jlaffy / scalop Goto Github PK

Hi,
I'm trying to install the scalop package, using
R version 4.2.1
Platform: x86_64-apple-darwin19.6.0 (64-bit)
devtools::install_github("jlaffy/scalop")

But I get the following error:

* installing *source* package ‘scalop’ ...
** using staged installation
** libs
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c init.c -o init.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c nd.c -o nd.o
nd.c:24:10: fatal error: 'S.h' file not found
#include "S.h"
         ^~~~~
1 error generated.
make: *** [nd.o] Error 1
ERROR: compilation failed for package ‘scalop’
* removing ‘/usr/local/lib/R/4.2/site-library/scalop’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/zs/_5szrr6j2zv3rm4r3xt4rhpxz58q7z/T//Rtmpbyuh0z/file71421bdf6ff0/scalop_1.1.0.tar.gz’ had non-zero exit status

Any idea what could explain this error?
Thank you for your help,
Kind regards,
Jenn

Hi, thanks for build this nice tool, Itay told me that I can use scalop::sigScores to calculate signature scores, but I didn't find any tutorial or guidance to calculate meta-programs(MP) score, could you give me some instruction to do this analysis? Appreciate it!

hello, I was running the scalp::sigscore to calculated 41 Meta-programes abundance, it has some problem, and I didn't know what the 'x' refer to?

re = sigScores(object, sigs = sigs)
Error in FUN(mat) : 'x' must be an array of at least two dimensions.

The object here is a single cell expression matrix(gene * cell), the sigs here is the 41 MP program list vector.
Do you know how to deal with it?
Thanks！

I am trying to install your other package, infercna, which is dependent on this package, scalop. But I keep running into this error:

nd.c:24:10: fatal error: S.h: No such file or directory
24 | #include "S.h"
| ^~~~~

I see there was a previous issue about this same problem that hasn't been solved, are there any updates?

hi team，

Some function in scalop as well as in infercna will use the split_by_sample_names, but there is no this function in the scalop package.
Would your team fix this problem.

Thanks!

This package is useful in classifying the genesets signature score in scRNA-seq data, but I meet the problem to use this. What's the flow to deal with a scRNA-seq matirx data? I can't find a vignettes in this package.