Unable to install after updating to R 4.4

[tomasnobrega]

Describe the bug

After updating to R 4.4 I am unable to install unigd

To Reproduce

install.packages("unigd")
remotes::install_github("nx10/unigd")

Screenshots

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘unigd’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/homebrew/lib/R/4.4/site-library/00LOCK-unigd/00new/unigd/libs/unigd.so':
  dlopen(/opt/homebrew/lib/R/4.4/site-library/00LOCK-unigd/00new/unigd/libs/unigd.so, 0x0006): symbol not found in flat namespace '__ZNSt13exception_ptr31__from_native_exception_pointerEPv'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/homebrew/lib/R/4.4/site-library/unigd’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmp2txVY6/file130f64fc83087/unigd_0.1.1.tar.gz’ had non-zero exit status

Environment

• OS: MacOS Sonoma 14.4.1 (23E224) (Apple chip)
• R version: 4.4
• unigd version: 0.1.1

Additional context

I installed all necessary system requirements described (https://nx10.github.io/unigd/articles/a00_installation.html#system-requirements) including XQuartz.

[tomasnobrega]

After some hours trying things, I was able to find a way around. Instead of installing with R, install from source:

Download the unigd_0.1.1.tgz from CRAN
Open the terminal, navigate to the folder and then type:

tar -zxvf unigd_0.1.1.tgz
R CMD INSTALL --verbose unigd

[adamaltmejd]

Having the same issue and for me installing 0.1.2 from the tarball here on Github did not help (maybe not surprising).

Error: package or namespace load failed for ‘unigd’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/adam/.R/packages/00LOCK-unigd-0.1.2/00new/unigd/libs/unigd.so':
  dlopen(/Users/adam/.R/packages/00LOCK-unigd-0.1.2/00new/unigd/libs/unigd.so, 0x0006): symbol not found in flat namespace '__ZNSt13exception_ptr31__from_native_exception_pointerEPv'
Error: loading failed
Execution halted
ERROR: loading failed

What did work was to remove my .R\Makevars which includes the following (to get OpenMP to work with data.table and fixest). So there must be some conflict with the settings there.

XC_LOC:=$(shell xcrun --show-sdk-path)
LLVM_LOC:=$(shell brew --prefix llvm)
GCC_LOC:=$(shell brew --prefix gcc)
GETTEXT_LOC:=$(shell brew --prefix gettext)
OMP_LOC:=$(shell brew --prefix libomp)

CC=$(LLVM_LOC)/bin/clang
CXX=$(LLVM_LOC)/bin/clang++
CXX11=$(LLVM_LOC)/bin/clang++
CXX14=$(LLVM_LOC)/bin/clang++
CXX17=$(LLVM_LOC)/bin/clang++
CXX1X=$(LLVM_LOC)/bin/clang++

OBJC=$(LLVM_LOC)/bin/clang
OBJCXX=$(LLVM_LOC)/bin/clang++

CFLAGS=-g -O2 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O2 -Wall -pedantic -std=c++11 -mtune=native -pipe
CXX11FLAGS=-g -O2 -Wall -pedantic -std=c++11 -mtune=native -pipe
CXX14FLAGS=-g -O2 -Wall -pedantic -std=c++14 -mtune=native -pipe
CXX17FLAGS=-g -O2 -Wall -pedantic -std=c++17 -mtune=native -pipe

LDFLAGS=-L"$(LLVM_LOC)/lib" -L"$(GETTEXT_LOC)/lib" -L/opt/homebrew/opt/libpng/lib -L/opt/homebrew/opt/libtiff/lib -L/opt/homebrew/opt/jpeg-turbo/lib -L/opt/homebrew/opt/zstd/lib -L/opt/homebrew/opt/mbedtls/lib -Wl,-rpath,$(LLVM_LOC)/lib --sysroot="$(XC_LOC)" -lomp
CPPFLAGS=-I"$(GETTEXT_LOC)/include" -I"$(LLVM_LOC)/include" -I/opt/homebrew/opt/libpng/include -I/opt/homebrew/opt/libtiff/include -I/opt/homebrew/opt/jpeg-turbo/include -I/opt/homebrew/opt/zstd/include -I/opt/homebrew/opt/mbedtls/include -isysroot "$(XC_LOC)" -I"$(OMP_LOC)/include" -Xclang -fopenmp

FC=$(GCC_LOC)/bin/gfortran
F77=$(GCC_LOC)/bin/gfortran
FLIBS=-L$(GCC_LOC)/lib/gcc/10/ -lm

[dongguaguaguagua]

Got the same issue on:

• MacOS Sonoma 14.4 with apple silicon
• R 4.4.1
• installing unigd 0.1.1 or 0.1.2

Installing the unigd tarball did not work on my device either.