ERROR; return code from pthread_create() is 22
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Entering edit mode
@943a2f3b
Last seen 7 weeks ago
Hong Kong

I am using rma function in the R package affy, but I have encountered the following error. I don't know how to handle it, please help me.Thank you so much.

these are my codes and R info:

files=list.files(path="./",pattern=".CEL")

exampl=read.affybatch(filenames=files[1])

exampl_expSet.RMAL=rma(exampl)

ERROR; return code from pthread_create() is 22

sessionInfo()

R version 4.3.3 (2024-02-29)

Platform: x86_64-conda-linux-gnu (64-bit)

Running under: Ubuntu 20.04.6 LTS

Matrix products: default

BLAS/LAPACK: /home/qcmu_mzk/anaconda3/envs/seurat/lib/libopenblasp-r0.3.27.so; LAPACK version 3.12.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] 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] hgu219cdf_2.18.0 makecdfenv_1.78.0 affyio_1.72.0
[4] affy_1.80.0 Biobase_2.62.0 BiocGenerics_0.48.1

loaded via a namespace (and not attached): [1] crayon_1.5.2 vctrs_0.6.5 httr_1.4.7
[4] cli_3.6.2 rlang_1.1.3 DBI_1.2.2
[7] png_0.1-8 bit_4.0.5 S4Vectors_0.40.2
[10] RCurl_1.98-1.14 Biostrings_2.70.3 stats4_4.3.3
[13] KEGGREST_1.42.0 bitops_1.0-7 fastmap_1.2.0
[16] GenomeInfoDb_1.38.8 IRanges_2.36.0 memoise_2.0.1
[19] BiocManager_1.30.23 compiler_4.3.3 preprocessCore_1.64.0
[22] RSQLite_2.3.6 blob_1.2.4 XVector_0.42.0
[25] R6_2.5.1 GenomeInfoDbData_1.2.11 AnnotationDbi_1.64.1
[28] tools_4.3.3 bit64_4.0.5 zlibbioc_1.48.2
[31] cachem_1.1.0

affy • 225 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States

Seems OK to me.

> dat <- ReadAffy()
> dat
AffyBatch object
size of arrays=744x744 features (20 kb)
cdf=HG-U219 (49386 affyids)
number of samples=5
number of genes=49386
annotation=hgu219
notes=
> eset <- rma(dat)
Background correcting
Normalizing
Calculating Expression
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] hgu219cdf_2.18.0   
[2] affy_1.82.0        
[3] BiocManager_1.30.23
[4] GEOquery_2.72.0    
[5] Biobase_2.64.0     
[6] BiocGenerics_0.50.0

You should upgrade to R-4.4.0 and the current version of Bioconductor. You can also use oligo for this array.

> dat2 <- read.celfiles(list.celfiles(listGzipped = TRUE))
Loading required package: pd.hg.u219
Attempting to obtain 'pd.hg.u219' from BioConductor website.
Checking to see if your internet connection works...
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
installing the source package 'pd.hg.u219'

trying URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/pd.hg.u219_3.12.0.tar.gz'
Content type 'application/x-gzip' length 15394307 bytes (14.7 MB)
downloaded 14.7 MB

* installing *source* package 'pd.hg.u219' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pd.hg.u219)

The downloaded source packages are in
    'C:\Users\jmacdon\AppData\Local\Temp\RtmpuiogAB\downloaded_packages'
Loading required package: pd.hg.u219
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Reading in : GSM7497389_39523.CEL.gz
Reading in : GSM7497390_39535.CEL.gz
Reading in : GSM7497391_39541.CEL.gz
Reading in : GSM7497392_39549.CEL.gz
Reading in : GSM7497393_39529.CEL.gz
> eset2 <- rma(dat2)
Background correcting
Normalizing
Calculating Expression
> all.equal(exprs(eset), exprs(eset2))
[1] TRUE
>

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