Package: src:r-bioc-oligo
Version: 1.66.0+ds-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
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[...]
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
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
I: R Package: oligo Version: 1.66.0
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 17:58:01 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-oligo-1.66.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-oligo-1.66.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean
. "--built-timestamp='Thu, 30 Nov 2023 17:58:01 +0100'"
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/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 DABG.c -o DABG.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/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 ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function ‘gzcountLines’:
ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible
pointer type [-Wincompatible-pointer-types]
18 | while (!gzeof(file)){
| ^~~~
| |
| struct gzFile_s **
In file included from ParserGzXYS.c:4:
/usr/include/zlib.h:1598:34: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1598 | ZEXTERN int ZEXPORT gzeof(gzFile file);
| ~~~~~~~^~~~
ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible
pointer type [-Wincompatible-pointer-types]
19 | gzgets(file, buffer, 1000);
| ^~~~
| |
| struct gzFile_s **
/usr/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len);
| ~~~~~~~^~~~
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:46:6: warning: assignment to ‘struct gzFile_s **’ from
incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’}
[-Wincompatible-pointer-types]
46 | fp = gzopen(currentFile, "rb");
| ^
ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible
pointer type [-Wincompatible-pointer-types]
50 | gzgets(fp, buffer, LINEMAX);
| ^~
| |
| struct gzFile_s **
/usr/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len);
| ~~~~~~~^~~~
ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible
pointer type [-Wincompatible-pointer-types]
51 | gzclose(fp);
| ^~
| |
| struct gzFile_s **
/usr/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1634 | ZEXTERN int ZEXPORT gzclose(gzFile file);
| ~~~~~~~^~~~
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:134:6: warning: assignment to ‘struct gzFile_s **’ from
incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’}
[-Wincompatible-pointer-types]
134 | fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
| ^
ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from
incompatible pointer type [-Wincompatible-pointer-types]
138 | gzclose(fp);
| ^~
| |
| struct gzFile_s **
/usr/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1634 | ZEXTERN int ZEXPORT gzclose(gzFile file);
| ~~~~~~~^~~~
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/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 ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:145:3: warning: ignoring return value of ‘fgets’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
145 | fgets(buffer, LINEMAX, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:320:3: warning: ignoring return value of ‘fgets’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
320 | fgets(buffer, LINEMAX, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/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 baseProfile.c -o baseProfile.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/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 basecontent.c -o basecontent.o
basecontent.c: In function ‘basecontent’:
basecontent.c:54:15: error: format not a string literal and no format arguments
[-Werror=format-security]
54 | error(errmess);
| ^~~~~~~
cc1: some warnings being treated as errors
make[2]: *** [/usr/lib/R/etc/Makeconf:195: basecontent.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘oligo’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-oligo/usr/lib/R/site-library/oligo’
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-oligo-1.66.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean
. "--built-timestamp='Thu, 30 Nov 2023 17:58:01 +0100'" returned exit code 1
make[1]: *** [debian/rules:7: override_dh_auto_install] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
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.
