Unable to install leafcutter R 4.2.1

[chesi]

Hi, I cannot install leafcutter on my Mac (M1) on R 4.2.1 following the provided instructions (https://davidaknowles.github.io/leafcutter/articles/Installation.html)

It fails at the last step, at compilation:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:12:10: fatal error:
'tbb/task_scheduler_init.h' file not found
#include <tbb/task_scheduler_init.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [stanExports_bb_glm.o] Error 1
ERROR: compilation failed for package ‘leafcutter’

• removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/leafcutter’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/f_/yvxrydm16lz5ytwnv_zfz2280000gn/T//Rtmp65Z1MH/file3a92b0ea725/leafcutter_0.2.9.tar.gz’ had non-zero exit status

Can you please help?

[caballero]

I have a similar error on Linux x64, I tried using R 3.5, 3.6, 4.0, and 4.2, version <4.0 have a dependency error for Hmisc/foreign, and for version >4.0 the error on StanHeaders is not fixable even using the dev version of Rstan and RstanHeaders.

[skywalker51616]

I have the same error using Linux x64 R 4.2.2.

[Yang-Yingshan]

I have the same error using Linux x64 R 4.2.0，do you have the answer

[jackhump]

The following worked for me recently on R 4.2 on an M1 macbook:

install.packages("remotes")
remotes::install_github("stan-dev/rstantools")
remotes::install_github("davidaknowles/leafcutter/leafcutter", ref = "psi_2019")

[chesi]

I just tried it, it doesn’t work for me: clang: error: the clang compiler does not support '-mtune=native' make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘leafcutter’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/leafcutter’ Warning message: In i.p(...) : installation of package ‘/var/folders/f_/yvxrydm16lz5ytwnv_zfz2280000gn/T//RtmpxqG8Tr/filea74e35f4c05c/leafcutter_0.2.8.tar.gz’ had non-zero exit status From: Jack Humphrey ***@***.***> Date: Wednesday, August 16, 2023 at 11:00 AM To: davidaknowles/leafcutter ***@***.***> Cc: Alessandra ***@***.***>, Author ***@***.***> Subject: Re: [davidaknowles/leafcutter] Unable to install leafcutter R 4.2.1 (Issue #239) The following worked for me recently on R 4.2 on an M1 macbook: install.packages("remotes") remotes::install_github("stan-dev/rstantools") remotes::install_github("davidaknowles/leafcutter/leafcutter", ref = "psi_2019") — Reply to this email directly, view it on GitHub<#239 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADBMUUBKSMFZQTLWM3N4D5TXVTOABANCNFSM6AAAAAAZRVXM2A>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[tcashby]

I make no promises but after about 6 hours of trying to make this work here's the version that finally started working:

mamba install -c conda-forge r-base=4.2.1 r-rcpp=1.0.10 r-rstan=2.21.7 r-stanheaders=2.21.0-7 r-devtools

Then, install the things it's missing, but don't update anything.

Like I say, your mileage may vary, but this is what got it working for me.

[CodeOfSascha]

@tcashby Thanks! It worked.

I'd like to propose the following steps i did:

mamba install -c bioconda bioconductor-biobase
mamba install -c bioconda bioconductor-dirichletmultinomial
R -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")'

When asked, i declined updating any packages...

[Chasingwind-Z]

@CodeOfSascha I'd like to know what version of R you have.