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Troubleshooting

Exceret

2025-09-23

Source: vignettes/Troubleshooting.Rmd
Troubleshooting.Rmd

Overview

This vignette provides solutions to common problems you might encounter when using this package. If you cannot find your problem here, please file an issue on our GitHub repository.

Error in normalize.quantiles(dataset0) : ERROR; return code from pthread_create() is 22

To solve this problem, you need to install preprocessCore without threading support. Try:

git clone https://github.com/bmbolstad/preprocessCore.git
cd preprocessCore
R CMD INSTALL --configure-args="--disable-threading"  .

or

BiocManager::install(
  "preprocessCore",
  configure.args = "--disable-threading",
  force = TRUE
)

See bioconductor_docker/issues/22, Scissor/issues/15 for more details.

Error at alpha=0.05:subscript out of bounds

Error in Scissor.v5.optimized():

! object ‘fit0’ not found

This may be due to two reasons: first, a mismatch in the dimensions of the bulk expression data and the phenotype data; second, incorrect column names in the survival phenotype data leading to a failure to match.

To check dimension mismatch：

ncol(your_bulk_data) == nrow(your_phenotype_data) # should be TRUE

all(unique(colnames(your_bulk_data)) == unique(rownames(your_bulk_data))) # should be TRUE

all(order(colnames(your_bulk_data)) == order(rownames(your_phenotype_data))) # should be TRUE

Survival phenotype column names should be formatted as time and status, ensuring correct capitalization and spelling:

head(survival_phenotype) # case-sensitive
#           time status
# GSM70130 34.80      0
# GSM70131 35.67      0
# GSM70136 43.37      0
# GSM70138 60.77      0
# GSM70140 33.80      1
# GSM70144 58.53      0

Error in function_name():

! lazy-load database ‘/home/user/R/x86_64-pc-linux-gnu-library/4.4/SigBridgeR/R/SigBridgeR. rdb’ is corrupt

An error occurred during installation, causing the package to be corrupted. Try reinstalling the package:

# I reccomend restarting R/RStudio before reinstalling
remove.packages("SigBridgeR")

detach("package:SigBridgeR", unload = TRUE)

if (!requireNamespace("remotes")) {
  install.packages("remotes")
}
remotes::install_github("WangLabCSU/SigBridgeR")

Error:

! Invalid syntax: ‘c(scissor_umap, scpas_umap)’

As far as I know, this is due to the R environment being contaminated, which prevents the use of %<-%. You can try restarting the R environment or clean up the environment.

# restart R/RStudio
.rs.api.restartSession()
rm(list = ls(all.names = TRUE))

Error:

! Detected n gene(s) with zero variance:

ℹ “gene name(s)”

This is due to the presence of genes with zero variance in the bulk expression data when you are using scPP and binary phenotype. This indicates that the expression levels of one (or several) genes are nearly identical across different samples. You should check your data.

✖ [2025/09/23 08:53:51] Fewer than 20% of the genes in the gene sets are included in the rankings.Check wether the gene IDs in the ‘rankings’ and ‘geneSets’ match.

ℹ [2025/09/23 08:53:51] scPP screening exit.

This issue arises from the single-cell processing, which filtered out too many genes and cells. Consider Adjusting min_cells and min_features to a smaller value.:

seurat = SCPreProcess(
  sc = mat_exam,
  min_cells = 200, 
  min_features = 3,
  quality_control.pattern = "^MT-",
  scale_features = rownames(mat_exam),
  dims = 1:20,
  resolution = 0.1
)