Problem installing VelocytoR in macOS

Question

Problem installing VelocytoR in macOS

Opened this issue 3 years ago · 12 comments

Hello

I have tried to install VelocytoR in macOS ( on a MacBook Pro M1 series). But When I run below line I faced with following error :

library(devtools)
install_github("velocyto-team/velocyto.R")

The error appear in R :

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o velocyto.R.so RcppExports.o points_within.o routines.o -lboost_filesystem -lboost_system -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lboost_filesystem
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [velocyto.R.so] Error 1
ERROR: compilation failed for package ‘velocyto.R’

How can I fix it !?

Answer 1 · 2021-05-31T15:29:40.000Z

Hello,

I got the same issue but managed to fix it by first installing the following packages from CRAN:
boostr and hdf5r
and then running again
library(devtools)
install_github("velocyto-team/velocyto.R")

Is this working for you?

Answer 2 · 2021-08-20T14:58:57.000Z

Hello. I'm also using the M1 MacBook, and I had spent hours struggling with exactly the same error message with you.
I've just solved this problem. I'm not sure if my solution could help you, but give it a try!

Install boost packages using homebrew
(Perhaps the problem with -lboost-filesystem arises because this boost package is not installed. )

brew install boost

My boost package was installed in this path : /opt/homebrew/Cellar/boost/ and the version is 1.76.0.

Now, you should directly modify the Makevars file in this github. Fork this github to your repository.
In your repo, go to the src folder, and open the Makevars file. At the end of the PKG_LIBS statement, you should add a path to the lib directory that exists within the boost package you just installed. So, change the Makevars file like this.

CXX_STD = CXX11
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
PKG_LIBS=-lboost_filesystem -lboost_system   -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS)  $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L /opt/homebrew/Cellar/boost/1.76.0/lib/

Try again to install the velocyto.R using your github repo in the Rstudio.

install_github("ssun1116/velocyto.R")

This is all! Hope this instructions work well 🙏

Answer 3 · 2021-09-18T02:48:05.000Z

I fix it by using a process similar to https://github.com/kharchenkolab/conos/wiki/Installing-Conos-for-Mac-OS.
i.e., modify my Makevars files to the following:

XCBASE:=$(shell xcrun --show-sdk-path)
LLVMBASE:=$(shell brew --prefix llvm)
GCCBASE:=$(shell brew --prefix gcc)
GETTEXT:=$(shell brew --prefix gettext)

CC=$(LLVMBASE)/bin/clang -fopenmp
CXX=$(LLVMBASE)/bin/clang++ -fopenmp
CXX11=$(LLVMBASE)/bin/clang++ -fopenmp
CXX14=$(LLVMBASE)/bin/clang++ -fopenmp
CXX17=$(LLVMBASE)/bin/clang++ -fopenmp
CXX1X=$(LLVMBASE)/bin/clang++ -fopenmp

CPPFLAGS=-isystem "$(LLVMBASE)/include" -isysroot "$(XCBASE)"
LDFLAGS=-L"$(LLVMBASE)/lib" -L"$(GETTEXT)/lib" --sysroot="$(XCBASE)"

FC=$(GCCBASE)/bin/gfortran -fopenmp
F77=$(GCCBASE)/bin/gfortran -fopenmp
FLIBS=-L$(GCCBASE)/lib/gcc/9/ -lm

Answer 4 · 2022-04-01T02:41:57.000Z

I am using M1Pro MacBook. I solved this question by combining the methods of ssun1116 and MikaQiao.

1.brew install boost
/opt/homebrew/Cellar/boost/（install path）

2.mkdir ~/.R
3.touch Makevars

4.vi Makevars

CXX_STD = CXX11
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
PKG_LIBS=-lboost_filesystem -lboost_system -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS) $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L /opt/homebrew/Cellar/boost/1.76.0/lib/

5.install_github("ssun1116/velocyto.R")

Answer 5 · 2022-06-25T08:06:04.000Z

Hello. I'm also using the M1 MacBook, and I had spent hours struggling with exactly the same error message with you. I've just solved this problem. I'm not sure if my solution could help you, but give it a try! (I am not really good at English, so it can be a little difficult to understand.)

Install boost packages using homebrew
(Perhaps the problem with -lboost-filesystem arises because this boost package is not installed. )
brew install boost
My boost package was installed in this path : /opt/homebrew/Cellar/boost/ and the version is 1.76.0.

Now, you should directly modify the Makevars file in this github. Fork this github to your repository.

In your repo, go to the src folder, and open the Makevars file. At the end of the PKG_LIBS statement, you should add a path to the lib directory that exists within the boost package you just installed. So, change the Makevars file like this.
CXX_STD = CXX11
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
PKG_LIBS=-lboost_filesystem -lboost_system   -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS)  $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L /opt/homebrew/Cellar/boost/1.76.0/lib/
Try again to install the velocyto.R using your github repo in the Rstudio.
install_github("ssun1116/velocyto.R")
This is all! Hope this instructions work well 🙏

Your solution works very well on my M1 MAC, thanks for sharing it!!!

Answer 6 · 2022-10-13T21:49:43.000Z

If you are only installing this package to use the SeuratWrappers vignette on RNA velocity using scVelo link then you only need the read.loom.matrices function, for which the code is below. So just copy that into R studio as a formula and use 'read.loom.matrices' instead of 'ReadVelocity'. You don't need this package for the rest.

read.loom.matrices <- function(file, engine='hdf5r') {
if (engine == 'h5'){
cat('reading loom file via h5...\n')
f <- h5::h5file(file,mode='r');
cells <- f["col_attrs/CellID"][];
genes <- f["row_attrs/Gene"][];
dl <- c(spliced="/layers/spliced",unspliced="/layers/unspliced",ambiguous="/layers/ambiguous");
if("/layers/spanning" %in% h5::list.datasets(f)) {
dl <- c(dl,c(spanning="/layers/spanning"))
}
dlist <- lapply(dl,function(path) {
m <- as(f[path][],'dgCMatrix'); rownames(m) <- genes; colnames(m) <- cells; return(m)
})
h5::h5close(f)
return(dlist)
} else if (engine == 'hdf5r') {
cat('reading loom file via hdf5r...\n')
f <- hdf5r::H5File$new(file, mode='r')
cells <- f[["col_attrs/CellID"]][]
genes <- f[["row_attrs/Gene"]][]
dl <- c(spliced="layers/spliced",
unspliced="layers/unspliced",
ambiguous="layers/ambiguous")
if("layers/spanning" %in% hdf5r::list.datasets(f)) {
dl <- c(dl, c(spanning="layers/spanning"))
}
dlist <- lapply(dl, function(path) {
m <- as(t(f[[path]][,]),'dgCMatrix')
rownames(m) <- genes; colnames(m) <- cells;
return(m)
})
f$close_all()
return(dlist)
}
else {
warning('Unknown engine. Use hdf5r or h5 to import loom file.')
return(list())
}
}

Answer 7 · 2022-12-01T04:48:12.000Z

Hello. I'm also using the M1 MacBook, and I had spent hours struggling with exactly the same error message with you. I've just solved this problem. I'm not sure if my solution could help you, but give it a try!

Install boost packages using homebrew
(Perhaps the problem with -lboost-filesystem arises because this boost package is not installed. )
brew install boost
My boost package was installed in this path : /opt/homebrew/Cellar/boost/ and the version is 1.76.0.

Now, you should directly modify the Makevars file in this github. Fork this github to your repository.

In your repo, go to the src folder, and open the Makevars file. At the end of the PKG_LIBS statement, you should add a path to the lib directory that exists within the boost package you just installed. So, change the Makevars file like this.
CXX_STD = CXX11
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
PKG_LIBS=-lboost_filesystem -lboost_system   -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS)  $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L /opt/homebrew/Cellar/boost/1.76.0/lib/
Try again to install the velocyto.R using your github repo in the Rstudio.
install_github("ssun1116/velocyto.R")
This is all! Hope this instructions work well 🙏

Thank you! This solution is good and it works

Answer 8 · 2023-01-13T10:41:31.000Z

Anyone managed to solve this on Ubuntu? I have boost installed and libs in /usr/lib/x86_64-linux-gnu/ but adding -L /usr/lib/x86_64-linux-gnu/ to Makevars doesn't solve the installation error.

Answer 9 · 2023-02-28T22:31:05.000Z

Hello. I'm also using the M1 MacBook, and I had spent hours struggling with exactly the same error message with you. I've just solved this problem. I'm not sure if my solution could help you, but give it a try!

Install boost packages using homebrew
(Perhaps the problem with -lboost-filesystem arises because this boost package is not installed. )
brew install boost
My boost package was installed in this path : /opt/homebrew/Cellar/boost/ and the version is 1.76.0.

Now, you should directly modify the Makevars file in this github. Fork this github to your repository.

In your repo, go to the src folder, and open the Makevars file. At the end of the PKG_LIBS statement, you should add a path to the lib directory that exists within the boost package you just installed. So, change the Makevars file like this.
CXX_STD = CXX11
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
PKG_LIBS=-lboost_filesystem -lboost_system   -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS)  $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L /opt/homebrew/Cellar/boost/1.76.0/lib/
Try again to install the velocyto.R using your github repo in the Rstudio.
install_github("ssun1116/velocyto.R")
This is all! Hope this instructions work well 🙏

This solution works. Thanks!!

Answer 10 · 2023-03-18T09:40:19.000Z

use 'brew --prefix boost' to find where the boost is installed

Answer 11 · 2023-08-24T20:16:15.000Z

@ssun1116

Thank you so much! I was able to install the package with your assistance.

Answer 12 · 2024-05-08T13:59:49.000Z

Modified my ~/.R/Makevars to include following line:

PKG_LIBS=-lboost_filesystem -lboost_system -lstdc++ -L /opt/homebrew/Cellar/boost/1.85.0/lib/

Make sure to modify above code accordingly to the version of boost that you have installed with brew. The directory is for Silicon Mac, the brew directory for Intel Mac would be something similar to /usr/local/var/homebrew/... instead.