issue with scibet

[kguion1]

I have been struggling to install the scibet package. I was able to run the scMAGIC atlas version with no issues. However, I now want to try using a reference dataset which does look like it uses the scibet package. When I use devtools::install_github("PaulingLiu/scibet") it fails to compile with the error no DLL was created. Looking through their installation instructions (http://scibet.cancer-pku.cn/installation.html), they mention that scibet is for linux and I was able to install their zwj-tina/scibetR for Windows. However, this is not recognized by the scMAGIC function and so I am still unable to run.

I have tried the scibet GitHub issues page as well as other online forums and have been unsuccessful.

Have you addressed this problem before and have any suggestions?

[Drizzle-Zhang]

I'm sorry for not considering Windows users. I have update the scMAGIC, and you can run scMGAIC again according to the steps in README.

[jolynljj]

I'm sorry for not considering Windows users. I have update the scMAGIC, and you can run scMGAIC again according to the steps in README.

Hi, I am also a windows user trying to use ScMAGIC. Following the instructions on readme still did not resolve the problem for me. It still calls the error that scibet package is not found.

[antoine4ucsd]

Hello I am having the same kind of issue with a Mac (last gen) I did try to install the following packges first as instructed here:http://scibet.cancer-pku.cn/installation.html

install.packages("Rcpp")
install.packages("RcppEigen")
install.packages("ggsci")
install.packages("viridis")
install.packages("tidyverse")

but I still get this error

devtools::install_github("PaulingLiu/scibet") 

Installing package into '/Users/me/Library/R/x86_64/4.2/library'
(as 'lib' is unspecified)
* installing *source* package ‘scibet’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Ofast -ffast-math -march=native -fopenmp -I'/Users/me/Library/R/x86_64/4.2/library/Rcpp/include' -I'/Users/me/Library/R/x86_64/4.2/library/RcppEigen/include' -I'/Users/me/Library/R/x86_64/4.2/library/tidyverse/include' -I'/Users/me/Library/R/x86_64/4.2/library/viridis/include' -I'/Users/me/Library/R/x86_64/4.2/library/ggsci/include' -I'/Users/me/Library/R/x86_64/4.2/library/ggplot2/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Users/me/Library/R/x86_64/4.2/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/me/Library/R/x86_64/4.2/library/RcppEigen/include/RcppEigenForward.h:25:
In file included from /Users/me/opt/miniconda3/bin/../include/c++/v1/iterator:586:
In file included from /Users/me/opt/miniconda3/bin/../include/c++/v1/__debug:14:
In file included from /Users/me/opt/miniconda3/bin/../include/c++/v1/iosfwd:98:
In file included from /Users/me/opt/miniconda3/bin/../include/c++/v1/__mbstate_t.h:29:
/Users/me/opt/miniconda3/bin/../include/c++/v1/wchar.h:123:15: fatal error: 'wchar.h' file not found
#include_next <wchar.h>
              ^~~~~~~~~
1 error generated.
make: *** [/Library/Frameworks/R.framework/Resources/etc/Makeconf:175: RcppExports.o] Error 1
ERROR: compilation failed for package ‘scibet’
* removing ‘/Users/me/Library/R/x86_64/4.2/library/scibet’
Warning message:
In i.p(...) :
  installation of package '/var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T//Rtmp4jwvWW/file429d4949a232/scibet_1.0.tar.gz' had non-zero exit status

thank you!

[NDeeSeee]

Hello everyone,

After much collaboration and numerous trials, I've managed to install the scibet R package on MacOS (M1), utilizing OpenMP support. In the spirit of collective problem-solving, I'm excited to share a detailed guide and the scripts I've developed to assist anyone encountering similar hurdles.

Key Steps:

1. Install Homebrew Packages: You’ll need llvm and gcc. Ensure they are in your PATH.
2. Configure Makevars: Set the correct paths to Clang and GFortran in your ~/.R/Makevars.
3. Set Environment Variables: Adjust PATH, LDFLAGS, and CPPFLAGS to include Homebrew paths.
4. I've written a detailed step-by-step guide in a README.md and a bash script generate_report.sh to collect your system
5. setup which you can find in the attached files.

Attachments:

R_setup_files.zip contains setup_report.txt, generate_report.sh, and README.md.

• setup_report.txt: This file contains my working environment setup.
• generate_report.sh: A script you can run to generate your system's report.
• README.md: The step-by-step installation guide.

Please note, my Makevars configurations are at the very bottom of the setup_report.txt. These settings were pivotal to the successful installation. Ensure that in your case, all directories and paths are appropriate and reflect your system's structure.

Usage: Extract the ZIP file and run bash generate_report.sh in your terminal to produce a report of your configuration. Follow the instructions in the README.md to set up your environment.

Contribution: I hope it can assist others in the community. If you have improvements or suggestions, please share!