[R-pkg-team] Bug#1103198: r-bioc-cner: FTBFS: ucsc/common.c:360:9: error: too many arguments to function 'free'
Santiago Vila
sanvila at debian.org
Tue Apr 15 01:19:44 BST 2025
Package: src:r-bioc-cner
Version: 1.42.0+dfsg-2
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
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-cner/ -O--buildsystem=R
I: R Package: CNEr Version: 1.42.0
I: Building using R version 4.5.0-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 13 Jan 2025 20:58:15 +0100
mkdir -p /<<BUILDDIR>>/r-bioc-cner-1.42.0\+dfsg/debian/r-bioc-cner/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-cner-1.42.0\+dfsg/debian/r-bioc-cner/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 20:58:15 +0100'"
* installing *source* package ‘CNEr’ ...
** this is package ‘CNEr’ version ‘1.42.0’
files ‘inst/doc/CNEr.html’, ‘inst/doc/PairwiseWholeGenomeAlignment.html’ are missing
files ‘tests/testthat/test_Axt.R’, ‘tests/testthat/test_CNE.R’, ‘tests/testthat/test_GRangePairs.R’, ‘tests/testthat/test_ceScan.R’ have the wrong MD5 checksums
** using staged installation
** libs
using C compiler: ‘gcc (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_CNEr.c -o R_init_CNEr.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c -o io.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ceScan.c -o ceScan.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/axt.c -o ucsc/axt.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/binRange.c -o ucsc/binRange.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/chain.c -o ucsc/chain.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -g -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘slUniqify’:
ucsc/common.c:360:9: error: too many arguments to function ‘free’
360 | free(el);
| ^~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:202: ucsc/common.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 ‘CNEr’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-cner/usr/lib/R/site-library/CNEr’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-cner-1.42.0\+dfsg/debian/r-bioc-cner/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 20:58:15 +0100'" returned exit code 1
make: *** [debian/rules:6: 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/202504/
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 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 add an affects on src:r-bioc-cner, so that this is still
visible in the BTS web page for this package.
Thanks.
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