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RfastOfficial / Rfast

A collection of Rfast functions for data analysis. Note 1: The vast majority of the functions accept matrices only, not data.frames. Note 2: Do not have matrices or vectors with have missing data (i.e NAs). We do no check about them and C++ internally transforms them into zeros (0), so you may get wrong results. Note 3: In general, make sure you give the correct input, in order to get the correct output. We do no checks and this is one of the many reasons we are fast.
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Can't install package #110

Open yesitsjess opened 1 month ago

yesitsjess commented 1 month ago

Describe the bug install.packages("Rfast")

* installing *source* package ‘Rfast’ ...
** package ‘Rfast’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’
using C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’
using C++17
g++ -std=gnu++17 -I"/software/R_v4.3.0_Rocky8/lib64/R/include" -DNDEBUG -I../inst/include -I'/tmp_mnt/filer1/.../R_lib_v4.3.0_seurat/Rcpp/include' -I'/tmp_mnt/filer1/../R_lib_v4.3.0_seurat/RcppArmadillo/include' -I'/tmp_mnt/filer1/../R_lib_v4.3.0_seurat/RcppParallel/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c Coeff.cpp -o Coeff.o
In file included from ../inst/include/Rfast/templates.h:10,
                 from ../inst/include/Rfast/matrix.hpp:14,
                 from ../inst/include/Rfast.h:5,
                 from mn.h:4,
                 from Coeff.cpp:4:
../inst/include/Rfast/parallel.h:20:10: fatal error: execution: No such file or directory
 #include <execution>
          ^~~~~~~~~~~
compilation terminated.
make: *** [/software/R_v4.3.0_Rocky8/lib64/R/etc/Makeconf:200: Coeff.o] Error 1
ERROR: compilation failed for package ‘Rfast’

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Carolina-Toste commented 1 month ago

Hi. I'm not part of the developing team but I had a similar problem. Have you tried updating your GCC compiler to a later version and modifying your compilation flags in Makevars and try installing Rfast again. You can check this Stack Overflow post - Although this guides you to configure Apple Silicon compilers, it might guide you in the right direction

ManosPapadakis95 commented 1 month ago

Just update your gcc! You have a very old version. The newest gcc is better and creates better optimised code. The last version is 12.X. If I remember correctly you need something greater than 9.X.

ManosPapadakis95 commented 1 month ago

Hi. I'm not part of the developing team but I had a similar problem. Have you tried updating your GCC compiler to a later version and modifying your compilation flags in Makevars and try installing Rfast again. You can check this Stack Overflow post - Although this guides you to configure Apple Silicon compilers, it might guide you in the right direction

Why you had to change the Makevars file?

Carolina-Toste commented 1 month ago

Hi. I'm not part of the developing team but I had a similar problem. Have you tried updating your GCC compiler to a later version and modifying your compilation flags in Makevars and try installing Rfast again. You can check this Stack Overflow post - Although this guides you to configure Apple Silicon compilers, it might guide you in the right direction

Why you had to change the Makevars file?

I recently bought an M3 Mac and downloaded R from CRAN. When compiling the Rfast package I encountered an error where the linker couldn't find the path for gfortran . I followed the steps in the above link and that solved my issue.