Re: rpmbuild goes crazy writing duplicate files in /cd/usr/.... "Identical binaries are copied, not linked"...

Without a reproducer it is difficult to help.

Best regards

On Tue, May 13, 2008 at 8:26 PM, Paul Johnson <[email protected]> wrote:

> On Fedora 8 with rpm-devel-4.4.2.2-7.fc8, I'm having trouble getting a
> package to build. The program compiles in a shell if I just do the
> usual configure & make & make install, but when I try to use a spec
> file to build it, a lot of macros come into play and I'm having a hard
> time tracking them down.
>
> Please look down 30 lines for the extract debug-info line that
> suddenly inserts the letters "/cd" into the middle of the path, and
> then "duplicate" files get sent to /usr... and /cd/usr... in the
> buildroot.  I'm quite baffled!
>
> test -z "/usr/lib/pkgconfig" || /bin/mkdir -p
> "/var/tmp/jags-1.0.2-root/usr/lib/pkgconfig"
>  /usr/bin/install -c -m 644 'jags.pc'
> '/var/tmp/jags-1.0.2-root/usr/lib/pkgconfig/jags.pc'
> make[2]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/etc'
> make[1]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/etc'
> Making install in win32
> make[1]: Entering directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32'
> Making install in lapack
> make[2]: Entering directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32/lapack'
> make[3]: Entering directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32/lapack'
> make[3]: Nothing to be done for `install-exec-am'.
> make[3]: Nothing to be done for `install-data-am'.
> make[3]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32/lapack'
> make[2]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32/lapack'
> make[2]: Entering directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32'
> make[3]: Entering directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32'
> make[3]: Nothing to be done for `install-exec-am'.
> make[3]: Nothing to be done for `install-data-am'.
> make[3]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32'
> make[2]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32'
> make[1]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2/win32'
> make[1]: Entering directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2'
> make[2]: Entering directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2'
> make[1]: Leaving directory
> `/home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2'
> + /usr/lib/rpm/find-debuginfo.sh
> /home/pauljohn/LinuxDownloads/redhat/BUILD/JAGS-1.0.2
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/libexec/jags-terminal
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/lib/libjags.so.1.0.2
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/lib/JAGS/modules/bugs.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/lib/JAGS/modules/dic.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/lib/JAGS/modules/msm.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/lib/JAGS/modules/mix.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/lib/JAGS/modules/basemod.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/usr/lib/libjrmath.so.0.0.0
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/libexec/jags-terminal
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/libexec/jags-terminal
>   and  /usr/libexec/jags-terminal
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/lib/libjags.so.1.0.2
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/lib/libjags.so.1.0.2
>   and  /usr/lib/libjags.so.1.0.2
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/lib/JAGS/modules/bugs.so
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/lib/JAGS/modules/bugs.so
>   and  /usr/lib/JAGS/modules/bugs.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/lib/JAGS/modules/dic.so
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/lib/JAGS/modules/dic.so
>   and  /usr/lib/JAGS/modules/dic.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/lib/JAGS/modules/msm.so
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/lib/JAGS/modules/msm.so
>   and  /usr/lib/JAGS/modules/msm.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/lib/JAGS/modules/mix.so
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/lib/JAGS/modules/mix.so
>   and  /usr/lib/JAGS/modules/mix.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/lib/JAGS/modules/basemod.so
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/lib/JAGS/modules/basemod.so
>   and  /usr/lib/JAGS/modules/basemod.so
> extracting debug info from
> /var/tmp/jags-1.0.2-root/cd/usr/lib/libjrmath.so.0.0.0
> *** WARNING: identical binaries are copied, not linked:
>        /cd/usr/lib/libjrmath.so.0.0.0
>   and  /usr/lib/libjrmath.so.0.0.0
> symlinked /usr/lib/debug/usr/lib/libjrmath.so.0.0.0.debug to
> /usr/lib/debug/usr/lib/libjrmath.so.debug
> symlinked /usr/lib/debug/usr/lib/libjags.so.1.0.2.debug to
> /usr/lib/debug/usr/lib/libjags.so.debug
> symlinked /usr/lib/debug/usr/lib/libjags.so.1.0.2.debug to
> /usr/lib/debug/usr/lib/libjags.so.1.debug
> symlinked /usr/lib/debug/usr/lib/libjrmath.so.0.0.0.debug to
> /usr/lib/debug/usr/lib/libjrmath.so.0.debug
> symlinked /usr/lib/debug/cd/usr/lib/libjrmath.so.0.0.0.debug to
> /usr/lib/debug/cd/usr/lib/libjrmath.so.debug
> symlinked /usr/lib/debug/cd/usr/lib/libjags.so.1.0.2.debug to
> /usr/lib/debug/cd/usr/lib/libjags.so.debug
> symlinked /usr/lib/debug/cd/usr/lib/libjags.so.1.0.2.debug to
> /usr/lib/debug/cd/usr/lib/libjags.so.1.debug
> symlinked /usr/lib/debug/cd/usr/lib/libjrmath.so.0.0.0.debug to
> /usr/lib/debug/cd/usr/lib/libjrmath.so.0.debug
> cpio: JAGS-0.98.0/src/lib/compiler/scanner.cc: Cannot stat: No such
> file or directory
> cpio: JAGS-1.0.2/src/terminal/.libs/jags-terminalS.c: Cannot stat: No
> such file or directory
> 2653 blocks
> + /usr/lib/rpm/check-buildroot
> + /usr/lib/rpm/redhat/brp-compress
> + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
> + /usr/lib/rpm/redhat/brp-strip-comment-note /usr/bin/strip
> /usr/bin/objdump
> + /usr/lib/rpm/brp-python-bytecompile
> + /usr/lib/rpm/redhat/brp-python-hardlink
> + /usr/lib/rpm/redhat/brp-java-repack-jars
> Processing files: jags-1.0.2-1f8pj
> Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.15765
> + umask 022
> + cd /home/pauljohn/LinuxDownloads/redhat/BUILD
> + cd JAGS-1.0.2
> + DOCDIR=/var/tmp/jags-1.0.2-root/usr/share/doc/jags-1.0.2
> + export DOCDIR
> + rm -rf /var/tmp/jags-1.0.2-root/usr/share/doc/jags-1.0.2
> + /bin/mkdir -p /var/tmp/jags-1.0.2-root/usr/share/doc/jags-1.0.2
> + cp -pr AUTHORS COPYING ChangeLog INSTALL NEWS README TODO
> /var/tmp/jags-1.0.2-root/usr/share/doc/jags-1.0.2
> + exit 0
> Provides: basemod.so basemod.so.debug bugs.so bugs.so.debug dic.so
> dic.so.debug libjags.so.1 libjags.so.1.0.2.debug libjrmath.so.0
> libjrmath.so.0.0.0.debug mix.so mix.so.debug msm.so msm.so.debug
> Requires(interp): /bin/sh /bin/sh /sbin/ldconfig /sbin/ldconfig
> Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1
> rpmlib(PayloadFilesHavePrefix) <= 4.0-1
> Requires(pre): /bin/sh
> Requires(post): /sbin/ldconfig ldconfig
> Requires(preun): /bin/sh
> Requires(postun): /sbin/ldconfig ldconfig
> Requires: /bin/sh basemod.so bugs.so dic.so lapack libRmath
> libblas.so.3 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3)
> libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libgcc_s.so.1
> libgcc_s.so.1(GCC_3.0) libgcc_s.so.1(GCC_4.0.0) libjags.so.1
> libjrmath.so.0 liblapack.so.3 libm.so.6 libm.so.6(GLIBC_2.0)
> libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.1)
> libstdc++.so.6(GLIBCXX_3.4) mix.so msm.so rtld(GNU_HASH)
> Processing files: jags-debuginfo-1.0.2-1f8pj
> Provides: basemod.so.debug bugs.so.debug dic.so.debug
> libjags.so.1.0.2.debug libjrmath.so.0.0.0.debug mix.so.debug
> msm.so.debug
> Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1
> rpmlib(PayloadFilesHavePrefix) <= 4.0-1
> Requires: basemod.so bugs.so dic.so libjags.so.1 libjrmath.so.0 mix.so
> msm.so
> Checking for unpackaged file(s): /usr/lib/rpm/check-files
> /var/tmp/jags-1.0.2-root
> error: Installed (but unpackaged) file(s) found:
>   /cd/usr/bin/jags
>   /cd/usr/include/JAGS/Console.h
>   /cd/usr/include/JAGS/JRmath.h
>   /cd/usr/include/JAGS/Module.h
>   /cd/usr/include/JAGS/compiler/Compiler.h
>   /cd/usr/include/JAGS/compiler/ConstantFactory.h
>   /cd/usr/include/JAGS/compiler/Counter.h
>   /cd/usr/include/JAGS/compiler/CounterTab.h
>   /cd/usr/include/JAGS/compiler/LogicalFactory.h
>   /cd/usr/include/JAGS/compiler/MixtureFactory.h
>   /cd/usr/include/JAGS/compiler/NodeFactory.h
>   /cd/usr/include/JAGS/compiler/ParseTree.h
>   /cd/usr/include/JAGS/distribution/DistScalar.h
>   /cd/usr/include/JAGS/distribution/DistScalarRmath.h
>   /cd/usr/include/JAGS/distribution/DistTab.h
>   /cd/usr/include/JAGS/distribution/Distribution.h
>   /cd/usr/include/JAGS/distribution/RNG.h
>   /cd/usr/include/JAGS/distribution/RNGFactory.h
>   /cd/usr/include/JAGS/distribution/RmathRNG.h
>   /cd/usr/include/JAGS/function/FuncTab.h
>   /cd/usr/include/JAGS/function/Function.h
>   /cd/usr/include/JAGS/function/InverseLinkFunc.h
>   /cd/usr/include/JAGS/function/ScalarFunc.h
>   /cd/usr/include/JAGS/graph/AggNode.h
>   /cd/usr/include/JAGS/graph/ConstantNode.h
>   /cd/usr/include/JAGS/graph/DeterministicNode.h
>   /cd/usr/include/JAGS/graph/DevianceNode.h
>   /cd/usr/include/JAGS/graph/Graph.h
>   /cd/usr/include/JAGS/graph/GraphMarks.h
>   /cd/usr/include/JAGS/graph/LogicalNode.h
>   /cd/usr/include/JAGS/graph/MixtureNode.h
>   /cd/usr/include/JAGS/graph/Node.h
>   /cd/usr/include/JAGS/graph/NodeError.h
>   /cd/usr/include/JAGS/graph/StochasticNode.h
>   /cd/usr/include/JAGS/model/BUGSModel.h
>   /cd/usr/include/JAGS/model/Model.h
>   /cd/usr/include/JAGS/model/Monitor.h
>   /cd/usr/include/JAGS/model/MonitorFactory.h
>   /cd/usr/include/JAGS/model/NodeArray.h
>   /cd/usr/include/JAGS/model/SymTab.h
>   /cd/usr/include/JAGS/sampler/DensityMethod.h
>   /cd/usr/include/JAGS/sampler/DensitySampler.h
>   /cd/usr/include/JAGS/sampler/Linear.h
>   /cd/usr/include/JAGS/sampler/Metropolis.h
>   /cd/usr/include/JAGS/sampler/RWMetropolis.h
>   /cd/usr/include/JAGS/sampler/Sampler.h
>   /cd/usr/include/JAGS/sampler/SamplerFactory.h
>   /cd/usr/include/JAGS/sampler/SingletonFactory.h
>   /cd/usr/include/JAGS/sampler/Slicer.h
>   /cd/usr/include/JAGS/sarray/Range.h
>   /cd/usr/include/JAGS/sarray/RangeIterator.h
>   /cd/usr/include/JAGS/sarray/SArray.h
>   /cd/usr/include/JAGS/util/dim.h
>   /cd/usr/include/JAGS/util/integer.h
>   /cd/usr/include/JAGS/util/logical.h
>   /cd/usr/include/JAGS/util/nainf.h
>   /cd/usr/lib/JAGS/modules/basemod.la
>   /cd/usr/lib/JAGS/modules/basemod.so
>   /cd/usr/lib/JAGS/modules/bugs.la
>   /cd/usr/lib/JAGS/modules/bugs.so
>   /cd/usr/lib/JAGS/modules/dic.la
>   /cd/usr/lib/JAGS/modules/dic.so
>   /cd/usr/lib/JAGS/modules/mix.la
>   /cd/usr/lib/JAGS/modules/mix.so
>   /cd/usr/lib/JAGS/modules/msm.la
>   /cd/usr/lib/JAGS/modules/msm.so
>   /cd/usr/lib/libjags.la
>   /cd/usr/lib/libjags.so
>   /cd/usr/lib/libjags.so.1
>   /cd/usr/lib/libjags.so.1.0.2
>   /cd/usr/lib/libjrmath.la
>   /cd/usr/lib/libjrmath.so
>   /cd/usr/lib/libjrmath.so.0
>   /cd/usr/lib/libjrmath.so.0.0.0
>   /cd/usr/lib/pkgconfig/jags.pc
>   /cd/usr/libexec/jags-terminal
>   /usr/libexec/jags-terminal
>
>
> RPM build errors:
>    Installed (but unpackaged) file(s) found:
>   /cd/usr/bin/jags
>   /cd/usr/include/JAGS/Console.h
>   /cd/usr/include/JAGS/JRmath.h
>   /cd/usr/include/JAGS/Module.h
>   /cd/usr/include/JAGS/compiler/Compiler.h
>   /cd/usr/include/JAGS/compiler/ConstantFactory.h
>   /cd/usr/include/JAGS/compiler/Counter.h
>   /cd/usr/include/JAGS/compiler/CounterTab.h
>   /cd/usr/include/JAGS/compiler/LogicalFactory.h
>   /cd/usr/include/JAGS/compiler/MixtureFactory.h
>   /cd/usr/include/JAGS/compiler/NodeFactory.h
>   /cd/usr/include/JAGS/compiler/ParseTree.h
>   /cd/usr/include/JAGS/distribution/DistScalar.h
>   /cd/usr/include/JAGS/distribution/DistScalarRmath.h
>   /cd/usr/include/JAGS/distribution/DistTab.h
>   /cd/usr/include/JAGS/distribution/Distribution.h
>   /cd/usr/include/JAGS/distribution/RNG.h
>   /cd/usr/include/JAGS/distribution/RNGFactory.h
>   /cd/usr/include/JAGS/distribution/RmathRNG.h
>   /cd/usr/include/JAGS/function/FuncTab.h
>   /cd/usr/include/JAGS/function/Function.h
>   /cd/usr/include/JAGS/function/InverseLinkFunc.h
>   /cd/usr/include/JAGS/function/ScalarFunc.h
>   /cd/usr/include/JAGS/graph/AggNode.h
>   /cd/usr/include/JAGS/graph/ConstantNode.h
>   /cd/usr/include/JAGS/graph/DeterministicNode.h
>   /cd/usr/include/JAGS/graph/DevianceNode.h
>   /cd/usr/include/JAGS/graph/Graph.h
>   /cd/usr/include/JAGS/graph/GraphMarks.h
>   /cd/usr/include/JAGS/graph/LogicalNode.h
>   /cd/usr/include/JAGS/graph/MixtureNode.h
>   /cd/usr/include/JAGS/graph/Node.h
>   /cd/usr/include/JAGS/graph/NodeError.h
>   /cd/usr/include/JAGS/graph/StochasticNode.h
>   /cd/usr/include/JAGS/model/BUGSModel.h
>   /cd/usr/include/JAGS/model/Model.h
>   /cd/usr/include/JAGS/model/Monitor.h
>   /cd/usr/include/JAGS/model/MonitorFactory.h
>   /cd/usr/include/JAGS/model/NodeArray.h
>   /cd/usr/include/JAGS/model/SymTab.h
>   /cd/usr/include/JAGS/sampler/DensityMethod.h
>   /cd/usr/include/JAGS/sampler/DensitySampler.h
>   /cd/usr/include/JAGS/sampler/Linear.h
>   /cd/usr/include/JAGS/sampler/Metropolis.h
>   /cd/usr/include/JAGS/sampler/RWMetropolis.h
>   /cd/usr/include/JAGS/sampler/Sampler.h
>   /cd/usr/include/JAGS/sampler/SamplerFactory.h
>   /cd/usr/include/JAGS/sampler/SingletonFactory.h
>   /cd/usr/include/JAGS/sampler/Slicer.h
>   /cd/usr/include/JAGS/sarray/Range.h
>   /cd/usr/include/JAGS/sarray/RangeIterator.h
>   /cd/usr/include/JAGS/sarray/SArray.h
>   /cd/usr/include/JAGS/util/dim.h
>   /cd/usr/include/JAGS/util/integer.h
>   /cd/usr/include/JAGS/util/logical.h
>   /cd/usr/include/JAGS/util/nainf.h
>   /cd/usr/lib/JAGS/modules/basemod.la
>   /cd/usr/lib/JAGS/modules/basemod.so
>   /cd/usr/lib/JAGS/modules/bugs.la
>   /cd/usr/lib/JAGS/modules/bugs.so
>   /cd/usr/lib/JAGS/modules/dic.la
>   /cd/usr/lib/JAGS/modules/dic.so
>   /cd/usr/lib/JAGS/modules/mix.la
>   /cd/usr/lib/JAGS/modules/mix.so
>   /cd/usr/lib/JAGS/modules/msm.la
>   /cd/usr/lib/JAGS/modules/msm.so
>   /cd/usr/lib/libjags.la
>   /cd/usr/lib/libjags.so
>   /cd/usr/lib/libjags.so.1
>   /cd/usr/lib/libjags.so.1.0.2
>   /cd/usr/lib/libjrmath.la
>   /cd/usr/lib/libjrmath.so
>   /cd/usr/lib/libjrmath.so.0
>   /cd/usr/lib/libjrmath.so.0.0.0
>   /cd/usr/lib/pkgconfig/jags.pc
>   /cd/usr/libexec/jags-terminal
>   /usr/libexec/jags-terminal
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
>
> _______________________________________________
> Rpm-list mailing list
> [email protected]
> https://www.redhat.com/mailman/listinfo/rpm-list
>

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