GregorySchwartz / too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Home Page:https://gregoryschwartz.github.io/too-many-cells/

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too-many-cells not installed on MacOSX Sierra

elusito opened this issue · comments

I tried to install too-many-cells on MacOS X Sierra without success.

It fails building gtk 0.14 that is required.

I also followed instructions here: https://wiki.haskell.org/Gtk2Hs/Mac i.e. I tried
to use cabal install gtk -f have-quartz-gtk although for OS X Mavericks but again it failed.

It installs automatically gtk 0.15.

Any suggestion?

Thank you in advance

Can you post the error output?

Yes:

gtk-0.14.10: configure
gtk-0.14.10: build
Progress 1/5

-- While building package gtk-0.14.10 using:
/private/var/folders/lv/2jj3qhdn7wz4t58kgm0m14bmgc_64f/T/stack-aaff458a906ff1bc/gtk-0.14.10/.stack-work/dist/x86_64-osx/Cabal-2.2.0.1/setup/setup --builddir=.stack-work/dist/x86_64-osx/Cabal-2.2.0.1 build --ghc-options " -ddump-hi -ddump-to-file -fdiagnostics-color=always"
Process exited with code: ExitFailure 1

In the attached log file the details.

Thank you in advance

gtk-0.14.10.log

I don't have a Mac so FYI I won't have a way to test this (worst case scenario you can use docker which won't have these issues).

First, did you use this command in the too-many-cells folder with stack? Something like stack install --ghc-options "-fhave-quartz-gtk".

Also try stack install --flag gtk:have-quartz-gtk from commercialhaskell/stack#807.

So while solved the gtk-0.14.10 build another error occurs:

Building library for too-many-cells-0.1.3.0..
[ 3 of 21] Compiling TooManyCells.Matrix.Types ( src/TooManyCells/Matrix/Types.hs, .stack-work/dist/x86_64-osx/Cabal-2.2.0.1/build/TooManyCells/Matrix/Types.o )
: can't load .so/.DLL for: /Users/Username/.stack/snapshots/x86_64-osx/lts-12.0/8.4.3/lib/x86_64-osx-ghc-8.4.3/libHShmatrix-gsl-0.19.0.1-Gni665xmjpQJJA5D3St61G-ghc8.4.3.dylib (dlopen(/Users/lusito.eleonora/.stack/snapshots/x86_64-osx/lts-12.0/8.4.3/lib/x86_64-osx-ghc-8.4.3/libHShmatrix-gsl-0.19.0.1-Gni665xmjpQJJA5D3St61G-ghc8.4.3.dylib, 5): Library not loaded: /usr/local/opt/gsl/lib/libgsl.23.dylib
Referenced from: /Users/Username/.stack/snapshots/x86_64-osx/lts-12.0/8.4.3/lib/x86_64-osx-ghc-8.4.3/libHShmatrix-gsl-0.19.0.1-Gni665xmjpQJJA5D3St61G-ghc8.4.3.dylib
Reason: image not found)

Do you have the GNU Scientific Library dependency? If not first install that and the rest of the dependencies in the installation section of https://gregoryschwartz.github.io/too-many-cells/. I don't know the exact names of the Mac equivalents. If it still doesn't work, let me know!

Any updates or should I close this issue?

still not working. we stopped trying to install it

That's unfortunate. I will try to get hold of a Mac to try and sort this out. In the meantime, have you tried the Docker? Mac people have had success using that instead of compiling from scratch.

Oh yes Docker! So, I cannot use it on our cluster because it is installed on a dedicated server and in development and we, users, don't have access. I then installed it on my Mac but since I deal with 30.000 cells I have some resources issues. Probably I can try using a subset of cells at least to verify that it works.

I was able to build on macOS with no issue using the commands I put into the documentation in Installation -> macOS (https://gregoryschwartz.github.io/too-many-cells/). Please try it out and see if it solves your problem!

It works on this end, so if you are still having difficulty please re-open this issue.