[Debichem-devel] Bug#695553: Bug#695553: tandem-mass: FTBFS: cannot stat `debian/tmp/bin/tandem': No such file or directory

Filippo Rusconi lopippo at debian.org
Wed Jan 9 21:18:20 UTC 2013


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-devel at 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-devel at lists.alioth.debian.org>
> +Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
> +XSBC-Original-Maintainer: The Debichem Group <debichem-devel at lists.alioth.debian.org>
>  Uploaders: Filippo Rusconi <lopippo at 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-devel at 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 <lopippo at debian.org>
Author of ``massXpert''     at http://www.massxpert.org
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: Digital signature
URL: <http://lists.alioth.debian.org/pipermail/debichem-devel/attachments/20130109/a77ae82f/attachment.pgp>


More information about the Debichem-devel mailing list