Your message dated Tue, 25 Nov 2025 22:51:37 +0000
with message-id <[email protected]>
and subject line Bug#1112687: fixed in spaln 3.0.7+dfsg-1
has caused the Debian Bug report #1112687,
regarding spaln FTCBFS: uses -l flags in Makefile dependencies
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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--
1112687: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1112687
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: spaln
Version: 3.0.2+dfsg-2
Tags: patch upstream
User: [email protected]
Usertags: ftcbfs
spaln fails to cross build from source, because lists -l flags for
linking libraries in Makefile dependencies. Doing so invokes a behavior
where make looks up the library using a built-in library search path.
This path is architecture-dependent and is one reason for make not being
Multi-Arch: foreign. In any case, make does not succeed at looking up
e.g. -lz as it tries /usr/lib/${DEB_BUILD_MULTIARCH} but not
/usr/lib/${DEB_HOST_MULTIARCH} where it would actually reside.
Generally, listing such dependencies bears little benefit. I'm attaching
a patch that splits out these flags from the CLIB, SLIB and ULIB
variables into a LIBRARIES variable such that they can still be passed
to the compiler but not listed as target dependencies. Once applying it
spaln cross builds successfully. Please consider applying it and also
forwarding it upstream as it benefits other cross compilation
distributions such as Yocto or PtxDist.
Helmut
--- spaln-3.0.2+dfsg.orig/src/Makefile.in
+++ spaln-3.0.2+dfsg/src/Makefile.in
@@ -23,7 +23,8 @@
PROG = $(PROG_B) $(PROG_A) $(PROG_F)
STDH = stdtype.h
-CLIB = clib.a -lpthread -lm -lz
+LIBRARIES = -lpthread -lm -lz
+CLIB = clib.a
SLIB = sblib.a $(CLIB)
ULIB = ublib.a $(SLIB)
@@ -88,36 +89,36 @@
ls $(SRC) $(HDR)
spaln: spaln.cc blksrc.o $(SLIB)
- $(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(ILIB) $(LDFLAGS)
+ $(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(ILIB) $(LIBRARIES) $(LDFLAGS)
sortgrcd: sortgrcd.cc $(SLIB)
- $(CXX) -o $@ sortgrcd.cc $(SLIB) $(ILIB) $(LDFLAGS)
+ $(CXX) -o $@ sortgrcd.cc $(SLIB) $(ILIB) $(LIBRARIES) $(LDFLAGS)
makdbs: makdbs.cc dbs.h seq.h bitpat.h $(SLIB)
- $(CXX) -o $@ makdbs.cc $(SLIB) $(ILIB) $(LDFLAGS)
+ $(CXX) -o $@ makdbs.cc $(SLIB) $(ILIB) $(LIBRARIES) $(LDFLAGS)
makmdm: makmdm.cc mdm.h $(CLIB)
- $(CXX) -o $@ makmdm.cc $(CLIB) $(ILIB) $(LDFLAGS)
+ $(CXX) -o $@ makmdm.cc $(CLIB) $(ILIB) $(LIBRARIES) $(LDFLAGS)
dvn: dvn.cc autocomp.h $(ULIB)
- $(CXX) -o $@ dvn.cc $(ULIB) $(ILIB)
+ $(CXX) -o $@ dvn.cc $(ULIB) $(ILIB) $(LIBRARIES)
exinpot: exinpot.cc codepot.h utilseq.h eijunc.h $(SLIB)
- $(CXX) -o $@ exinpot.cc $(SLIB) $(ILIB)
+ $(CXX) -o $@ exinpot.cc $(SLIB) $(ILIB) $(LIBRARIES)
kmers: kmers.cc $(SLIB)
- $(CXX) -o $@ kmers.cc $(SLIB) $(ILIB)
+ $(CXX) -o $@ kmers.cc $(SLIB) $(ILIB) $(LIBRARIES)
npssm: npssm.cc $(SLIB)
- $(CXX) -o $@ npssm.cc $(SLIB) $(ILIB)
+ $(CXX) -o $@ npssm.cc $(SLIB) $(ILIB) $(LIBRARIES)
rdn: rdn.cc $(ULIB)
- $(CXX) -o $@ rdn.cc $(ULIB) $(ILIB)
+ $(CXX) -o $@ rdn.cc $(ULIB) $(ILIB) $(LIBRARIES)
utn: utn.o $(ULIB)
- $(CXX) -o $@ utn.o $(ULIB) $(ILIB)
+ $(CXX) -o $@ utn.o $(ULIB) $(ILIB) $(LIBRARIES)
compild: compild.cc calcserv.h ildpdf.o $(CLIB)
- $(CXX) -o compild compild.cc ildpdf.o $(CLIB) -lm -lgsl -lgslcblas
+ $(CXX) -o compild compild.cc ildpdf.o $(CLIB) $(LIBRARIES) -lm -lgsl -lgslcblas
decompild: decompild.o ildpdf.o fitild.o $(CLIB)
- $(CXX) -o decompild decompild.o ildpdf.o fitild.o $(CLIB) -lgsl -lgslcblas
+ $(CXX) -o decompild decompild.o ildpdf.o fitild.o $(CLIB) $(LIBRARIES) -lgsl -lgslcblas
fitild: fitild.cc ildpdf.o $(CLIB)
- $(CXX) -o $@ -DMAIN fitild.cc ildpdf.o $(CLIB) \
+ $(CXX) -o $@ -DMAIN fitild.cc ildpdf.o $(CLIB) $(LIBRARIES) \
-L/usr/local/lib -lm -lgsl -lgslcblas
plotild: plotild.cc ildpdf.o $(CLIB)
- $(CXX) -o plotild plotild.cc ildpdf.o $(CLIB) -lm -lgsl -lgslcblas
+ $(CXX) -o plotild plotild.cc ildpdf.o $(CLIB) $(LIBRARIES) -lm -lgsl -lgslcblas
clib.o: clib.cc stdtype.h
iolib.o: iolib.cc stdtype.h
--- End Message ---
--- Begin Message ---
Source: spaln
Source-Version: 3.0.7+dfsg-1
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
spaln, 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 spaln 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: Tue, 25 Nov 2025 23:14:46 +0100
Source: spaln
Architecture: source
Version: 3.0.7+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1112687
Changes:
spaln (3.0.7+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version 3.0.7+dfsg. (Closes: #1112687)
* d/copyright: bump upstream copyright year.
* d/control: declare compliance to standards version 4.7.2.
* d/control: drop redundant Rules-Requires-Root: no.
* d/watch: convert to v5 Github template.
* hardening.patch: refresh.
* portability.patch: refresh.
* d/patches/*: normalize the Last-Update timestamp.
* d/t/run-unit-test: adjust test per upstream recommendations.
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