My system information is given below
sessionInfo ()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] hugene10sttranscriptcluster.db_8.5.0 hugene10stprobeset.db_8.5.0
[3] org.Hs.eg.db_3.4.0 hugene10stv1probe_2.18.0
[5] AnnotationDbi_1.36.2 IRanges_2.8.2
[7] S4Vectors_0.12.2 hugene10stv1cdf_2.18.0
[9] gcrma_2.46.0 affy_1.52.0
[11] GEOquery_2.40.0 Biobase_2.34.0
[13] BiocGenerics_0.20.0 BiocInstaller_1.24.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 XVector_0.14.1 splines_3.3.2
[4] zlibbioc_1.20.0 bit_1.1-12 R6_2.2.2
[7] rlang_0.1.4 blob_1.1.0 httr_1.3.1
[10] tcltk_3.3.2 tools_3.3.2 DBI_0.7
[13] digest_0.6.12 bit64_0.9-7 tibble_1.3.4
[16] preprocessCore_1.36.0 affyio_1.44.0 bitops_1.0-6
[19] RCurl_1.95-4.8 memoise_1.1.0 RSQLite_2.0
[22] Biostrings_2.42.1 XML_3.98-1.9 pkgconfig_2.0.1
I am following a work flow to do gene expression analysis from BioConductor packages. during my analysis i go through the source("http://bioconductor.org/biocLite.R") and biocLite("GEOquery") command but, during the command of sapply I am getting the following error message
getGEOSuppFiles("GSE10329")
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE10nnn/GSE10329/suppl/
OK trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE10nnn/GSE10329/suppl//GSE10329_RAW.tar'
Content type 'application/x-tar' length 122982400 bytes (117.3 MB)
downloaded 117.3 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE10nnn/GSE10329/suppl//filelist.txt'
Content type 'text/plain' length 1389 bytes
downloaded 1389 bytes
untar("GSE10329/GSE10329_RAW.tar", exdir="data")
cels = list.files("data/", pattern = "CEL")
sapply(paste("data", cels, sep="/"), gunzip)
Error in FUN(X[[i]], ...) :
Argument 'filename' and 'destname' are identical: data/GSM261030.CEL
cels = list.files("data/", pattern = "CEL")
sapply(paste("data", cels, sep="/"), gunzip)
Error in FUN(X[[i]], ...) :
Argument 'filename' and 'destname' are identical: data/GSM261030.CEL
cels = list.files("data/", pattern = "CEL")
