Comments (12)
@JenniferWUSTL , This is more complicated than I initially thought. The following worked for me.
Step 1
Download a ZIP Conos source package by clicking the green down load button and unzip
Step 2
In the Conos source folder, search and get into the src folder, and locate Makevars file. Double click on it and see if Textedit will kicking to open Makvars. Look for a line starting with PKG_LIBS and add CXX_STD = CXX11 like a following;
PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -ln2 -lleidenalg -lm
$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) $(PKGB_PATH)/igraph$(DYLIB_EXT) **CXX_STD = CXX11** MkInclude = $(R_HOME)/etc${R_ARCH}/Makeconf
After this close the file and get back into R.
Step 3
Create your Makevars in ~/.R directory by your favorite text editor (I use nano) and cut and paste following;
LLVM_LOC = /usr/local/opt/llvm
C = $(LLVM_LOC)/bin/clang -fopenmp
CXX = $(LLVM_LOC)/bin/clang++ -fopenmp
CXX1X = $(LLVM_LOC)/bin/clang++ -fopenmp
CXX11 = $(LLVM_LOC)/bin/clang++ -fopenmp
CFLAGS = -O3 -Wall -mtune=native -march=native -Ofast -pedantic -mtune=native -pipe
CXXFLAGS = -O3 -Wall -mtune=native -march=native -Ofast -pedantic -mtune=native -pipe
CXX1XFLAGS = -O3 -Wall -mtune=native -march=native -Ofast -pedantic -mtune=native -pipe
CXX11FLAGS = -O3 -Wall -mtune=native -march=native -Ofast -pedantic -mtune=native -pipe
#LDFLAGS = CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
Make sure location of llvm is right in LLVM_LOC = /usr/local/opt/llvm
(this is where my llvm is located,).
Step3
Back in R studio or whatever R interface you are using, fire a following;
install.packages("/Users/akihikohohji/Downloads/conos-master", repos = NULL, type = "source")
That should do it. But at the end the compiler will mostly likely complain that it can't find igraph.dyllib. If this is the case, then you just follow this link, #11 (comment)
I hope this helps. If this does not work, I would suggest a nuclear option, clean install Catalina, which I did and everything started working just fine.
from conos.
Thank you @evanbiederstedt ! That worked! :)
from conos.
Possibly, you have two compilers in your system: one with openmp support and one without. Can you please check that path for the new compiler corresponds to the path, which is shown in the compilation logs?
from conos.
How do I obtain the compilation log?
from conos.
When you install the package, it shows installation progress, and compilation log is a part of it. The same place where you saw the error message you posted above. Indeed "clang: error: unsupported option '-fopenmp'" is just the end of the compilation log.
from conos.
You must have Makevars in ~/.R in which CF or CXX FLAGS has "-fopenmp". You can rename Makevars to Makevars.old and reinstall.
from conos.
@akhst7 We have tried to update the Makevars and clang+++ to the newest version and added the CF and CXX flags but unfortunately continue to get the same warning.
from conos.
Related: #64
from conos.
I've added a wiki page here: https://github.com/kharchenkolab/conos/wiki/Installing-Conos-for-Mac-OS
from conos.
Hi all,
I've been struggling with this as well. Recently installed R 4.0 on a new computer with Catalina. Ultimately, I was able to install PAGODA2, but still running into issues with conos.
I followed the instructions in the wiki page posted above ("Installing Conos for Mac OS"), but still no go.
When I try installing using R by running
devtools::install_github('kharchenkolab/conos')
I get the following error:
clang: error: unsupported option '-fopenmp'
make[1]: *** [base.o] Error 1
make: *** [sublibraries] Error 1
ERROR: compilation failed for package ‘conos’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/conos’
Error: Failed to install 'conos' from GitHub:
(converted from warning) installation of package ‘/var/folders/g0/v1bzrcmn6kx6zpnx83d6_yv80000gp/T//RtmposCVMf/file48c325b0013c/conos_1.3.0.tar.gz’ had non-zero exit status
When I clone the repo and try installing this method:
R CMD install conos*.tar.gz
I get the following error:
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
clang-10: error: no such file or directory: '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/igraph/libs/igraph.dylib'
make: *** [conos.so] Error 1
ERROR: compilation failed for package ‘conos’
Any help would be much appreciated!
from conos.
Hi @haircell
The master branch of conos still hasn't been updated in some time; we're working on a release soon. I believe that's why you are running into this error:
clang-10: error: no such file or directory: '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/igraph/libs/igraph.dylib'
make: *** [conos.so] Error 1
ERROR: compilation failed for package ‘conos’
In principle, this was fixed with the following PR: #64
When cloning the repo, please switch to the dev branch for the time being, i.e.
git clone https://github.com/kharchenkolab/conos.git
cd conos
git checkout dev
R CMD build .
R CMD install conos*.tar.gz
Hope that helps. Update: I've also explicitly updated the master branch to include these changes.
from conos.
Conos is now on CRAN. https://cran.r-project.org/web/packages/conos/index.html
Please install with install.packages('conos')
to access the binaries.
The Mac OS binaries are there. I've updated the wiki accordingly: https://github.com/kharchenkolab/conos/wiki/Installing-conos-for-Mac-OS
from conos.
Related Issues (20)
- Wrong legend while using custom palette HOT 3
- Downsample from each cluster HOT 3
- Cell subsetting error HOT 4
- docker build fails HOT 1
- 'adjustedRand not in load table' HOT 6
- conos install error igraph.so not found HOT 16
- getDifferentialGenes for selected groups? HOT 6
- shared NN variant of $buildGraph HOT 5
- findSubcommunities HOT 7
- Rstudio session crash when making Conos object (LeidenAlg cluster estimation) HOT 11
- Running Conos functions across multiple nodes/computers HOT 1
- How to get predicted cell types? HOT 2
- why I can't find the "velocityInfoConos" function in conos(v1.4.6)? HOT 5
- largeVis embedding does not utilize n.cores argument HOT 5
- Feeding output from getPerCellTypeDE into Heatmap HOT 2
- Integration of multi-modal data based on a joint space
- Prepare for upcoming Seurat v5 release HOT 1
- Attaching metadata from Seurat Objects HOT 1
- Adding MetaData to Conos Object HOT 1
- Using SCT assays HOT 6
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from conos.