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SebKrantz / collapse

Advanced and Fast Data Transformation in R
https://sebkrantz.github.io/collapse/
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error during install #550

Open robin-sto opened 6 months ago

robin-sto commented 6 months ago

Hello,

I am trying to install collapse in an R/4.2.1 environment via BiocManager::install. I am getting this error:

gcc -std=gnu11 -I"/usr/local/lib64/R/include" -DNDEBUG -I'/usr/local/lib64/R/library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c fmean.c -o fmean.o fmean.c: In function ‘fmean_double_omp_impl’: fmean.c:37:30: error: expected ‘#pragma omp’ clause before ‘simd’

pragma omp parallel for simd num_threads(nthreads) reduction(+:mean,n)

                          ^

fmean.c:45:28: error: expected ‘#pragma omp’ clause before ‘simd’

pragma omp parallel for simd num_threads(nthreads) reduction(+:mean)

this repeats for a while.

Can you help me?

SebKrantz commented 6 months ago

Hi, this means OpenMP, your C/C++ compiler, or both are outdated, see #417. So either update them or install collapse without OpenMP.

SebKrantz commented 6 months ago

Ok, so since this issue has occurred multiple times, and updating your compiler may be tedious, I have just created a branch "no_parallel_simd" that should solve your problem: 

remotes::install_github("SebKrantz/collapse", ref = "no_parallel_simd")
robin-sto commented 6 months ago

Thank you.

[cid:7a8e49e7-1f0d-46c0-b5bc-12d6957dd27f] Robin Storch, M.Ed.

Systems Engineer

IS Research IT

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Cincinnati Children's 3333 Burnet Avenue, Cincinnati, OH 45229

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From: Sebastian Krantz @.> Sent: Thursday, March 21, 2024 1:05 PM To: SebKrantz/collapse @.> Cc: Storch, Robin @.>; Author @.> Subject: Re: [SebKrantz/collapse] error during install (Issue #550)

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Ok, so since this issue has occurred multiple times, and updating your compiler may be tedious, I have just created a branch "no_parallel_simd" that should solve your problem:

remotes::install_github("SebKrantz/collapse", ref = "no_parallel_simd")

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