chrchang
commented
3 years ago I'm guessing your R installation is configured with nonstandard C/C++ compilation flags. Is there a ~/.R/Makevars file?
Closed Fnyasimi closed 3 years ago
chrchang
commented
3 years ago I'm guessing your R installation is configured with nonstandard C/C++ compilation flags. Is there a ~/.R/Makevars file?
Fnyasimi
commented
3 years ago I have inspected that path and I don't have the directory or the file
chrchang
commented
3 years ago Can you post more of the compile log, including the compile flags for the failed step? I'm unable to reproduce your failure on any machine I have access to.
If one of the flags is "-march=native", can you also post or send me the output of running "<name of C++ compiler used by R> -march=native -Q --help=target" on the command line?
Fnyasimi
commented
3 years ago The command gcc -march=native -Q --help=target
The output
The following options are target specific:
-m128bit-long-double [enabled]
-m16 [disabled]
-m32 [disabled]
-m3dnow [disabled]
-m3dnowa [disabled]
-m64 [enabled]
-m80387 [enabled]
-m8bit-idiv [disabled]
-m96bit-long-double [disabled]
-mabi= sysv
-mabm [enabled]
-maccumulate-outgoing-args [disabled]
-maddress-mode= long
-madx [disabled]
-maes [enabled]
-malign-data= compat
-malign-double [disabled]
-malign-functions= 0
-malign-jumps= 0
-malign-loops= 0
-malign-stringops [enabled]
-mandroid [disabled]
-march= haswell
-masm= att
-mavx [enabled]
-mavx2 [enabled]
-mavx256-split-unaligned-load [enabled]
-mavx256-split-unaligned-store [enabled]
-mavx5124fmaps [disabled]
-mavx5124vnniw [disabled]
-mavx512bw [disabled]
-mavx512cd [disabled]
-mavx512dq [disabled]
-mavx512er [disabled]
-mavx512f [disabled]
-mavx512ifma [disabled]
-mavx512pf [disabled]
-mavx512vbmi [disabled]
-mavx512vl [disabled]
-mavx512vpopcntdq [disabled]
-mbionic [disabled]
-mbmi [disabled]
-mbmi2 [disabled]
-mbranch-cost= 3
-mcld [disabled]
-mclflushopt [enabled]
-mclwb [disabled]
-mclzero [disabled]
-mcmodel= [default]
-mcpu=
-mcrc32 [disabled]
-mcx16 [enabled]
-mdispatch-scheduler [disabled]
-mdump-tune-features [disabled]
-mf16c [disabled]
-mfancy-math-387 [enabled]
-mfentry [disabled]
-mfma [disabled]
-mfma4 [disabled]
-mforce-drap [disabled]
-mfp-ret-in-387 [enabled]
-mfpmath= sse
-mfsgsbase [enabled]
-mfunction-return= keep
-mfused-madd
-mfxsr [enabled]
-mgeneral-regs-only [disabled]
-mglibc [enabled]
-mhard-float [enabled]
-mhle [enabled]
-miamcu [disabled]
-mieee-fp [enabled]
-mincoming-stack-boundary= 0
-mindirect-branch-register [disabled]
-mindirect-branch= keep
-minline-all-stringops [disabled]
-minline-stringops-dynamically [disabled]
-mintel-syntax
-mlarge-data-threshold=<number> 65536
-mlong-double-128 [disabled]
-mlong-double-64 [disabled]
-mlong-double-80 [enabled]
-mlwp [disabled]
-mlzcnt [enabled]
-mmemcpy-strategy=
-mmemset-strategy=
-mmitigate-rop [disabled]
-mmmx [enabled]
-mmovbe [enabled]
-mmpx [disabled]
-mms-bitfields [disabled]
-mmusl [disabled]
-mmwaitx [disabled]
-mno-align-stringops [disabled]
-mno-default [disabled]
-mno-fancy-math-387 [disabled]
-mno-push-args [disabled]
-mno-red-zone [disabled]
-mno-sse4 [disabled]
-mnop-mcount [disabled]
-momit-leaf-frame-pointer [disabled]
-mpc32 [disabled]
-mpc64 [disabled]
-mpc80 [disabled]
-mpclmul [enabled]
-mpcommit [disabled]
-mpku [disabled]
-mpopcnt [enabled]
-mprefer-avx128 [disabled]
-mpreferred-stack-boundary= 0
-mprefetchwt1 [disabled]
-mprfchw [enabled]
-mpush-args [enabled]
-mrdpid [disabled]
-mrdrnd [enabled]
-mrdseed [enabled]
-mrecip [disabled]
-mrecip=
-mrecord-mcount [disabled]
-mred-zone [enabled]
-mregparm= 6
-mrtd [disabled]
-mrtm [disabled]
-msahf [enabled]
-msgx [disabled]
-msha [disabled]
-mskip-rax-setup [disabled]
-msoft-float [disabled]
-msse [enabled]
-msse2 [enabled]
-msse2avx [disabled]
-msse3 [enabled]
-msse4 [enabled]
-msse4.1 [enabled]
-msse4.2 [enabled]
-msse4a [disabled]
-msse5
-msseregparm [disabled]
-mssse3 [enabled]
-mstack-arg-probe [disabled]
-mstack-protector-guard= tls
-mstackrealign [disabled]
-mstringop-strategy= [default]
-mstv [enabled]
-mtbm [disabled]
-mtls-dialect= gnu
-mtls-direct-seg-refs [enabled]
-mtune-ctrl=
-mtune= generic
-muclibc [disabled]
-mveclibabi= [default]
-mvect8-ret-in-mem [disabled]
-mvzeroupper [enabled]
-mx32 [disabled]
-mxop [disabled]
-mxsave [enabled]
-mxsavec [disabled]
-mxsaveopt [disabled]
-mxsaves [disabled]
Known assembler dialects (for use with the -masm= option):
att intel
Known ABIs (for use with the -mabi= option):
ms sysv
Known code models (for use with the -mcmodel= option):
32 kernel large medium small
Valid arguments to -mfpmath=:
387 387+sse 387,sse both sse sse+387 sse,387
Known indirect branch choices (for use with the -mindirect-branch=/-mfunction-return= options):
keep thunk thunk-extern thunk-inline
Known data alignment choices (for use with the -malign-data= option):
abi cacheline compat
Known vectorization library ABIs (for use with the -mveclibabi= option):
acml svml
Known address mode (for use with the -maddress-mode= option):
long short
Known stack protector guard (for use with the -mstack-protector-guard= option):
global tls
Valid arguments to -mstringop-strategy=:
byte_loop libcall loop rep_4byte rep_8byte rep_byte unrolled_loop vector_loop
Known TLS dialects (for use with the -mtls-dialect= option):
gnu gnu2
That is super-weird: no Intel or AMD processor should have -mavx2 without -mbmi. What is the output of "cat /proc/cpuinfo | grep 'name' | uniq"?
Fnyasimi
commented
3 years ago model name : Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
chrchang
commented
3 years ago Thanks. It looks like -march=native can indeed misdetect processor features on a VM.
I've tried to address this with commit 43e41bc ; can you check if install_github works now?
Fnyasimi
commented
3 years ago This works!
Thank you so much
I am trying to install the cindex from r using the command
install_github("chrchang/plink-ng", subdir="/2.0/cindex")but I am running to this error below;OS Ubuntu 18.04 R version 3.6.3
Assistance with this error will be appreciated