Troubleshooting

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:

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

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
)

Warning in info$envs : partial match of ‘envs’ to ‘envs directories’

Error in reticulate::use_condaenv():

! Unable to locate conda environment ‘r-reticulate-degas’.

For some reason (maybe r session is contaminated), reticulate cannot find the relevant environment. One solution is to pass in the Python path of the environment instead of the environment name.

envs <- ListPyEnv()
head(envs) # goes like this
#                                                            name                                                  python  type
# /home/user/miniconda3                                       base                         /home/user/miniconda3/bin/python conda
# /home/user/miniconda3/envs/r-reticulate-degas r-reticulate-degas /home/user/miniconda3/envs/r-reticulate-degas/bin/python conda

For example, if I want to use the r-reticulate-degas environment, I can pass its Python location to reticulate::use_condaenv().

py_path <- envs[envs$name == "r-reticulate-degas", "python"]
# /home/user/miniconda3/envs/r-reticulate-degas/bin/python
reticulate::use_condaenv(py_path)

Traceback (most recent call last):

File “/home/user/R/Project/R_code/SigBridgeR/Tmp/tmp/BlankClassMTL.py”, line 1, in

import tensorflow as tf #NEED

ModuleNotFoundError: No module named ‘tensorflow’

Warning in file(file, “r”) :

cannot open file ‘tmp//Activations.csv’: No such file or directory

This is due to the issue with the tensorflow package. Use the following method to check if the tensorflow package can be imported.

# make sure you are using the correct python, i.e. r-reticulate-degas
import sys

sys.executable  # in an environment, it should be something like /home/user/miniconda3/envs/r-reticulate-degas/bin/python3

import tensorflow as tf

tf.__version__

# make sure you've entered the Conda environment you want to check, i.e. r-reticulate-degas
conda list tensorflow

# packages in environment at /home/user/miniconda3/envs/r-reticulate-degas:                                                               
#                                                                                                                                        
# Name                     Version          Build               Channel                                                                  
# tensorflow                 2.4.1            mkl_py39h4683426_0
# tensorflow-base            2.4.1            mkl_py39h43e0292_0
# tensorflow-estimator       2.6.0            py39he80948d_0      https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

If the output is ModuleNotFoundError: No module named 'tensorflow', you need to install the tensorflow package, and strictly control the version of the package (version 2.4.1 has been tested and is feasible)

Exceret

2025-10-31

Overview

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

Error at alpha=0.05:subscript out of bounds

Error in `Scissor.v5.optimized()`:

! object ‘fit0’ not found

Error in `function_name()`:

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

Error:

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

Error:

! Detected n gene(s) with zero variance:

ℹ “gene name(s)”

✖ $2025/09/23 08:53:51$ 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.

Warning in info$envs : partial match of ‘envs’ to ‘envs directories’

Error in `reticulate::use_condaenv()`:

! Unable to locate conda environment ‘r-reticulate-degas’.

Traceback (most recent call last):

File “/home/user/R/Project/R_code/SigBridgeR/Tmp/tmp/BlankClassMTL.py”, line 1, in

import tensorflow as tf #NEED

ModuleNotFoundError: No module named ‘tensorflow’

Warning in file(file, “r”) :

cannot open file ‘tmp//Activations.csv’: No such file or directory

Troubleshooting

Exceret

2025-10-31

Overview

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

Error at alpha=0.05:subscript out of bounds

Error in Scissor.v5.optimized():

! object ‘fit0’ not found

Error in function_name():

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

Error:

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

Error:

! Detected n gene(s) with zero variance:

ℹ “gene name(s)”

✖ 2025/09/2308:53:512025/09/23 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 2025/09/2308:53:512025/09/23 08:53:51 scPP screening exit.

Warning in info$envs : partial match of ‘envs’ to ‘envs directories’

Error in reticulate::use_condaenv():

! Unable to locate conda environment ‘r-reticulate-degas’.

Traceback (most recent call last):

File “/home/user/R/Project/R_code/SigBridgeR/Tmp/tmp/BlankClassMTL.py”, line 1, in

import tensorflow as tf #NEED

ModuleNotFoundError: No module named ‘tensorflow’

Warning in file(file, “r”) :

cannot open file ‘tmp//Activations.csv’: No such file or directory

Error in `Scissor.v5.optimized()`:

Error in `function_name()`:

✖ $2025/09/23 08:53:51$ 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.

Error in `reticulate::use_condaenv()`: