What am I missing for proper installation?

[AditiBhandari04]

Hi Torsten

I am stuck with installing Haploblocker in R-4.4. Manually installed both RandomFieldUtils_1.2.5 and Haploblockr_1.7.01.zip. Still being stonewalled with errors. What am I missing?

library(RandomFieldsUtils)
install.packages("C:\Users\aditi.bhandari\Downloads\HaploBlocker_1.7.01.zip", repos = NULL, type = "source")
Installing package into ‘C:/Users/aditi.bhandari/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
package 'HaploBlocker' successfully unpacked and MD5 sums checked
library(HaploBlocker)
Error: package or namespace load failed for ‘HaploBlocker’:
.onLoad failed in loadNamespace() for 'HaploBlocker', details:
call: fun(libname, pkgname)
error: DLL requires the use of native symbols

[tpook92]

Dear Aditi,

sorry for the late response and thanks for reporting the issue. The previous version of HaploBlocker was only working for R 4.3.0 and lower as RandomFieldsUtils was only developed for that. I just released a new version of HaploBlocker and RandomFieldsUtils that should be compatible with newer versions. Please ensure that Rtools is installed on your system (this is not an R package but a separate software) that you can download at https://cran.r-project.org/bin/windows/Rtools/

Best regards
Torsten

[chabrault]

Dear Torsten,

I am also having troubles installing HaploBlocker (I am under R 4.5.1). I am stuck because I need RandomFieldsUtils > 1.4 and I have the version 1.2.5. Do you know where can I find the latest version?

[tpook92]

@chabrault you can find the most recent version of RandomFieldsUtils in this Github repository for download at https://github.com/tpook92/HaploBlocker/blob/master/RandomFieldsUtils_1.5.1.1.tar.gz

[chabrault]

That works, thank you!

[AditiBhandari04]

Thanks a lot, Torsten! It works well for me now. Greatly appreciate your follow-up.

[matt-shenton]

Here with ubuntu 22.04: (Rtools not necessary for Linux?) RandomFieldsUtils_1.5.1.1.tar.gz won't go. "solve_RFU_61.cu:36:10: fatal error: Basic_utils_local.h: No such file or directory"
Thanks in advance!

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[Previously saved workspace restored]

install.packages("RandomFieldsUtils_1.5.1.1.tar.gz", type="source",repos=NULL)

• installing source package ‘RandomFieldsUtils’ ...
  ** using staged installation
  checking whether the C++ compiler works... yes
  checking for C++ compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether the compiler supports GNU C++... yes
  checking whether x86_64-conda-linux-gnu-c++ -std=gnu++17 accepts -g... yes
  checking for x86_64-conda-linux-gnu-c++ -std=gnu++17 option to enable C++11 features... none needed
  configure: value of 'CROSS' is 'noflags'.
  checking whether __cpuid is available... no
  checking whether cpuid works under asm... yes (linux)
  checking whether '-march=native' can be used... yes
  configure: value of 'USE_GPU' is 'try'.
  checking whether CUDA_HOME is set... no -- using /usr/local/cuda
  checking for /usr/local/cuda/bin/nvcc... yes
  configure: yes
  checking for /usr/local/cuda/lib64/libcublas.so... yes
  checking SIMD options for some CC files... avx512f avx2 avx sse41 ssse3 sse3 sse2
  checking which downwards controls might be used... .
  configure: default compilation option is -march=native -DLINUXCPUID -DLINUXDEFAULT -DGPU_NEEDS=Inone -DUSEGPU -DMEMisALIGNED=Nan
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  using C compiler: ‘x86_64-conda-linux-gnu-cc (conda-forge gcc 15.1.0-4) 15.1.0’
  using C++ compiler: ‘x86_64-conda-linux-gnu-c++ (conda-forge gcc 15.1.0-4) 15.1.0’
  /usr/local/cuda/bin/nvcc --generate-code arch=compute_61,code=sm_61 --generate-code arch=compute_70,code=sm_70 --generate-code arch=compute_75,code=sm_75 --generate-code arch=compute_80,code=sm_80 --generate-code arch=compute_86,code=sm_86 -std=c++14 -Xcompiler -fopenmp -DSCHLATHERS_MACHINE --expt-extended-lambda -I /home/mashus096/miniconda3/envs/haploblocker1.7/lib/R/include -I/usr/local/cuda/include -I./cutlass -Xcompiler -fpic -DUSEGPU -g -x cu -c solve_RFU_61.cu -o solve_RFU_61.o
  solve_RFU_61.cu:36:10: fatal error: Basic_utils_local.h: No such file or directory
  36 | #include "Basic_utils_local.h"
  | ^~~~~~~~~~~~~~~~~~~~~
  compilation terminated.
  make: *** [Makevars:38: solve_RFU_61.o] Error 1
  ERROR: compilation failed for package ‘RandomFieldsUtils’
• removing ‘/home/mashus096/miniconda3/envs/haploblocker1.7/lib/R/library/RandomFieldsUtils’
  Warning message:
  In install.packages("RandomFieldsUtils_1.5.1.1.tar.gz", type = "source", :
  installation of package ‘RandomFieldsUtils_1.5.1.1.tar.gz’ had non-zero exit status

[tpook92]

@matt-shenton sorry for the late response. where you able to get it running? I was not able to reproduce the issue on my side and dont think this error is on RandomFieldsUtils but on the setup of your miniconda3 environment.

[matt-shenton]

@matt-shenton sorry for the late response. where you able to get it running? I was not able to reproduce the issue on my side and dont think this error is on RandomFieldsUtils but on the setup of your miniconda3 environment.

No problem, thanks a lot for the reply. No, still not managed to get it working. Is Basic_utils_local.h a file from the package? Or should be generated from elsewhere? I made a new environment including just R-4.5.1 from conda-forge.