Your message dated Sun, 21 Dec 2025 01:02:05 +0000
with message-id <[email protected]>
and subject line Bug#1112688: fixed in skesa 2.4.0-7
has caused the Debian Bug report #1112688,
regarding skesa FTCBFS: uses variable CC for the C++ compiler
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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--
1112688: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1112688
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: skesa
Version: 2.4.0-6
Tags: patch upstream
User: [email protected]
Usertags: ftcbfs
skesa fails to cross build from source, because debhelper overrides CC
with a C cross compilere while the upstream build system uses the CC
variable to contain a C++ compiler. I suggest adapting upstream source
code to use the more common CXX variable and am attaching a patch for
your convenience. If upstream does not like this patch, you may instead
try:
override_dh_auto_build:
dh_auto_build -- CC='$$(CXX)'
Helmut
--- skesa-2.4.0.orig/Makefile
+++ skesa-2.4.0/Makefile
@@ -39,7 +39,11 @@
NGS_INCL := -I $(NGS_PATH)/include
NGS_LIB := -L $(NGS_PATH)/lib64
-CC = c++ -std=c++11 -fdiagnostics-color=never
+ifeq ($(origin CXX),default)
+CXX = c++
+endif
+CFLAGS += -std=c++11 -fdiagnostics-color=never
+LDLAGS += -std=c++11 -fdiagnostics-color=never
CFLAGS += -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
-fomit-frame-pointer $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
@@ -54,7 +58,7 @@
-lrt -ldl -lm -lpthread -lz
%.o: %.cpp
- $(CC) -c -o $@ $< $(CFLAGS)
+ $(CXX) -c -o $@ $< $(CFLAGS)
binaries=skesa gfa_connector kmercounter
@@ -69,15 +73,15 @@
skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile
skesa: skesa.o glb_align.o
- $(CC) -o $@ $^ $(LIBS) $(LDFLAGS)
+ $(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
gfa_connector.o: gfa.hpp glb_align.hpp common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp graphdigger.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile
gfa_connector: gfa_connector.o glb_align.o
- $(CC) -o $@ $^ $(LIBS)
+ $(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
kmercounter.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile
kmercounter: kmercounter.o glb_align.o
- $(CC) -o $@ $^ $(LIBS)
+ $(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
$(NGS_DIR)/ngs.done:
--- End Message ---
--- Begin Message ---
Source: skesa
Source-Version: 2.4.0-7
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
skesa, 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.
Andreas Tille <[email protected]> (supplier of updated skesa 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: Sat, 20 Dec 2025 23:12:25 +0100
Source: skesa
Architecture: source
Version: 2.4.0-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1112688
Changes:
skesa (2.4.0-7) unstable; urgency=medium
.
[ Andreas Tille ]
* d/watch: version=5
* Standards-Version: 4.7.2 (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
.
[ Helmut Grohne ]
* Do not use variable CC for the C++ compiler
Closes: #1112688
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