error

[Bao110110]

excuse me ,I am facing an issue when running CIBERSORT package: when I try this:

library(CIBERSORT)

sig_matrix <- system.file("extdata", "LM22.txt", package = "CIBERSORT")

mixture_file <- system.file("extdata", "exampleForLUAD.txt", package = "CIBERSORT")

data(LM22)
LM22[1:4,1:4]#547 22
#      B cells naive B cells memory Plasma cells T cells CD8
#ABCB4     555.71345       10.74423     7.225819     4.31128
#ABCB9      15.60354       22.09479   653.392328    24.22372
#ACAP1     215.30595      321.62102    38.616872  1055.61338
#ACHE       15.11795       16.64885    22.123737    13.42829

data(mixed_expr)
mixed_expr[1:4,1:4]#[1] 20501     5
#      TCGA-05-4244-01 TCGA-05-4249-01 TCGA-05-4250-01 TCGA-05-4382-01
#A1BG          26.0302        120.1349         50.8597        145.9037
#A1CF           0.0000          0.3220          0.0000          0.0000
#A2BP1          1.7454          1.6098          0.0000          0.0000
#A2LD1        135.5022         89.0629        151.1332        112.0685

and running it:

> results <- cibersort(sig_matrix = LM22, mixture_file = mixed_expr,perm = 1000,QN = T)
Error in normalize.quantiles(Y) : 
  ERROR; return code from pthread_create() is 22

how can I do for this error? hoping your help ......

[tbwxmu]

you may need check this https://github.com/Bioconductor/bioconductor_docker/issues/22 The following manual installation of preprocessCore fixes the issue

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