Installation failure: Scissor, SigBridgeR, and scPAS all fail to compile (RcppExports.o, cc1plus warnings treated as errors)

[lisch7]

Hi, thank you very much for developing these useful packages!

I am trying to install several related packages (Scissor, SigBridgeR, scPAS) from GitHub, but all of them fail during compilation. The errors suggest issues with C++ compilation (Rcpp / Makeconf).

▶ 1. Scissor

devtools::install_github("sunduanchen/Scissor")

Error:

make: *** [/usr/lib/R/etc/Makeconf:211: RcppExports.o] Error 1
ERROR: compilation failed for package ‘Scissor’
* removing ‘/data2/refdir/Rlib_4.5/Scissor’
installation ... had non-zero exit status

▶ 2. scPAS

devtools::install_github("aiminXie/scPAS")

Error:

cc1plus: some warnings being treated as errors
make: *** [/usr/lib/R/etc/Makeconf:211: RcppExports.o] Error 1
ERROR: compilation failed for package ‘scPAS’
* removing ‘/data2/refdir/Rlib_4.5/scPAS’

I used remotes::install_github("WangLabCSU/SigBridgeR") to install packages and nothing changed.

Could you please offer some help?

Thanks a lot!

[lisch7]

My environment:

> sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Shanghai
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cli_3.6.5

loaded via a namespace (and not attached):
 [1] desc_1.4.3        R6_2.5.1          devtools_2.4.6    fastmap_1.2.0     magrittr_2.0.4    glue_1.8.0        cachem_1.1.0      remotes_2.5.0     memoise_2.0.1     lifecycle_1.0.4   ps_1.9.1         
[12] processx_3.8.6    sessioninfo_1.2.3 callr_3.7.6       pak_0.9.0         vctrs_0.6.5       pkgload_1.4.1     compiler_4.5.0    purrr_1.1.0       rstudioapi_0.17.1 tools_4.5.0       pkgbuild_1.4.8   
[23] curl_7.0.0        ellipsis_0.3.2    rlang_1.1.6       fs_1.6.6          usethis_3.2.1

[ShixiangWang]

@lisch7 Hi

Thanks for your report. Based on your limited report about the compilation error and using the latest R version, I guess this error was raised by unsupported C/C++ compilation library. Please try updaing the C/C++ compiler refer to the blog https://cloud.tencent.com/developer/article/1937953.

[ShixiangWang]

Closing. Please file a new issue if necessary.