debian.org> - 2024-05-17 22:50 +0200
Bug#1071346: marked as pending in r-bioc-rsamtools "Michael R. Crusoe" <noreply@salsa.debian.org> - 2024-07-11 16:40 +0200
Processed: Bug#1071346 marked as pending in r-bioc-rsamtools "Debian Bug Tracking System" <owner@bugs.debian.org> - 2024-07-11 16:40 +0200
Bug#1071346: marked as done (r-bioc-rsamtools: FTBFS: samtools_patch.c:37:13: error: format not a string literal and no format arguments) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2024-07-14 20:40 +0200
| From | Santiago Vila <sanvila@debian.org> |
|---|---|
| Date | 2024-05-17 22:50 +0200 |
| Subject | Bug#1071346: r-bioc-rsamtools: FTBFS: samtools_patch.c:37:13: error: format not a string literal and no format arguments |
| Message-ID | <IFcGR-e26K-83@gated-at.bofh.it> |
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.
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| From | "Michael R. Crusoe" <noreply@salsa.debian.org> |
|---|---|
| Date | 2024-07-11 16:40 +0200 |
| Subject | Bug#1071346: marked as pending in r-bioc-rsamtools |
| Message-ID | <IZ37I-1nQy-13@gated-at.bofh.it> |
| In reply to | #363806 |
Control: tag -1 pending Hello, Bug #1071346 in r-bioc-rsamtools reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/r-pkg-team/r-bioc-rsamtools/-/commit/42a4bdcf3a6b82497a449fd65592f0bfe8caf153 ------------------------------------------------------------------------ new upstream version fixes FTBFS. Closes: #1071346 ------------------------------------------------------------------------ (this message was generated automatically) -- Greetings https://bugs.debian.org/1071346
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| From | "Debian Bug Tracking System" <owner@bugs.debian.org> |
|---|---|
| Date | 2024-07-11 16:40 +0200 |
| Subject | Processed: Bug#1071346 marked as pending in r-bioc-rsamtools |
| Message-ID | <IZ37I-1nQy-21@gated-at.bofh.it> |
| In reply to | #363806 |
Processing control commands: > tag -1 pending Bug #1071346 [src:r-bioc-rsamtools] r-bioc-rsamtools: FTBFS: samtools_patch.c:37:13: error: format not a string literal and no format arguments Added tag(s) pending. -- 1071346: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1071346 Debian Bug Tracking System Contact owner@bugs.debian.org with problems
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| From | "Debian Bug Tracking System" <owner@bugs.debian.org> |
|---|---|
| Date | 2024-07-14 20:40 +0200 |
| Subject | Bug#1071346: marked as done (r-bioc-rsamtools: FTBFS: samtools_patch.c:37:13: error: format not a string literal and no format arguments) |
| Message-ID | <J0ciD-282h-57@gated-at.bofh.it> |
| In reply to | #363806 |
[Multipart message — attachments visible in raw view] — view raw
Your message dated Sun, 14 Jul 2024 18:38:01 +0000 with message-id <E1sT46j-0035NY-UR@fasolo.debian.org> and subject line Bug#1071346: fixed in r-bioc-rsamtools 2.20.0+dfsg-1~0exp has caused the Debian Bug report #1071346, regarding r-bioc-rsamtools: FTBFS: samtools_patch.c:37:13: error: format not a string literal and no format arguments 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner@bugs.debian.org immediately.) -- 1071346: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1071346 Debian Bug Tracking System Contact owner@bugs.debian.org with problems
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