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MiNAA aligns a pair of networks based their topologies and biologies.

License: MIT License

Makefile 0.66% C++ 85.03% Shell 0.52% Batchfile 0.25% R 1.04% Python 8.04% TeX 4.46%

graal graph-algorithm graphlets interaction-network microbiome network-alignment orca

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reednel becheler salix-d stevemk14ebr rosaaghdam

minaa's Issues

makefile error

Hi!

I was trying to install minaa on windows 10.
I tried with Ubuntu LTS (seemed less complicated than figuring out mingw) and got this error:

~/minaa$ make
g++ -O3 -g -c -Wall -Wextra -ansi -pedantic -std=c++20 -Iinclude -o obj/minaa.o src/minaa.cpp
make: g++: No such file or directory
make: *** [Makefile:26: obj/minaa.o] Error 127

Sometimes linux on Windows has a hard time with paths, so I tried with mingw, I got this error:

~\minaa>make
g++ -O3 -g -c -Wall -Wextra -ansi -pedantic -std=c++20 -Iinclude -o obj/minaa.o src/minaa.cpp
process_begin: CreateProcess(NULL, g++ -O3 -g -c -Wall -Wextra -ansi -pedantic -std=c++20 -Iinclude -o obj/minaa.o src/minaa.cpp, ...) failed.
make (e=2): The system cannot find the file specified.
make: *** [Makefile:26: obj/minaa.o] Error 2

Turns out the file not found was g++...

So apparently, having or installing 'make' on Ubuntu doesn't mean you also have g++ already. I installed it with sudo apt install g++.
For the windows install, the link from the guide in the readme wasn't working for me, so I got mingw-get from https://sourceforge.net/projects/mingw/. Also, since I got minwg with RTools, I had to make sure, make.exe and g++.exe got install in the same mingw folder else, they doesn't find each other.
After that, it work with both mingw and Ubuntu LTS.

In the compilation section it says 'any method for compiling C++ should suffice', but maybe, I'd add a note about needing g++ specifically since that's what your makefile uses. I would also add it to the unix method.

Output name error on Windows

So running the example command: ./minaa.exe example/G.csv example/H.csv
I got this error:

ERROR:
 Unable to create output folder alignments\example/G-example/H-2023_11_26-18_56_14\

The problem is at line 39 of file_io.cpp:

auto si = file.find_last_of("\\") + 1;

For windows you're looking for the last backslash but your example code uses slash.

If I run ./minaa.exe example\\G.csv example\\H.csv instead it works, but to avoid this you could simply check for the last backslash or slash ("\\|/") instead and then you could use the same command regardless of OS.

    /**
     * Returns the truncated name of the file.
     * 
     * @param file The file to truncate.
     * 
     * @return The truncated name of the file.
     */
    std::string name_file(std::string file)
    {
        auto si = file.find_last_of("\\|/") + 1;
        auto ei = file.find_last_of(".");
        auto file_name = file.substr(si, ei - si);
        return file_name;
    }

Rebuilt with this code ^ and got no error.

Reproducing simulations: can not install SpiecEasi

Hi! 😄 I can not install SpiecEasy package on my Macos Ventura.

The https://github.com/zdk123/SpiecEasi repo mentions the problem but the proposed solution (running xcode-select --install) did not work for me.

Would you know how to solve this?

> install_github("zdk123/SpiecEasi")
Downloading GitHub repo zdk123/SpiecEasi@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/22/scsyyfyx7dxfxfzv6gptfws00000gn/T/RtmpLUOwLs/remotes29936fe1d57b/zdk123-SpiecEasi-bc33288/DESCRIPTION’ ...
─  preparing ‘SpiecEasi’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Removed empty directory ‘SpiecEasi/inst’
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘SpiecEasi_1.1.2.tar.gz’
   
* installing *source* package ‘SpiecEasi’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c ADMM.cpp -o ADMM.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c matops.cpp -o matops.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c sqrtNewton.cpp -o sqrtNewton.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c svthresh.cpp -o svthresh.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SpiecEasi.so ADMM.o RcppExports.o matops.o sqrtNewton.o svthresh.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [SpiecEasi.so] Error 1
ERROR: compilation failed for package ‘SpiecEasi’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/SpiecEasi’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/22/scsyyfyx7dxfxfzv6gptfws00000gn/T//RtmpLUOwLs/file29933da0cb77/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

Thank you ! :D

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