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Re: [rsf-devel] Installation errors when running make install within RSFSRC on Mac os
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From: Luke D. <dec...@gm...> - 2018-11-02 01:33:46
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Here is the error from the last good program compilation: gcc -o build/plot/lib/vplot.os -c -O2 -x c -std=gnu99 -Wall -pedantic -fPIC -Ibuild/include -I/opt/local/include build/plot/lib/vplot.c gcc -o build/plot/lib/libdrsfplot.dylib -framework Accelerate -dynamiclib build/plot/lib/axis.os build/plot/lib/coltab.os build/plot/lib/contour.os build/plot/lib/gainpar.os build/plot/lib/plot.os build/plot/lib/stdplot.os build/plot/lib/vplot.os -Lbuild/lib -L/opt/local/lib -ldrsf -lm -lmx -lfftw3f -lfftw3f_threads -lfftw3_threads ld: warning: text-based stub file /System/Library/Frameworks//Accelerate.framework/Accelerate.tbd and library file /System/Library/Frameworks//Accelerate.framework/Accelerate are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//vecLib.framework/Versions/A/vecLib.tbd and library file /System/Library/Frameworks//vecLib.framework/Versions/A/vecLib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparse.tbd and library file /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparse.dylib are out of sync. Falling back to library file for linking. Install file: "build/plot/lib/libdrsfplot.dylib" as "/Users/luke/madagascar/lib/libdrsfplot.dylib" /opt/local/bin/install_name_tool -change build/api/c/libdrsf.dylib /Users/luke/madagascar/lib/libdrsf.dylib /Users/luke/madagascar/lib/libdrsfplot.dylib /opt/local/bin/install_name_tool: object: /Users/luke/madagascar/lib/libdrsfplot.dylib malformed object (unknown load command 8) scons: *** [/Users/luke/madagascar/lib/libdrsfplot.dylib] Error 1 scons: building terminated because of errors. make: *** [install] Error 2 Thanks, Luke > On Nov 1, 2018, at 8:32 PM, Luke Decker <dec...@gm...> wrote: > > Completing a MacPorts Migration fixes the numpy issue: > > https://trac.macports.org/wiki/Migration <https://trac.macports.org/wiki/Migration> > > However, the original problem of installation not completing remains (and is actually amplified — I lost the env.sh file when reinstalling MacPorts so now the Mac doesn’t recognize Madagascar programs. > > Thanks, > Luke > >> On Nov 1, 2018, at 5:58 PM, Zhicheng Geng <zhi...@ut... <mailto:zhi...@ut...>> wrote: >> >> Hi, >> >> The current system version of my Mac is macOS Mojave and I reinstalled the latest version Madagascar last night successfully. >> >> Luke, can you send the error message so that I can try to find out why the configure file doesn’t work? >> >> And regarding the problem Karl is having right now, I think you aren't using the latest Madagascar. >> The line #include <vecLib/clapack.h> has already been commented since Sep. 6. >> >> Currently, the sfpen can’t work with pipe, but you can use sfpen to open a vpl file. >> If it shows black, you can try fullscreen. It works on my Mac. >> >> Zhicheng >> >>> On Nov 1, 2018, at 15:17, Luke Decker <dec...@gm... <mailto:dec...@gm...>> wrote: >>> >>> Interesting. I’m getting more problems with the Mac too — I have noticed that the configure file no longer recognizes numpy either. Are you having this problem as well? >>> Luke >>> >>>> On Nov 1, 2018, at 3:14 PM, Karl Schleicher <k_s...@ho... <mailto:k_s...@ho...>> wrote: >>>> >>>> OK. Bill woke men up, but I do no have much to add. Here is the story of my recent story trying to build on a Mac. >>>> >>>> I purchased a new Mac in August and tried to install Madagascar. I followed the directions at reproduciblity.org <http://reproduciblity.org/> in Advanced installation. Everything build pretty easily, but sfpen did not work. This is test and some print from the terminal: >>>> sfspike n1=1000 k1=300 | sfbandpass fhi=2 phase=y | sfwiggle clip=0.02 title="Welcome to Madagascar" | >>>> sfpen >>>> produces the error message: >>>> Abort trap: 6 >>>> and a "Problem Report for sfpen" window appears that says: >>>> sfpen quite unexpectantly. >>>> click Reopen to open the application again. This report will be sent to Apple automaticly >>>> >>>> Problem is in sfpen. I plotted the .vpl from sfwiggle with this sequence: >>>> >>>> sfspike n1=1000 k1=300 | sfbandpass fhi=2 phase=y | sfwiggle clip=0.02 title="Welcome to Madagascar" > spike.vpl >>>> vpconvert spike.vpl format=gif >>>> open spike.gif >>>> >>>> >>>> In the past when I had problem with sfpen it was the program was not created because X11 libraries were missing. I tried a few things, posted to ref-devl and rsf-users but did not get help. >>>> >>>> Last week I decided to installed mojave. I do not remember the error message, but decided I need to update Xcode by reinstalling from the App Store. I followed the Advanced installation instructions at reproducibility.org <http://reproducibility.org/>. I opened Xcode and installed the command line tools. I reran ./configure and ran make install and get a message: >>>> clang -o build/pens/main/gdpen.o -c -O2 -DGIFANIM -Ibuild/include -I/opt/local/include build/pens/main/gdpen.c >>>> In file included from build/pens/main/gdpen.c:23: >>>> In file included from build/pens/main/../include/extern.h:4: >>>> build/include/rsf.h:5504:10: fatal error: 'vecLib/clapack.h' file not found >>>> #include <vecLib/clapack.h> >>>> >>>> I tried again, running all the steps in the advanced installation for Mac in reproducibility.org <http://reproducibility.org/>. Tried googling. I have a copy of clapack.h, but not found by the compiler. I also tried gcc, which fails the same way. >>>> >>>> That is where I am today. Still using my old Mac and my Linux tower. I'm interested in some tips. >>>> >>>> Karl >>>> From: symes <sy...@ri... <mailto:sy...@ri...>> >>>> Sent: Tuesday, October 30, 2018 3:17 PM >>>> To: rsf...@li... <mailto:rsf...@li...> >>>> Subject: Re: [rsf-devel] Installation errors when running make install within RSFSRC on Mac os >>>> >>>> I have heard something like this from Karl. Have been putting off >>>> updating to Mojave for precisely this reason. >>>> >>>> Quoting Luke Decker <dec...@gm... <mailto:dec...@gm...>>: >>>> >>>> > When I try to install Madagascar on my Mac, I get the following >>>> > issues towards the end of compilation : >>>> > >>>> > /opt/local/bin/install_name_tool -change build/api/c/libdrsf.dylib >>>> > /Users/luke/madagascar/lib/libdrsf.dylib >>>> > /Users/luke/madagascar/lib/libdrsfplot.dylib >>>> > /opt/local/bin/install_name_tool: object: >>>> > /Users/luke/madagascar/lib/libdrsfplot.dylib malformed object >>>> > (unknown load command 8) >>>> > scons: *** [/Users/luke/madagascar/lib/libdrsfplot.dylib] Error 1 >>>> > scons: building terminated because of errors. >>>> > make: *** [install] Error 2 >>>> > >>>> > >>>> > I recently updated to MojaveOS. Could this be causing the issue? >>>> > Is anyone else having this problem? >>>> > >>>> > Thanks, >>>> > Luke >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> RSF-devel mailing list >>>> RSF...@li... <mailto:RSF...@li...> >>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frsf-devel&data=02%7C01%7C%7C39f29d69041d4b4a95c608d63ea7d97e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636765287954190763&sdata=L2goocZO17gb8IKaJc%2BY9AKCAnIsuxyOuBhgsg%2BdyNY%3D&reserved=0 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frsf-devel&data=02%7C01%7C%7C39f29d69041d4b4a95c608d63ea7d97e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636765287954190763&sdata=L2goocZO17gb8IKaJc%2BY9AKCAnIsuxyOuBhgsg%2BdyNY%3D&reserved=0> >>>> _______________________________________________ >>>> RSF-devel mailing list >>>> RSF...@li... <mailto:RSF...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/rsf-devel <https://lists.sourceforge.net/lists/listinfo/rsf-devel> >>> >>> _______________________________________________ >>> RSF-devel mailing list >>> RSF...@li... <mailto:RSF...@li...> >>> https://lists.sourceforge.net/lists/listinfo/rsf-devel <https://lists.sourceforge.net/lists/listinfo/rsf-devel> >> > |
