Still unable to compile 9.1.beta1 on macos 10.15 (catalina)

[Andrew]

On sage-release Justin C Walker has reported successfully compiled sage 9.1.beta1 on a 2019 MBP, 8-core Core i9 running 10.5.2.

I am running 10.5.2 on 2016 MBP, 4-core Core i7 and, as previously reported, I whenever I try to compile I get stuck with:

Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-build'):
* package: givaro-4.1.1
  log file: /usr/local/src/sage/logs/pkgs/givaro-4.1.1.log
  build directory: /usr/local/src/sage/local/var/tmp/sage/build/givaro-4.1.1

Evidentally, I have screwed something up but for the life of me I can't figure what. Previously I did success in getting 8.9 to compille on a similarly configured imac in my office but I could not compile 9.1.beta0 there either. (I'm travelling at the moment so I haven'ttried to troubleshoot the imac yet...I was hoping that it would compile in my office and that I could then compare the install logs, but that didn't work out.)

Last time I asked on sage-dev no one was able to figure out what my problem was. I am posting again in the hope that some one will be able to suggest doing something different now. The givaro log file and the full install log are attached.

I am trying to compile using:

    make distclean;
    CC=clang CXX=clang++ FC=gfortran ./configure;
    MAKE="make -j4" make build

I have installed xcode and the command line tools, I have accepted the xcode licence, opened xcode, run xcode-select --install etc.

My system specs are:

sw_vers:
  ProductName:    Mac OS X
  ProductVersion:    10.15.2
  BuildVersion:    19C57
/usr/bin/xcodebuild -version
  Xcode 11.3.1
  Build version 11C504

I am using homebrew (list of installed homebrew fomrula below)

I have tried uninstalling xcode and the command-line tools and then reinstalling it. Uninstalling and then reinstalling all the homebrew packages. I have tried removing anything vaguely objectionable from my path and have trolled through stackexchange applying potential fixes without luck.

The problem seems to be that sage is not finding the header files. I don't any compiler flags (CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS, ...), set although I have tried various combinations of these without success.

Any suggestions would be very much appreciated!

Andrew

--

The homebrew packages that  have installed are:

adns            glog            libunistring        poppler
alluxio            gmp            libusb            python
aom            gnu-sed            libvidstab        python@2
arb            gnupg            libvorbis        qpdf
aspell            gnutls            libvpx            qt
autoconf        gpatch            libyaml            r
automake        graphite2        little-cms2        readline
bash            gsl            lua            rsync
bash-completion        harfbuzz        lzo            rtmpdump
boost            icu4c            macvim            rubberband
cairo            ilmbase            make            ruby
ceres-solver        imagemagick        metis            sdl2
cimg            isl            mpfi            shared-mime-info
cmake            jpeg            mpfr            snappy
coreutils        lame            nettle            speex
cscope            leptonica        node            sqlite
djvu2pdf        libass            npth            suite-sparse
djvulibre        libassuan        nspr            swig
eigen            libbluray        nss            tbb
ffmpeg            libde265        ntl            tesseract
fish            libdvdcss        numpy            texinfo
flac            libevent        openblas        the_silver_searcher
flint            libffi            opencore-amr        theora
fontconfig        libgcrypt        opencv            tkdiff
freetype        libgpg-error        openexr            unbound
frei0r            libheif            openjpeg        unrar
fribidi            libidn2            openssl            webkit2png
gawk            libksba            openssl@1.1        webp
gcc            libmpc            opus            wget
gd            libogg            p11-kit            x264
gdbm            libomp            p7zip            x265
gettext            libpng            pari            xvid
gflags            libsamplerate        pcre            xz
ghostscript        libsndfile        pcre2            yarn
giflib            libsoxr            perl            yasm
git            libtasn1        pinentry
git-extras        libtiff            pixman
glib            libtool            pkg-config

[François Bissey]

It looks to me like there could be a bad interaction between compiler headers (probably installed by brew)
in /usr/local and system headers.
If it is not then I would think there could be a bug for upstream givaro.

François

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> <install.log.gz><givaro-4.1.1.log>

[Justin C. Walker]

> On Jan 25, 2020, at 15:21 , Andrew <andrew...@gmail.com> wrote:
>
> On sage-release Justin C Walker has reported successfully compiled sage 9.1.beta1 on a 2019 MBP, 8-core Core i9 running 10.5.2.
>
> I am running 10.5.2 on 2016 MBP, 4-core Core i7 and, as previously reported, I whenever I try to compile I get stuck with:

To echo François, it looks like homebrew and Xcode don’t play well together.

In my case, I do have Xcode 3.x installed, but I don’t use Homebrew or MacPorts, or any of those package managers.

Does Homebrew really install “/usr/include”? That seems to be asking for trouble…

I don’t have anything to add at this point.

Justin

--
Justin C. Walker, Curmudgeon at Large
Director
Institute for the Enhancement of the Director's Income
-----------
Nobody knows the trouble I've been
-----------

[Dima Pasechnik]

On Sun, Jan 26, 2020 at 12:03 AM 'Justin C. Walker' via sage-devel
<sage-...@googlegroups.com> wrote:
>
>
>
> > On Jan 25, 2020, at 15:21 , Andrew <andrew...@gmail.com> wrote:
> >
> > On sage-release Justin C Walker has reported successfully compiled sage 9.1.beta1 on a 2019 MBP, 8-core Core i9 running 10.5.2.
> >
> > I am running 10.5.2 on 2016 MBP, 4-core Core i7 and, as previously reported, I whenever I try to compile I get stuck with:
>
> To echo François, it looks like homebrew and Xcode don’t play well together.
>
> In my case, I do have Xcode 3.x installed, but I don’t use Homebrew or MacPorts, or any of those package managers.
>
> Does Homebrew really install “/usr/include”? That seems to be asking for trouble…

no, certainly not, all goes either in /usr/local or even more obscure prefixes.

>
> I don’t have anything to add at this point.
>
> Justin
>
> --
> Justin C. Walker, Curmudgeon at Large
> Director
> Institute for the Enhancement of the Director's Income
> -----------
> Nobody knows the trouble I've been
> -----------
>
>
>

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[Andrew]

Thanks Justin, François and Dima, your comments were helpful. I used to quaranteen brew from my sage builds but I stopped doing this because others managed to compile sage along side homebrew, and even recommended which packages to install, and I was able to do this before macos 10.15. When I ran into problems with catalina I tried using brew to uninstall all of the homebrew packages, but I don't think that I checked to see if the directories in /usr/local were empty, perhaps they weren't.

In any case, after renaming the brew directories in /usr/local (specifically the bin, include, lib and opt directories), I can compile sage again! :)

When I have some time I will remove brew completely and then add everything back in slowly and try to isolate and better understand the problem.

Andrew

[Dima Pasechnik]

Why would you want to remove Brew---unless you enjoy building gfortran
and gmp from source ? :-)

I'd rather suggest we make an effort to create and use as many Brew
packages (perhaps from our own) Brew (formulae) repo.
I've just transferred the repo with few Brew formulae I wrote to sagemath org:

https://github.com/sagemath/homebrew-science

It's really not hard to create/tweak these formulae, in fact...

Cheers
Dima

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[Andrew]

 Hi Dima,

> Why would you want to remove Brew---unless you enjoy building gfortran
> and gmp from source ? :-)

I definitely do not want to remove brew but the fact is that I could not compile sage while it it was present because of an unidentified conflict.

Note that I did not say that I removed brew but, instead, that I renamed the directories to compile sage. Once I sage finished compiling I restored the directory names so that brew and sage are both happy now. Next time I need to build sage my bash build function will temporarily rename the directories again. As I said, when I have some time I will try and track work out what was causing my problem but for now this is a good enough work around.

I've just transferred the repo with few Brew formulae I wrote to sagemath org:

https://github.com/sagemath/homebrew-science

I was not able to install some of these formulas earlier, with similar compile problems. I can try and reproduce this and post as an issue on your repository if you like.

Andrew