Package: src:r-bioc-sparsearray
Version: 1.2.4+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-sparsearray/ -O--buildsystem=R
I: R Package: SparseArray Version: 1.2.4
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Tue, 20 Feb 2024 14:27:12 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-sparsearray-1.2.4\+dfsg/debian/r-bioc-sparsearray/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-sparsearray-1.2.4\+dfsg/debian/r-bioc-sparsearray/usr/lib/R/site-library
--clean . "--built-timestamp='Tue, 20 Feb 2024 14:27:12 +0100'"
* installing *source* package ‘SparseArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
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
-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 ExtendableJaggedArray.c -o ExtendableJaggedArray.o
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
-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
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
-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_SparseArray.c -o R_init_SparseArray.o
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
-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 Rvector_summarization.c -o Rvector_summarization.o
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
-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 Rvector_utils.c -o Rvector_utils.o
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
-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
-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
-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 SBT_utils.c -o SBT_utils.o
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
-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 SVT_SparseArray_class.c -o SVT_SparseArray_class.o
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
-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 SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
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
-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 SparseArray_Math_methods.c -o SparseArray_Math_methods.o
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
-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 SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o
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
-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 SparseArray_abind.c -o SparseArray_abind.o
SparseArray_abind.c: In function ‘concatenate_SVTs’:
SparseArray_abind.c:109:46: warning: format ‘%s’ expects argument of type ‘char
*’, but argument 2 has type ‘int’ [-Wformat=]
109 | error("input object %s is an invalid
SVT_SparseArray",
| ~^
| |
| char *
| %d
110 | n + 1);
| ~~~~~
| |
| int
SparseArray_abind.c:114:46: warning: format ‘%s’ expects argument of type ‘char
*’, but argument 2 has type ‘int’ [-Wformat=]
114 | error("input object %s is an invalid
SVT_SparseArray",
| ~^
| |
| char *
| %d
115 | n + 1);
| ~~~~~
| |
| int
SparseArray_abind.c: In function ‘concatenate_leaf_vectors’:
SparseArray_abind.c:146:46: warning: format ‘%s’ expects argument of type ‘char
*’, but argument 2 has type ‘int’ [-Wformat=]
146 | error("input object %s is an invalid
SVT_SparseArray",
| ~^
| |
| char *
| %d
147 | n + 1);
| ~~~~~
| |
| int
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
-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 SparseArray_aperm.c -o SparseArray_aperm.o
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
-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 SparseArray_class.c -o SparseArray_class.o
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
-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 SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
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
-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 SparseArray_subassignment.c -o SparseArray_subassignment.o
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
-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 SparseArray_subsetting.c -o SparseArray_subsetting.o
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
-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 SparseArray_summarization.c -o SparseArray_summarization.o
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
-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 SparseMatrix_mult.c -o SparseMatrix_mult.o
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
-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
-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
-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 coerceVector2.c -o coerceVector2.o
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
-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 leaf_vector_Arith.c -o leaf_vector_Arith.o
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
-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 leaf_vector_Compare.c -o leaf_vector_Compare.o
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
-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 leaf_vector_Logic.c -o leaf_vector_Logic.o
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
-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 leaf_vector_dotprod.c -o leaf_vector_dotprod.o
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
-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 leaf_vector_summarization.c -o leaf_vector_summarization.o
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
-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 leaf_vector_utils.c -o leaf_vector_utils.o
leaf_vector_utils.c: In function ‘_new_leaf_vector’:
leaf_vector_utils.c:33:17: error: format not a string literal and no format
arguments [-Werror=format-security]
33 | error(msg);
| ^~~~~
leaf_vector_utils.c:37:17: error: format not a string literal and no format
arguments [-Werror=format-security]
37 | error(msg);
| ^~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: leaf_vector_utils.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 ‘SparseArray’
* removing
‘/<<PKGBUILDDIR>>/debian/r-bioc-sparsearray/usr/lib/R/site-library/SparseArray’
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-sparsearray-1.2.4\+dfsg/debian/r-bioc-sparsearray/usr/lib/R/site-library
--clean . "--built-timestamp='Tue, 20 Feb 2024 14:27:12 +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.
