示例代码报错——找不到c++

[Guangxin-Xu]

作者您好，您的工作对GWAS和scRNA-seq结合研究非常有帮助 自己的配置如下： R: R_4.2.2 Seurat: 5.0.1 ggpubr: 0.6.0 目前我在windows中的Rstudio下重复示例代码时遇到如下问题： ` devtools::install_github("sulab-wmu/scPagwas")

library(scPagwas)

system.time(

1.start to run the wrapper functions for example.

Pagwas_data<-scPagwas_main(Pagwas = NULL, gwas_data =system.file("extdata", "GWAS_summ_example.txt", package = "scPagwas"), # The GWAS Summary statistics files Single_data =system.file("extdata", "scRNAexample.rds", package = "scPagwas"),# scRNA-seq data in seruat format with "RNA" assays and normalized. output.prefix="test", # the prefix name for output files output.dirs="scPagwastest_output",# the directory file's name for output block_annotation = block_annotation_hg37,# gene position in chromosome is provided by package. default is hg38, block_annotation_hg37 is hg37. assay="RNA", # the assays for scRNA-seq data to use. Pathway_list=Genes_by_pathway_kegg,# pathway list is provided by package, including gene symbols. n.cores=1, iters_singlecell = 10, chrom_ld = chrom_ld,# The LD data is provided by package. singlecell=T, # Whether to run the singlecell process. celltype=T# Whether to run the celltype process. ) ) `

报错如下： `

------ Fri Jun 14 11:52:11 2024 ------## *** 1st: Single_data_input function start! ****

Start to read the single cell data! Start to filter single cell data! Input single cell data! 10 cell types are remain, after filter! done!

------ Fri Jun 14 11:52:12 2024 ------## *** 2nd: Pathway_pcascore_run function start!! ****

/bin/sh: x86_64-conda-linux-gnu-c++: command not found make: *** [file922b79531c1e.o] Error 127 x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/data/nas2/software/miniconda3/envs/R_4.2.2/lib/R/include" -DNDEBUG -I"/data/nas2/software/miniconda3/envs/R_4.2.2/lib/R/library/Rcpp/include" -I"/tmp/RtmpIGGYU6/sourceCpp-x86_64-conda-linux-gnu-1.0.10" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/nas2/software/miniconda3/envs/R_4.2.2/include -I/data/nas2/software/miniconda3/envs/R_4.2.2/include -Wl,-rpath-link,/data/nas2/software/miniconda3/envs/R_4.2.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/nas2/software/miniconda3/envs/R_4.2.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1671440533574/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/data/nas2/software/miniconda3/envs/R_4.2.2=/usr/local/src/conda-prefix -c file922b79531c1e.cpp -o file922b79531c1e.o Error in Rcpp::sourceCpp(code = "\n#include \nusing namespace Rcpp;\n\n\n// [[Rcpp::export]]\nIntegerMatrix asMatrix(NumericVector rp,\n NumericVector cp,\n NumericVector z,\n int nrows,\n int ncols){\n\n int k = z.size() ;\n\n IntegerMatrix mat(nrows, ncols);\n\n for (int i = 0; i < k; i++){\n mat(rp[i],cp[i]) = z[i];\n }\n\n return mat;\n}\n") : Error 1 occurred building shared library. Timing stopped at: 2.32 11.08 9.228 `

我看说是x86_64-conda-linux-gnu-c++: command not found这个命令没有找到，查询git其他咨询后，尝试过conda install gxx_linux-64命令也无法解决

能否麻烦您看看有没有其他解决方式呢，您所做的工作对我们非常重要，期待您的答复，谢谢！

[Guangxin-Xu]

已解决是环境中少了这个东西，运行那个命令报错是因为没有安装权限