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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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parallel.h fatal error #92

Open albenstein opened 6 months ago

albenstein commented 6 months ago

Describe the bug When try to install Rfast with Rstudio (R 4.1.2), get error like attached file: rfast.error.txt

Expected behavior

  1. The correct result I expected is the package is installed.

Desktop (please complete the following information):

albenstein commented 6 months ago

I could install Rfast 2.0.6 version. Cannot install 2.0.9 and 2.1.0 versions.

ManosPapadakis95 commented 6 months ago

I cannot help for your OS. Try remove the parallel from the header file and compile by yourself.

ric-osorio commented 5 months ago

I believe it happens in any CentOS or similar. I try from a fresh install and same happens. I can stick with Rfast: 2.0.8 but I'm sure 2.1.0 has some important fixes...

AlexandreGGS commented 5 months ago

I cant install the last version on a CentOS server.

I can install the 2.0.8, thx to last comment.

remotes::install_version("Rfast", version = "2.0.8")
tdhock commented 5 months ago

I have same issue https://github.com/tdhock/data.table-revdeps/issues/11

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)’
ManosPapadakis95 commented 5 months ago

If anyone want to help then check the branch Parallel and compile it. I have add checks for red hat OS.

ric-osorio commented 5 months ago

Still not... ![Uploading replicate.jpg…]()

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devtools::install_github("RfastOfficial/Rfast",ref = "Parallel") Downloading GitHub repo RfastOfficial/Rfast@Parallel ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/opt/GIT/tmp/RtmphAw955/remotes253a56ef0fde5/RfastOfficial-Rfast-30347e8/DESCRIPTION’ (335ms) ─ preparing ‘Rfast’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ installing the package to process help pages

─ installing source package ‘Rfast’ ... 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"/opt/R/4.3.0/lib/R/include" -DNDEBUG -I../inst/include -I'/home/byspectra/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/home/byspectra/R/x86_64-pc-linux-gnu-library/4.3/RcppArmadillo/include' -I'/home/byspectra/R/x86_64-pc-linux-gnu-library/4.3/RcppParallel/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -fdiagnostics-color=always -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

^~~ compilation terminated. make: *** [/opt/R/4.3.0/lib/R/etc/Makeconf:200: Coeff.o] Error 1 ERROR: compilation failed for package ‘Rfast’ ─ removing ‘/opt/GIT/tmp/RtmpI2kk8J/Rinst2549e40bddee3/Rfast’

ERROR: package installation failed Error: Failed to install 'Rfast' from GitHub: ! System command 'R' failed

tdhock commented 5 months ago

For me the error does not happen with a more recent version of gcc (12.3.0), so I believe the solution is to upgrade gcc.

tdhock commented 5 months ago

oldest version of gcc used by current CRAN checks is 10.4.0 (most are actually newer, 12 or 13), https://cloud.r-project.org/web/checks/check_flavors.html so that is probably why this error is not showing up on CRAN, https://cloud.r-project.org/web/checks/check_results_Rfast.html

tdhock commented 5 months ago

for others who are having this issue, can you try upgrading gcc to see if that fixes the issue? If so, then I believe we can close this issue.

ric-osorio commented 5 months ago

It worked! Thanks. gcc 12 guys:

sudo dnf install gcc-toolset-12 scl enable gcc-toolset-12 bash

and then install/upgrade

@tdhock thanks for the tip!

ManosPapadakis95 commented 5 months ago

To make the C++ parallel play you need to have cpp version >= 20160 except MacOS. So everyone just update your GCC to the latest. You want this. Newer compiler means more speed.