Your message dated Sun, 07 Aug 2022 09:08:21 +0000
with message-id <[email protected]>
and subject line Bug#1015467: fixed in lagan 2.0-9
has caused the Debian Bug report #1015467,
regarding lagan: ftbfs with LTO (link time optimization) enabled
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.
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--
1015467: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1015467
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:lagan
Version: 2.0-8
Severity: minor
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-lto
This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled. For a background
for LTO please see
https://wiki.debian.org/ToolChain/LTO
The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures. The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.
To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:
export DEB_BUILD_MAINT_OPTIONS = optimize=+lto
Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:
export DEB_BUILD_MAINT_OPTIONS = optimize=-lto
or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/lagan_2.0-8_unstable_dpkglto.log
The last lines of the build log are at the end of this report.
[...]
| ~~~~~~^~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp:97:11: warning: ignoring return value of ‘char* fgets(char*,
int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
97 | fgets (buffer, 105, file);
| ~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3
-Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -flto=auto
-ffat-lto-objects -Wl,-z,relro
utils/overlay.c: In function ‘read_align’:
utils/overlay.c:119:10: warning: implicit declaration of function ‘isspace’
[-Wimplicit-function-declaration]
119 | if (!isspace(currchar)) {
| ^~~~~~~
utils/overlay.c:5:1: note: include ‘<ctype.h>’ or provide a declaration of
‘isspace’
4 | #include <string.h>
+++ |+#include <ctype.h>
5 |
utils/overlay.c:120:19: warning: implicit declaration of function ‘toupper’
[-Wimplicit-function-declaration]
120 | checkchar = toupper(currchar);
| ^~~~~~~
utils/overlay.c:120:19: note: include ‘<ctype.h>’ or provide a declaration of
‘toupper’
utils/overlay.c:109:3: warning: ignoring return value of ‘fgets’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
109 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/ccPpSXbd.ltrans0.ltrans.o: in function `main':
./src/utils/scorecontigs.c:296: undefined reference to `print'
/usr/bin/ld: /tmp/ccPpSXbd.ltrans0.ltrans.o:./src/utils/scorecontigs.c:283:
undefined reference to `print'
/usr/bin/ld: /tmp/ccPpSXbd.ltrans0.ltrans.o:./src/utils/scorecontigs.c:283:
undefined reference to `print'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:46: ../utils/scorecontigs] Error 1
make[2]: *** Waiting for unfinished jobs....
utils/Glue.cpp: In function ‘void calculateScoreMatrix(int)’:
utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to
‘char*’ [-Wwrite-strings]
64 | char *alpha = "ATCG";
| ^~~~~~
utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to
‘char*’ [-Wwrite-strings]
11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
| ^~~~~~~~~~~~~~~
utils/Glue.cpp:72:22: note: in expansion of macro ‘NUCLEOTIDE_MATRIX_FILE’
72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE);
| ^~~~~~~~~~~~~~~~~~~~~~
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’,
but argument 3 has type ‘void *’ [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’,
but argument 3 has type ‘void *’ [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’:
utils/Glue.cpp:44:9: warning: ignoring return value of ‘char* fgets(char*, int,
FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
44 | fgets (line, 1024, file);
| ~~~~~~^~~~~~~~~~~~~~~~~~
utils/Glue.cpp:52:12: warning: ignoring return value of ‘int fscanf(FILE*,
const char*, ...)’ declared with attribute ‘warn_unused_result’
[-Wunused-result]
52 | fscanf (file, "%1s", &(line[0]));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
utils/Glue.cpp:54:14: warning: ignoring return value of ‘int fscanf(FILE*,
const char*, ...)’ declared with attribute ‘warn_unused_result’
[-Wunused-result]
54 | fscanf (file, "%d", &k);
| ~~~~~~~^~~~~~~~~~~~~~~~
utils/Glue.cpp:59:10: warning: ignoring return value of ‘int fscanf(FILE*,
const char*, ...)’ declared with attribute ‘warn_unused_result’
[-Wunused-result]
59 | fscanf (file, "%d%d", &gapopen, &gapcont);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j8 "INSTALL=install --strip-program=true"
returned exit code 2
make[1]: *** [debian/rules:10: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: lagan
Source-Version: 2.0-9
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
lagan, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated lagan package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 07 Aug 2022 13:59:54 +0530
Source: lagan
Architecture: source
Version: 2.0-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1015467
Changes:
lagan (2.0-9) unstable; urgency=medium
.
* Team upload.
* Propagate hardening flags in src/glocal
* Add patch to fix FTBFS with lto (Closes: #1015467)
* d/p/hardening.patch: quote LDFLAGS so as to
pass all relevant flags in makefile w/o confusing make
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