bioconductor-oligo glib(?) build issue, "pthread_create() is 22" unless glib is pinned

[darintay]

Hi, hope this is the right place for this!

I'm hitting an unusual pthread_create error using bioconductor-oligo installed from bioconda.
If I pin to an older glib version the error goes away.
I think this means there's some sort of ABI dependency issue?

(It's not clear to me if the specific glib version is directly fixing the issue here, or just one of the transitive dependencies)

### Failing environment, no glib pin ###
$ conda create -n olitest --strict-channel-priority -c conda-forge -c bioconda -c defaults bioconductor-oligo
$ conda activate olitest
$ Rscript  ~/test.R
================================================================================
Welcome to oligo version 1.46.0
================================================================================
Background correcting
Error in basicRMA(pms, pns, TRUE, TRUE, verbose = TRUE) : 
  ERROR; return code from pthread_create() is 22

### Working environment, glib pinned ###
$ conda create -n olitest --strict-channel-priority -c conda-forge -c bioconda -c defaults bioconductor-oligo glib=2.56
$ conda activate olitest
$ Rscript  ~/test.R
================================================================================
Welcome to oligo version 1.46.0
================================================================================
Background correcting
Normalizing
Calculating Expression

### test.R  (example from https://rdrr.io/bioc/oligo/man/basicRMA.html) ###
library('oligo')
pms <- 2^matrix(rnorm(1000), nc=20)
colnames(pms) <- paste("sample", 1:20, sep="")
pns <- rep(letters[1:10], each=5)
res <- basicRMA(pms, pns, TRUE, TRUE)
res[, 1:3]

I've tested this on ubuntu (14.04 and 16.04).

[mpachkov]

I would like to add that I have similar issue (return code from pthread_create() is 22) with affy bioconductor package installed through bioconductor package manager inside conda environment. I tried different versions of R(3.6, 3.5) and openblas (0.3.6,0.3.7) but the problem persist. My problem is not directly connected with bioconda since these packages are coming from conda-forge but environment includes a few packages from bioconda and it means that bioconda packages dependent on conda-forge packages are affected. OS: CentOs 7.6

Thanks for the hint with pinning glib!

[bgruening]

@darintay could you please check the latest builds? Thanks.

[imerelli]

I have the same problem on CentOS Linux release 7.6.1810 (Core), inside a conda environment:

eset_object <- justRMA(filenames = infofile$Arrayname, sampleNames = infofile$Samplename, cdfname = "hugene10sthsentrezgcdf") # change the cdf file name

Error in just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description, :
ERROR; return code from pthread_create() is 22

[b-niu]

return code from pthread_create() is 22

Same issue in CentOS 7...

[J-81]

To add important context to my commit reference:
I was unable to pin glib to 2.56 (conflicts on my end) but did find out pinning to 2.58 did not resolve the issue on my end.

Pinning openblas to 0.3.3 as mentioned on the below stackoverflow did fix the issue on my end:
https://stackoverflow.com/questions/61629861/error-return-code-from-pthread-create-is-22