Error in gc.sample.stats

Eric Blanc

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Dec 12, 2023, 6:37:18 AM12/12/23

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Hi,

I encountered the following error extracting the normalised coverage:

library(sequenza)

# Follow sequenza documentation https://bitbucket.org/sequenzatools/sequenza/src/master/
args <- list(

file="sample.seqz.gz",

assembly="hg38",

chromosome.list=sprintf("chr%d", 1:22),

gamma=60,

kmin=50

)
seqz <- do.call(sequenza.extract, args=args)

Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)
Calls: do.call -> <Anonymous> -> gc.sample.stats -> chunk.apply

The session info is below:

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.7 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: $HOME/miniconda3/envs/sequenza/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0

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: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] sequenza_3.0.0

loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.2 rlang_1.1.2
[4] glue_1.6.2 S4Vectors_0.40.2 RCurl_1.98-1.13
[7] squash_1.0.9 stats4_4.3.2 hms_1.1.3
[10] fansi_1.0.6 tibble_3.2.1 bitops_1.0-7
[13] tzdb_0.4.0 IRanges_2.36.0 lifecycle_1.0.4
[16] GenomeInfoDb_1.38.1 compiler_4.3.2 pkgconfig_2.0.3
[19] XVector_0.42.0 pbapply_1.7-2 iotools_0.3-5
[22] R6_2.5.1 readr_2.1.4 utf8_1.2.4
[25] GenomeInfoDbData_1.2.11 seqminer_9.3 pillar_1.9.0
[28] parallel_4.3.2 GenomicRanges_1.54.1 magrittr_2.0.3
[31] tools_4.3.2 zlibbioc_1.48.0 copynumber_1.15.0
[34] BiocGenerics_0.48.1

I believe that the problem arises because the argument names of function itools::chunk.apply have changed since version 0.3-3. I believe that, in function sequenza::gc.sample.stats, the argument parallel of the call to chunk.apply should be renamed CH.PARALLEL.

Thanks for your package,

Best,

Eric

Francesco Favero

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Dec 12, 2023, 4:57:50 PM12/12/23

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Hi Eric,

You are correct. The immediate solutions are to roll back iotools or fix the code in a local branch.

You can send a PR and I’ll push it to main.

We are developing a newer branch that doesn’t use iotools, so hopefully we will push this out of restricted access soon.

Best

Francesco

Fong Chun Chan

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Jan 5, 2024, 7:50:32 PM1/5/24

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Ran into the issue. Thanks Eric for posting the solution.

I've created a PR (https://bitbucket.org/sequenzatools/sequenza/pull-requests/3) that includes the solution in hopes that it will help others avoid this in the futur.

Donkiss Zidane

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Mar 30, 2024, 7:56:38 AM3/30/24

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Donkiss Zidane

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Mar 31, 2024, 4:20:45 PM3/31/24

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