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fix: switch to R.utils::gunzip over removed GEOquery::gunzip #1

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fix: switch to R.utils::gunzip over removed GEOquery::gunzip #1

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8a8f0d4
fix: switch to R.utils::gunzip over removed GEOquery::gunzip
sof202 Jun 4, 2026
6550e80
chore: bump version
sof202 Jun 4, 2026
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: bigmelon
Type: Package
Title: Illumina methylation array analysis for large experiments
Version: 1.31.3
Version: 1.31.4
Authors@R: c(
person(c("Tyler", "J."), "Gorrie-Stone", role="aut"),
person("Ayden", "Saffari", role="aut"),
Expand All @@ -12,7 +12,7 @@ Description: Methods for working with Illumina arrays using gdsfmt.
License: GPL-3
Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4),
methods, minfi (>= 1.21.0), Biobase, methylumi
Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio
Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio, R.utils
Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter
LazyLoad: yes
Collate: zzz.R es2gds.R dasenGds.R dbGdsn.R dfsfitGdsn.R gds2mlumi.R
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -11,6 +11,7 @@ importFrom('stats', 'approx', 'coef', 'density', 'fivenum', 'lm',
'median', 'na.omit', 'sd', 'quantile', 'kmeans', 'prcomp')
importFrom('utils', 'data', 'file_test', 'packageVersion','untar', 'download.file', 'write.csv', 'packageDescription')
importFrom('GEOquery', 'getGEO')
importFrom('R.utils', 'gunzip')
importFrom('graphics', 'legend', 'plot', 'par')
importFrom('BiocGenerics', 'rownames')
importFrom('illuminaio', 'readIDAT')
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2 changes: 1 addition & 1 deletion R/GEOtoGDS.R
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Expand Up @@ -26,7 +26,7 @@ geotogds <- function(geo, gds=NULL, method = "wget", keepidat = F, keeptar = F,
barsgz <- dir(dest, recursive = TRUE)[grepl(".idat.gz", dir(dest, recursive = TRUE))]
message('Unpacking %s .idat files', length(barsgz))
for(z in barsgz){
GEOquery::gunzip(filename = paste0(dest, "/", z), destname = paste0(dest, "/", gsub(x = z, pattern = ".gz", replacement='')), remove = TRUE)
R.utils::gunzip(filename = paste0(dest, "/", z), destname = paste0(dest, "/", gsub(x = z, pattern = ".gz", replacement='')), remove = TRUE)
}
# if(tidy){
message('Removing packed files!')
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