error during install

[robin-sto]

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]

Hi, this means OpenMP, your C/C++ compiler, or both are outdated, see #417.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

[SebKrantz]

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]

Thank you. [cid:7a8e49e7-1f0d-46c0-b5bc-12d6957dd27f] Robin Storch, M.Ed. Systems Engineer IS Research IT Information Services Cincinnati Children's 3333 Burnet Avenue, Cincinnati, OH 45229 [cid:01b29a27-a78a-4b73-b5af-96482564b9f5]

…

________________________________ 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) This email originated from an EXTERNAL sender to CCHMC. Proceed with caution when replying, opening attachments, or clicking links in this message. 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") — Reply to this email directly, view it on GitHub<#550 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCEVDN54H265L33DVQG7A7DYZMHMRAVCNFSM6AAAAABFBZE5T6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJTGAZTSOJWGI>. You are receiving this because you authored the thread.Message ID: ***@***.***>