Greetings Tim, thanks for your report.
On Wed, Jan 09, 2013 at 01:44:07PM -0700, Tim Gardner wrote:
> Package: tandem-mass
> Version: 20121001-1
> Followup-For: Bug #695553
> User: ubuntu-de...@lists.ubuntu.com
> Usertags: origin-ubuntu raring ubuntu-patch
>
> Dear Maintainer,
>
> This patch updates debian/tandem-mass.install such that it
> copies the correct binary name.
Does the debian-makefile patch apply on your setup?
Relevant part of the patch
==========================
$ cat debian/patches/debian-makefile
--- a/src/Makefile_ubuntu
+++ b/src/Makefile_ubuntu
@@ -1,8 +1,8 @@
#makefile for c++ programs
#change the name of the executable to use for "any" project
-EXECUTABLE = ../bin/tandem.exe
-#EXECUTABLE = ../bin/p3.exe
+EXECUTABLE = ../bin/tandem
+#EXECUTABLE = ../bin/p3
LINKCC = $(CXX)
[...]
The patch changes the name of the built binary from `tandem.exe' to
`tandem' such that the binary to be installed is indeed tandem instead
of tandem.exe (which not only sounds terribly windowsish but also
contradicts the tradition that binaries have no extensions).
With this patch correctly applied, build the package is flawless.
Relevant part of the build log:
===============================
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
QUILT_PATCHES=debian/patches \
quilt --quiltrc /dev/null pop -a -R || test $? = 2
Removing patch fix-missing-include-string-h
Restoring src/mhistogram.h
Restoring src/mmotif.h
Restoring src/saxhandler.h
Restoring src/p3msequenceserver.cpp
Restoring src/mcleave.h
Restoring src/msequenceserver.cpp
Restoring src/base64.cpp
Removing patch debian-makefile
Restoring src/Makefile_ubuntu
No patches applied
rm -rf .pc debian/stamp-patched
dh_testdir
dh_testroot
dh_clean
rm -f debian/tandem-mass.substvars
rm -f debian/tandem-mass.*.debhelper
rm -rf debian/tandem-mass/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} \; \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \)
\)
rm -f *-stamp
rm -f bin/tandem
rm -f src/*.d src/*.o
rm -f build-stamp
dpkg-source -b tandem-mass-20121001
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: applying debian-makefile
dpkg-source: info: applying fix-missing-include-string-h
dpkg-source: info: building tandem-mass using existing
./tandem-mass_20121001.orig.tar.gz
dpkg-source: info: building tandem-mass in tandem-mass_20121001-1.debian.tar.gz
dpkg-source: info: building tandem-mass in tandem-mass_20121001-1.dsc
debian/rules build
dh_testdir
dh_prep
rm -f debian/tandem-mass.substvars
rm -f debian/tandem-mass.*.debhelper
rm -rf debian/tandem-mass/
cd src && /usr/bin/make -f Makefile_ubuntu
make[1]: Entering directory `/tmp/buildd/tandem-mass-20121001/src'
g++ -M -w -O2 xmltaxonomy.cpp > xmltaxonomy.d
g++ -M -w -O2 xmltaxonomy.cpp | sed s/\\.o/.d/ > xmltaxonomy.d
g++ -M -w -O2 xmlparameter.cpp > xmlparameter.d
g++ -M -w -O2 xmlparameter.cpp | sed s/\\.o/.d/ > xmlparameter.d
g++ -M -w -O2 tandem.cpp > tandem.d
g++ -M -w -O2 tandem.cpp | sed s/\\.o/.d/ > tandem.d
g++ -M -w -O2 stdafx.cpp > stdafx.d
g++ -M -w -O2 stdafx.cpp | sed s/\\.o/.d/ > stdafx.d
g++ -M -w -O2 saxtaxhandler.cpp > saxtaxhandler.d
g++ -M -w -O2 saxtaxhandler.cpp | sed s/\\.o/.d/ > saxtaxhandler.d
g++ -M -w -O2 saxtandeminputhandler.cpp > saxtandeminputhandler.d
g++ -M -w -O2 saxtandeminputhandler.cpp | sed s/\\.o/.d/ >
saxtandeminputhandler.d
g++ -M -w -O2 saxsaphandler.cpp > saxsaphandler.d
g++ -M -w -O2 saxsaphandler.cpp | sed s/\\.o/.d/ > saxsaphandler.d
g++ -M -w -O2 saxmzxmlhandler.cpp > saxmzxmlhandler.d
g++ -M -w -O2 saxmzxmlhandler.cpp | sed s/\\.o/.d/ > saxmzxmlhandler.d
g++ -M -w -O2 saxmzmlhandler.cpp > saxmzmlhandler.d
g++ -M -w -O2 saxmzmlhandler.cpp | sed s/\\.o/.d/ > saxmzmlhandler.d
g++ -M -w -O2 saxmzdatahandler.cpp > saxmzdatahandler.d
g++ -M -w -O2 saxmzdatahandler.cpp | sed s/\\.o/.d/ > saxmzdatahandler.d
g++ -M -w -O2 saxmodhandler.cpp > saxmodhandler.d
g++ -M -w -O2 saxmodhandler.cpp | sed s/\\.o/.d/ > saxmodhandler.d
g++ -M -w -O2 saxhandler.cpp > saxhandler.d
g++ -M -w -O2 saxhandler.cpp | sed s/\\.o/.d/ > saxhandler.d
g++ -M -w -O2 saxgamlhandler.cpp > saxgamlhandler.d
g++ -M -w -O2 saxgamlhandler.cpp | sed s/\\.o/.d/ > saxgamlhandler.d
g++ -M -w -O2 saxbiomlhandler.cpp > saxbiomlhandler.d
g++ -M -w -O2 saxbiomlhandler.cpp | sed s/\\.o/.d/ > saxbiomlhandler.d
g++ -M -w -O2 p3msequenceserver.cpp > p3msequenceserver.d
g++ -M -w -O2 p3msequenceserver.cpp | sed s/\\.o/.d/ > p3msequenceserver.d
g++ -M -w -O2 p3mprocess.cpp > p3mprocess.d
g++ -M -w -O2 p3mprocess.cpp | sed s/\\.o/.d/ > p3mprocess.d
g++ -M -w -O2 p3.cpp > p3.d
g++ -M -w -O2 p3.cpp | sed s/\\.o/.d/ > p3.d
g++ -M -w -O2 mxxcleavage.cpp > mxxcleavage.d
g++ -M -w -O2 mxxcleavage.cpp | sed s/\\.o/.d/ > mxxcleavage.d
g++ -M -w -O2 mtermmods.cpp > mtermmods.d
g++ -M -w -O2 mtermmods.cpp | sed s/\\.o/.d/ > mtermmods.d
g++ -M -w -O2 mspectrumcondition.cpp > mspectrumcondition.d
g++ -M -w -O2 mspectrumcondition.cpp | sed s/\\.o/.d/ > mspectrumcondition.d
g++ -M -w -O2 msequtilities.cpp > msequtilities.d
g++ -M -w -O2 msequtilities.cpp | sed s/\\.o/.d/ > msequtilities.d
g++ -M -w -O2 msequenceserver.cpp > msequenceserver.d
g++ -M -w -O2 msequenceserver.cpp | sed s/\\.o/.d/ > msequenceserver.d
g++ -M -w -O2 msequencecollection.cpp > msequencecollection.d
g++ -M -w -O2 msequencecollection.cpp | sed s/\\.o/.d/ > msequencecollection.d
g++ -M -w -O2 mscore_tandem.cpp > mscore_tandem.d
g++ -M -w -O2 mscore_tandem.cpp | sed s/\\.o/.d/ > mscore_tandem.d
g++ -M -w -O2 mscore.cpp > mscore.d
g++ -M -w -O2 mscore.cpp | sed s/\\.o/.d/ > mscore.d
g++ -M -w -O2 mreport.cpp > mreport.d
g++ -M -w -O2 mreport.cpp | sed s/\\.o/.d/ > mreport.d
g++ -M -w -O2 mrefine.cpp > mrefine.d
g++ -M -w -O2 mrefine.cpp | sed s/\\.o/.d/ > mrefine.d
g++ -M -w -O2 mprocess.cpp > mprocess.d
g++ -M -w -O2 mprocess.cpp | sed s/\\.o/.d/ > mprocess.d
g++ -M -w -O2 mpmods.cpp > mpmods.d
g++ -M -w -O2 mpmods.cpp | sed s/\\.o/.d/ > mpmods.d
g++ -M -w -O2 mplugin.cpp > mplugin.d
g++ -M -w -O2 mplugin.cpp | sed s/\\.o/.d/ > mplugin.d
g++ -M -w -O2 mpam.cpp > mpam.d
g++ -M -w -O2 mpam.cpp | sed s/\\.o/.d/ > mpam.d
g++ -M -w -O2 mbiomlreport.cpp > mbiomlreport.d
g++ -M -w -O2 mbiomlreport.cpp | sed s/\\.o/.d/ > mbiomlreport.d
g++ -M -w -O2 masscalc.cpp > masscalc.d
g++ -M -w -O2 masscalc.cpp | sed s/\\.o/.d/ > masscalc.d
g++ -M -w -O2 loadmspectrum.cpp > loadmspectrum.d
g++ -M -w -O2 loadmspectrum.cpp | sed s/\\.o/.d/ > loadmspectrum.d
g++ -M -w -O2 base64.cpp > base64.d
g++ -M -w -O2 base64.cpp | sed s/\\.o/.d/ > base64.d
make[1]: Leaving directory `/tmp/buildd/tandem-mass-20121001/src'
make[1]: Entering directory `/tmp/buildd/tandem-mass-20121001/src'
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o base64.o base64.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o loadmspectrum.o loadmspectrum.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o masscalc.o masscalc.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mbiomlreport.o mbiomlreport.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mpam.o mpam.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mplugin.o mplugin.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mpmods.o mpmods.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mprocess.o mprocess.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mrefine.o mrefine.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mreport.o mreport.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mscore.o mscore.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mscore_tandem.o mscore_tandem.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o msequencecollection.o
msequencecollection.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o msequenceserver.o msequenceserver.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o msequtilities.o msequtilities.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mspectrumcondition.o
mspectrumcondition.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mtermmods.o mtermmods.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o mxxcleavage.o mxxcleavage.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o p3.o p3.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o p3mprocess.o p3mprocess.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o p3msequenceserver.o p3msequenceserver.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxbiomlhandler.o saxbiomlhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxgamlhandler.o saxgamlhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxhandler.o saxhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxmodhandler.o saxmodhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxmzdatahandler.o saxmzdatahandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxmzmlhandler.o saxmzmlhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxmzxmlhandler.o saxmzxmlhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxsaphandler.o saxsaphandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxtandeminputhandler.o
saxtandeminputhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o saxtaxhandler.o saxtaxhandler.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o stdafx.o stdafx.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o tandem.o tandem.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o xmlparameter.o xmlparameter.cpp
g++ -w -O2 -D_FORTIFY_SOURCE=2 -c -o xmltaxonomy.o xmltaxonomy.cpp
g++ -w -O2 -o ../bin/tandem base64.o loadmspectrum.o masscalc.o mbiomlreport.o
mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o
mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o
mspectrumcondition.o mtermmods.o mxxcleavage.o p3.o p3mprocess.o
p3msequenceserver.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o
saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o
saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o
xmlparameter.o xmltaxonomy.o -lpthread -lm -lexpat
As you can see the binary that is created is indeed `tandem'.
Can you investigate please ?
Cheers,
Filippo
>
> *** /tmp/tmpHTnzCl/bug_body
> In Ubuntu, the attached patch was applied to achieve the following:
>
> Fix FTBS
>
> * Copy the correct binary in debian/tandem-mass.install
>
>
> Thanks for considering the patch.
>
>
> -- System Information:
> Debian Release: wheezy/sid
> APT prefers precise-updates
> APT policy: (500, 'precise-updates'), (500, 'precise-security'), (500,
> 'precise-proposed'), (500, 'precise'), (100, 'precise-backports')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 3.8.0-0-generic (SMP w/32 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> diff -Nru tandem-mass-20121001/debian/changelog
> tandem-mass-20121001/debian/changelog
> diff -Nru tandem-mass-20121001/debian/control
> tandem-mass-20121001/debian/control
> --- tandem-mass-20121001/debian/control 2012-11-20 11:57:06.000000000
> -0700
> +++ tandem-mass-20121001/debian/control 2013-01-09 13:33:51.000000000
> -0700
> @@ -1,7 +1,8 @@
> Source: tandem-mass
> Section: science
> Priority: optional
> -Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
> +Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
> +XSBC-Original-Maintainer: The Debichem Group
> <debichem-de...@lists.alioth.debian.org>
> Uploaders: Filippo Rusconi <lopi...@debian.org>
> Standards-Version: 3.9.3
> Build-Depends: debhelper (>= 7.0.50~),
> diff -Nru tandem-mass-20121001/debian/tandem-mass.install
> tandem-mass-20121001/debian/tandem-mass.install
> --- tandem-mass-20121001/debian/tandem-mass.install 2012-11-20
> 11:57:06.000000000 -0700
> +++ tandem-mass-20121001/debian/tandem-mass.install 2013-01-09
> 13:32:21.000000000 -0700
> @@ -1 +1 @@
> -bin/tandem usr/bin
> +bin/tandem.exe usr/bin
> _______________________________________________
> Debichem-devel mailing list
> debichem-de...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel
--
--
Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu
Researcher at CNRS and Debian Developer <lopi...@debian.org>
Author of ``massXpert'' at http://www.massxpert.org
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