Your message dated Fri, 30 Jan 2026 18:18:46 +0000
with message-id <[email protected]>
and subject line Bug#1107684: fixed in genometester 4.0+git20221122.71e6625-1
has caused the Debian Bug report #1107684,
regarding genometester FTCBFS: C vs C++ confusion
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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--
1107684: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1107684
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: genometester
Version: 4.0+git20200511.91cecb5+dfsg-1
Tags: patch upstream
User: [email protected]
Usertags: ftcbfs
genometester fails to cross build from source in a surprising way. It's
a compilation failure, but upon closer inspection the notable difference
is that the cross build used g++ whereas the native build used gcc.
dh_auto_build overrides CXX, which is the standard variable for the C++
compiler, but the upstream Makefile sets it to gcc. This also means that
the native build presently passes CXXFLAGS to the C compiler, which may
presently work but fail later. I suggest using the standard variables
with standard meanings. Once doing so it readily cross builds. I'm
attaching a patch (for forky) for your convenience.
Helmut
--- genometester-4.0+git20200511.91cecb5+dfsg.orig/src/Makefile
+++ genometester-4.0+git20200511.91cecb5+dfsg/src/Makefile
@@ -1,7 +1,7 @@
# Project: GenomeTester v4.0
VERSION = 4.0
-CXX = gcc
+CC = gcc
# C Files
@@ -127,42 +127,42 @@
INCS = -I.
BINS = glistmaker glistquery glistcompare
-#CXXFLAGS = $(INCS) $(DEBUGFLAGS) -Wall
-CXXFLAGS += $(INCS) $(RELEASEFLAGS) -Wall $(LDFLAGS)
+#CFLAGS = $(INCS) $(DEBUGFLAGS) -Wall
+CFLAGS += $(INCS) $(RELEASEFLAGS) -Wall $(LDFLAGS)
.PHONY: all all-before all-after clean clean-custom
all: all-before $(BINS) all-after
glistmaker: $(LISTMAKER_SOURCES)
- $(CXX) $(LISTMAKER_SOURCES) -o glistmaker $(LIBS) $(CXXFLAGS)
+ $(CC) $(LISTMAKER_SOURCES) -o glistmaker $(LIBS) $(CFLAGS)
glistmaker2: $(LISTMAKER2_SOURCES)
- $(CXX) $(LISTMAKER2_SOURCES) -o glistmaker2 $(LIBS) $(DEBUGFLAGS) -Wall
+ $(CC) $(LISTMAKER2_SOURCES) -o glistmaker2 $(LIBS) $(DEBUGFLAGS) -Wall
glistquery: $(LISTQUERY_SOURCES)
- $(CXX) $(LISTQUERY_SOURCES) -o glistquery $(LIBS) $(CXXFLAGS)
+ $(CC) $(LISTQUERY_SOURCES) -o glistquery $(LIBS) $(CFLAGS)
glistcompare: $(LISTCOMPARE_SOURCES)
- $(CXX) $(LISTCOMPARE_SOURCES) -o glistcompare $(LIBS) $(CXXFLAGS)
+ $(CC) $(LISTCOMPARE_SOURCES) -o glistcompare $(LIBS) $(CFLAGS)
gdistribution: $(GDISTRIBUTION_SOURCES)
- $(CXX) $(GDISTRIBUTION_SOURCES) -o gdistribution $(LIBS) $(CXXFLAGS)
+ $(CC) $(GDISTRIBUTION_SOURCES) -o gdistribution $(LIBS) $(CFLAGS)
gmer_counter: $(GMER_COUNTER_SOURCES)
- $(CXX) $(GMER_COUNTER_SOURCES) -o gmer_counter $(LIBS) $(CXXFLAGS) -Wall
+ $(CC) $(GMER_COUNTER_SOURCES) -o gmer_counter $(LIBS) $(CFLAGS) -Wall
gmer_caller: $(GMER_CALLER_SOURCES)
- $(CXX) $(GMER_CALLER_SOURCES) -o gmer_caller $(LIBS) $(CXXFLAGS) -Wall
+ $(CC) $(GMER_CALLER_SOURCES) -o gmer_caller $(LIBS) $(CFLAGS) -Wall
gassembler: $(GASSEMBLER_SOURCES)
- $(CXX) $(GASSEMBLER_SOURCES) -o gassembler $(LIBS) $(CXXFLAGS) -Wall
+ $(CC) $(GASSEMBLER_SOURCES) -o gassembler $(LIBS) $(CFLAGS) -Wall
distro: $(DISTRO_SOURCES)
- $(CXX) $(DISTRO_SOURCES) -o distro $(LIBS) $(CXXFLAGS) -Wall
+ $(CC) $(DISTRO_SOURCES) -o distro $(LIBS) $(CFLAGS) -Wall
aleq: $(ALEQ_SOURCES)
- $(CXX) $(ALEQ_SOURCES) -o aleq $(LIBS) $(CXXFLAGS) -Wall
+ $(CC) $(ALEQ_SOURCES) -o aleq $(LIBS) $(CFLAGS) -Wall
clean: clean-custom
rm -f *.o $(BINS)
--- genometester-4.0+git20200511.91cecb5+dfsg.orig/src/Makefile.gmer
+++ genometester-4.0+git20200511.91cecb5+dfsg/src/Makefile.gmer
@@ -1,7 +1,7 @@
# Project: GMER Caller
VERSION = 1.0
-CXX = gcc
+CC = gcc
# C Files
@@ -37,18 +37,18 @@
INCS = -I.
BINS = gmer_counter gmer_caller
-#CXXFLAGS = $(INCS) $(DEBUGFLAGS) -Wall
-CXXFLAGS = $(INCS) $(RELEASEFLAGS) -Wall
+#XFLAGS = $(INCS) $(DEBUGFLAGS) -Wall
+CFLAGS = $(INCS) $(RELEASEFLAGS) -Wall
.PHONY: all all-before all-after clean clean-custom
all: all-before $(BINS) all-after
gmer_counter: $(GMERCOUNTER_SOURCES)
- $(CXX) $(GMERCOUNTER_SOURCES) -o gmer_counter $(LIBS) $(CXXFLAGS) -Wall
+ $(CC) $(GMERCOUNTER_SOURCES) -o gmer_counter $(LIBS) $(CFLAGS) -Wall
gmer_caller: $(GMER_CALLER_SOURCES)
- $(CXX) $(GMER_CALLER_SOURCES) -o gmer_caller $(LIBS) $(CXXFLAGS) -Wall
+ $(CC) $(GMER_CALLER_SOURCES) -o gmer_caller $(LIBS) $(CFLAGS) -Wall
dist: $(GMERCOUNTER_SOURCES) $(GMER_CALLER_SOURCES)
mkdir fastgt_$(VERSION);
--- End Message ---
--- Begin Message ---
Source: genometester
Source-Version: 4.0+git20221122.71e6625-1
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
genometester, 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.
Étienne Mollier <[email protected]> (supplier of updated genometester 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: Fri, 30 Jan 2026 18:39:54 +0100
Source: genometester
Architecture: source
Version: 4.0+git20221122.71e6625-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1107684
Changes:
genometester (4.0+git20221122.71e6625-1) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* New upstream version
* d/watch:
- detect new versions on github
- version=5
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add missing build dependency on dh addon.
* Build-Depends: zlib1g-dev
* Standards-Version: 4.7.2 (routine-update)
.
[ Helmut Grohne ]
* Fix C vs C++ confusion by rather calling CC for C code
Closes: #1107684
.
[ Étienne Mollier ]
* default-wordlength.patch: new: set a sane default.
glistmaker defaults to have a wordlength of 0, out of the acceptable
length of 1 to 32. This patch restores the previous behavior, which
looks to have been to default to a wordlength of 16, given autopkgtest
expectations.
* gdistribution.patch: new: fix build failure of this binary.
* d/{install,rules}: build gassembler.
* buildflags.patch: new: improve hardening by passing CPP and LDFLAGS.
* d/patches/*: normalize Last-Update timestamps.
* d/control: drop redundant Priority: optional.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.3.
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Files:
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genometester_4.0+git20221122.71e6625-1.debian.tar.xz
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