Your message dated Tue, 5 Apr 2011 16:03:33 -0400
with message-id <20110405200333.gb15...@novo.onerussian.com>
and subject line Re: stimfit_0.10.13-1_amd64.changes ACCEPTED into unstable
has caused the Debian Bug report #620434,
regarding stimfit: FTBFS: undefined reference to dgemm_ from BLAS
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
620434: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=620434
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: stimfit
Version: 0.10.9-1
Severity: serious
Justification: fails to build from source
Per http://lists.debian.org/debian-devel-announce/2011/02/msg00011.html,
gcc now normally invokes ld with an option that directs it to consider
only libraries that explicitly appear on the command line. This change
affects stimfit as currently packaged, as it uses BLAS symbols without
directly linking against libblas. Previously, stimfit's use of LAPACK
would have sufficed to bring libbblas to the linker's attention as a
potential library of interest, but now that arrangement merely informs
the resulting error message:
/bin/bash ./libtool --tag=CXX --mode=link g++ -O2 -g -g -O2 -fPIC
-I/usr/lib/wx/include/gtk2-unicode-release-2.8 -I/usr/include/wx-2.8
-D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D__WXGTK__ -pthread -Wall -llapack
-L/usr/lib/python2.6 -lpython2.6 -Wl,-rpath,/usr/lib/stimfit -avoid-version -o
stimfit stimfit-channel.o stimfit-section.o stimfit-recording.o stimfit-core.o
stimfit-fitlib.o stimfit-measlib.o stimfit-asciilib.o stimfit-cfslib.o
stimfit-hdf5lib.o cfs.o stimfit-abflib.o stimfit-atflib.o stimfit-axglib.o
stimfit-hekalib.o stimfit-abffiles.o stimfit-csynch.o stimfit-filedesc.o
stimfit-FileReadCache.o stimfit-FileIO.o stimfit-abfheadr.o stimfit-abfhwave.o
stimfit-Oldheadr.o stimfit-abfutil.o stimfit-msbincvt.o stimfit-unix.o
stimfit-abferror.o stimfit-axatffio32.o stimfit-fileio2.o
stimfit-ProtocolReaderABF2.o stimfit-SimpleStringCache.o stimfit-abf2headr.o
stimfit-AxoGraph_ReadWrite.o stimfit-fileUtils.o stimfit-stringUtils.o
stimfit-byteswap.o lm.o Axb.o misc.o lmlec.o
lmbc.o stimfit-app.o stimfit-doc.o stimfit-stfcheckbox.o stimfit-copygrid.o
stimfit-graph.o stimfit-printout.o stimfit-parentframe.o stimfit-childframe.o
stimfit-view.o stimfit-table.o stimfit-zoom.o stimfit-cursorsdlg.o
stimfit-eventdlg.o stimfit-fitseldlg.o stimfit-smalldlgs.o stimfit-funclib.o
stimfit-usrdlg.o -pthread -lwx_baseu-2.8 -lwx_gtk2u_core-2.8
-lwx_gtk2u_adv-2.8 -lwx_gtk2u_aui-2.8 -lwx_baseu_net-2.8
./src/stfswig/libstf.la -lfftw3 -lhdf5 -lhdf5_hl ./src/app/libstimfit.a
libtool: link: g++ -O2 -g -g -O2 -fPIC
-I/usr/lib/wx/include/gtk2-unicode-release-2.8 -I/usr/include/wx-2.8
-D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D__WXGTK__ -pthread -Wall -Wl,-rpath
-Wl,/usr/lib/stimfit -o .libs/stimfit stimfit-channel.o stimfit-section.o
stimfit-recording.o stimfit-core.o stimfit-fitlib.o stimfit-measlib.o
stimfit-asciilib.o stimfit-cfslib.o stimfit-hdf5lib.o cfs.o stimfit-abflib.o
stimfit-atflib.o stimfit-axglib.o stimfit-hekalib.o stimfit-abffiles.o
stimfit-csynch.o stimfit-filedesc.o stimfit-FileReadCache.o stimfit-FileIO.o
stimfit-abfheadr.o stimfit-abfhwave.o stimfit-Oldheadr.o stimfit-abfutil.o
stimfit-msbincvt.o stimfit-unix.o stimfit-abferror.o stimfit-axatffio32.o
stimfit-fileio2.o stimfit-ProtocolReaderABF2.o stimfit-SimpleStringCache.o
stimfit-abf2headr.o stimfit-AxoGraph_ReadWrite.o stimfit-fileUtils.o
stimfit-stringUtils.o stimfit-byteswap.o lm.o Axb.o misc.o lmlec.o lmbc.o
stimfit-app.o stimfit-doc.o stimfit-stfcheckbox.o stimfit-copygrid.o s
timfit-graph.o stimfit-printout.o stimfit-parentframe.o stimfit-childframe.o
stimfit-view.o stimfit-table.o stimfit-zoom.o stimfit-cursorsdlg.o
stimfit-eventdlg.o stimfit-fitseldlg.o stimfit-smalldlgs.o stimfit-funclib.o
stimfit-usrdlg.o -pthread -llapack -L/usr/lib/python2.6 -lpython2.6
-lwx_baseu-2.8 -lwx_gtk2u_core-2.8 -lwx_gtk2u_adv-2.8 -lwx_gtk2u_aui-2.8
-lwx_baseu_net-2.8 ./src/stfswig/.libs/libstf.so /usr/lib/libfftw3.so
/usr/lib/libhdf5.so /usr/lib/libhdf5_hl.so ./src/app/libstimfit.a -pthread
-Wl,-rpath
-Wl,/build/buildd-stimfit_0.10.9-1-i386-5rQxiX/stimfit-0.10.9/debian/tmp/usr/lib/stimfit
/usr/bin/ld: misc.o: undefined reference to symbol 'dgemm_'
/usr/bin/ld: note: 'dgemm_' is defined in DSO //usr/lib/libblas.so.3gf so try
adding it to the linker command line
//usr/lib/libblas.so.3gf: could not read symbols: Invalid operation
collect2: ld returned 1 exit status
make[3]: *** [stimfit] Error 1
[Taken from
https://buildd.debian.org/fetch.cgi?pkg=stimfit&arch=i386&ver=0.10.9-1&stamp=1301667138&file=log&as=raw
]
Could you please link stimfit directly against libblas and double check
that you won't need to list any other libraries?
Thanks!
--- End Message ---
--- Begin Message ---
Version: 0.10.13-1
Hi Chris,
could you have a look at
https://buildd.debian.org/build.cgi?pkg=stimfit&dist=sid
there are issues while building for big endians and other ones on
kfreebsd ports
also with this email I am closing #620434 (BCCed to
620434-d...@bugs.debian.org so we do not continue emailing it with
follow up by mistake ;)) ) which was fixed in 0.10.13-1 -- package
built just fine, thanks!
On Mon, 04 Apr 2011, Debian FTP Masters wrote:
> Accepted:
> python-stfio_0.10.13-1_amd64.deb
> to main/s/stimfit/python-stfio_0.10.13-1_amd64.deb
> stimfit-dbg_0.10.13-1_amd64.deb
> to main/s/stimfit/stimfit-dbg_0.10.13-1_amd64.deb
> stimfit_0.10.13-1.debian.tar.gz
> to main/s/stimfit/stimfit_0.10.13-1.debian.tar.gz
> stimfit_0.10.13-1.dsc
> to main/s/stimfit/stimfit_0.10.13-1.dsc
> stimfit_0.10.13-1_amd64.deb
> to main/s/stimfit/stimfit_0.10.13-1_amd64.deb
> stimfit_0.10.13.orig.tar.gz
> to main/s/stimfit/stimfit_0.10.13.orig.tar.gz
--
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--- End Message ---
