Hi there,
I try to install Bioperl since some hours. A lot of fails I could solve by
myself, but now I'm stucking completely. Here's the error message:
gcc -c -I/sw/include -I/usr/X11/include -I.. -I/sw/include
-I/usr/X11/include -I/sw/include -fno-common -DPERL_DARWIN -no-cpp-precomp
-fno-strict-aliasing -pipe -fstack-protector -I/opt/local/include -O3
-DVERSION=\"804.032\" -DXS_VERSION=\"804.032\"
"-I/sw/lib/perl5-core/5.12.4/darwin-thread-multi-2level/CORE" -MD -Wall
-Wno-implicit-int -Wno-comment -Wno-unused -D__USE_FIXED_PROTOTYPES__
Canvas.c -o Canvas.o
clang: warning: argument unused during compilation: '-no-cpp-precomp'
rm -f ../blib/arch/auto/Tk/Canvas/Canvas.bundle
env MACOSX_DEPLOYMENT_TARGET=10.3 cc -L/sw/lib -bundle -undefined
dynamic_lookup -L/opt/local/lib -fstack-protector -o
../blib/arch/auto/Tk/Canvas/Canvas.bundle Canvas.o ../pTk/libpTk.a \
-lm \
chmod 755 ../blib/arch/auto/Tk/Canvas/Canvas.bundle
Manifying 101 pod documents
Manifying 1 pod document
Manifying 2 pod documents
Manifying 1 pod document
Manifying 1 pod document
Manifying 1 pod document
Manifying 1 pod document
Manifying 1 pod document
Manifying 3 pod documents
Manifying 2 pod documents
Manifying 5 pod documents
Sorry no HTML building yet
fink-package-precedence --depfile-ext='\.d' .
Scanning /\.d$/ dependency files...
./chnGlue.d
./encGlue.d
./evtGlue.d
./objGlue.d
./tixGlue.d
./Tk.d
./tkGlue.d
./tkGlue_f.d
./tkWin32Dll.d
./Canvas/Canvas.d
./Compound/Compound.d
./Entry/Entry.d
./Event/Event.d
./Event/eventWin32Dll.d
./Event/pTkCallback.d
./Event/tclAsync.d
./Event/tclEvent.d
./Event/tclNotify.d
./Event/tclPlatEvent.d
./Event/tclPlatNotfy.d
./Event/tclPlatTime.d
./Event/tclTimer.d
./HList/HList.d
./InputO/InputO.d
./IO/IO.d
./JPEG/imgJPEG.d
./JPEG/JPEG.d
./Listbox/Listbox.d
./Menubutton/Menubutton.d
./Mwm/Mwm.d
./NBFrame/NBFrame.d
./PNG/imgPNG.d
./PNG/PNG.d
./pTk/ClientWin.d
./pTk/imgBMP.d
./pTk/imgInit.d
./pTk/imgInt_f.d
./pTk/imgObj.d
./pTk/imgUtil.d
./pTk/imgWindow.d
./pTk/imgXBM.d
./pTk/imgXPM.d
./pTk/Lang_f.d
./pTk/ptkCanvGrid.d
./pTk/ptkCanvGroup.d
./pTk/stbDashCustom.d
./pTk/stbDiStyle.d
./pTk/stbDItem.d
./pTk/strGlue.d
./pTk/tclAsync.d
./pTk/tclDecls_f.d
./pTk/tclEvent.d
./pTk/tclHash.d
./pTk/tclNotify.d
./pTk/tclPreserve.d
./pTk/tclTimer.d
./pTk/tclUnixEvent.d
./pTk/tclUnixNotfy.d
./pTk/tclUnixTime.d
./pTk/tix_f.d
./pTk/tixCompat.d
./pTk/tixDiImg.d
./pTk/tixDiITxt.d
./pTk/tixDiStyle.d
./pTk/tixDItem.d
./pTk/tixDiText.d
./pTk/tixDiWin.d
./pTk/tixError.d
./pTk/tixForm.d
./pTk/tixFormMisc.d
./pTk/tixGrData.d
./pTk/tixGrFmt.d
./pTk/tixGrid.d
./pTk/tixGrRC.d
./pTk/tixGrSel.d
./pTk/tixGrSort.d
./pTk/tixGrUtl.d
./pTk/tixHLCol.d
./pTk/tixHLHdr.d
./pTk/tixHLInd.d
./pTk/tixHList.d
./pTk/tixImgCmp.d
./pTk/tixImgXpm.d
./pTk/tixImgXpm_f.d
./pTk/tixInputO.d
./pTk/tixInt_f.d
./pTk/tixList.d
./pTk/tixMwm.d
./pTk/tixNBFrame.d
./pTk/tixScroll.d
./pTk/tixSmpLs.d
./pTk/tixTList.d
./pTk/tixUnixDraw.d
./pTk/tixUnixWm.d
./pTk/tixUnixXpm.d
./pTk/tixUtils.d
./pTk/tixVars.d
./pTk/tk3d.d
./pTk/tk_f.d
./pTk/tkAtom.d
./pTk/tkBind.d
./pTk/tkBitmap.d
./pTk/tkButton.d
./pTk/tkCanvArc.d
./pTk/tkCanvas.d
./pTk/tkCanvBmap.d
./pTk/tkCanvImg.d
./pTk/tkCanvLine.d
./pTk/tkCanvPoly.d
./pTk/tkCanvPs.d
./pTk/tkCanvText.d
./pTk/tkCanvUtil.d
./pTk/tkCanvWind.d
./pTk/tkClipboard.d
./pTk/tkCmds.d
./pTk/tkColor.d
./pTk/tkConfig.d
./pTk/tkCursor.d
./pTk/tkDecls_f.d
./pTk/tkEntry.d
./pTk/tkError.d
./pTk/tkEvent.d
./pTk/tkEvent_f.d
./pTk/tkFileFilter.d
./pTk/tkFocus.d
./pTk/tkFont.d
./pTk/tkFrame.d
./pTk/tkGC.d
./pTk/tkGeometry.d
./pTk/tkGet.d
./pTk/tkGrab.d
./pTk/tkGrid.d
./pTk/tkImage.d
./pTk/tkImgBmap.d
./pTk/tkImgGIF.d
./pTk/tkImgPhoto.d
./pTk/tkImgPhoto_f.d
./pTk/tkImgPPM.d
./pTk/tkInt_f.d
./pTk/tkIntDecls_f.d
./pTk/tkIntPlatDecls_f.d
./pTk/tkIntXlibDecls_f.d
./pTk/tkListbox.d
./pTk/tkMenu.d
./pTk/tkMenubutton.d
./pTk/tkMenuDraw.d
./pTk/tkMessage.d
./pTk/tkObj.d
./pTk/tkOldConfig.d
./pTk/tkOption.d
./pTk/tkOption_f.d
./pTk/tkPack.d
./pTk/tkPanedWindow.d
./pTk/tkPlace.d
./pTk/tkPlatDecls_f.d
./pTk/tkPointer.d
./pTk/tkProperty.d
./pTk/tkRectOval.d
./pTk/tkScale.d
./pTk/tkScrollbar.d
./pTk/tkSelect.d
./pTk/tkSquare.d
./pTk/tkStubImg.d
./pTk/tkStyle.d
./pTk/tkText.d
./pTk/tkTextBTree.d
./pTk/tkTextDisp.d
./pTk/tkTextImage.d
./pTk/tkTextIndex.d
./pTk/tkTextMark.d
./pTk/tkTextTag.d
./pTk/tkTextWind.d
./pTk/tkTrig.d
./pTk/tkUndo.d
./pTk/tkUnix.d
./pTk/tkUnix3d.d
./pTk/tkUnixButton.d
./pTk/tkUnixColor.d
./pTk/tkUnixConfig.d
./pTk/tkUnixCursor.d
./pTk/tkUnixDialog.d
./pTk/tkUnixDraw.d
./pTk/tkUnixEmbed.d
./pTk/tkUnixEvent.d
./pTk/tkUnixFocus.d
./pTk/tkUnixFont.d
./pTk/tkUnixInit.d
./pTk/tkUnixKey.d
./pTk/tkUnixMenu.d
./pTk/tkUnixMenubu.d
./pTk/tkUnixScale.d
./pTk/tkUnixScrlbr.d
./pTk/tkUnixSelect.d
./pTk/tkUnixSend.d
./pTk/tkUnixWm.d
./pTk/tkUnixXft.d
./pTk/tkUnixXId.d
./pTk/tkUtil.d
./pTk/tkVisual.d
./pTk/tkWindow.d
./pTk/Xlib_f.d
./pTk/XrmOption.d
./Scale/Scale.d
./Scrollbar/Scrollbar.d
./Text/Text.d
./TixGrid/TixGrid.d
./TixPixmap/Pixmap.d
./TList/TList.d
./WinPhoto/WinPhoto.d
./Xlib/Xlib.d
./Xlib/X/X.d
Looking for incorrect headers in 211 dependency files...
Determining fink providers of 48 headers...
1 - 48
Found use of headers from 3 fink packages:
libjpeg9
libpng16
perl5124-core
Scanning binaries for incorrect dyld linking...
./blib/arch/auto/Tk/Tk.bundle uses /opt/local/lib/libX11.6.dylib
./blib/arch/auto/Tk/PNG/PNG.bundle uses /opt/local/lib/libz.1.dylib
Please fix build process to get consistent use of fink's libraries.
### execution of /tmp/fink.TXB5K failed, exit code 255
### execution of /tmp/fink.w3Bzn failed, exit code 255
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-tk-pm5124-804.032-1
(Reading database ... 37672 files and directories currently installed.)
Removing fink-buildlock-tk-pm5124-804.032-1 ...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-x86_64
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/dist-checkconflicts-pm5124_0.11-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/module-implementation-pm5124_0.09-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/module-runtime-conflicts-pm5124_0.001-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/package-stash-pm5124_0.37-1_darwin-x86_64.deb
Failed: phase compiling: tk-pm5124-804.032-1 failed
Before reporting any errors, please run "fink selfupdate" and try again.
If you continue to have issues, please check to see if the FAQ on Fink's
website solves the problem. If not, ask on one (not both, please) of
these mailing lists:
The Fink Users List <fink-us...@lists.sourceforge.net>
The Fink Beginners List <fink-beginners@lists.sourceforge.net>.
Please try to include the complete error message in your report. This
generally consists of a compiler line starting with e.g. "gcc" or "g++"
followed by the actual error output from the compiler.
Also include the following system information:
Package manager version: 0.38.5
Distribution version: selfupdate-rsync Fri May 22 21:07:54 2015, 10.7,
x86_64
Trees: local/main stable/main
Xcode.app: 4.2.1
Xcode command-line tools: 4.2.1
tk-pm5124-804.032-1 is set to build with only one job.
I changed already the name of /usr/local and made some fink selfupdates,
but nothing helps. Maybe you can find a solution?
Many thanks in advance,
Angela
--
Angela Noll, Dipl.-Biol.
Münster Graduate School of Evolution (MGSE)
Institute for Evolution and Biodiversity
University of Münster
Schlossplatz 6
D-48149 Münster
Website: http://www.uni-muenster.de/Evolution/mgse/people/angelanoll.html
<http://ieb.uni-muenster.de/mgsei/people/32>
Institute of Experimental Pathology
Center for Molecular Biology of Inflammation
University of Münster
Von-Esmarch-Straße 56
D-48149 Münster
Website: http://zmbe.uni-muenster.de/institutes/iep/iepschmitz_de.htm
Tel.: +49 251/83 52132
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