On quick glance this seems to indicate you are changing directories into the
package extdata probably using a setwd -
This should not be the case -
When I look at the code, set the path to read the file to the full path
location rather than switching into the directory that holds the data -
rawdata.path <- system.file(package = "DaMiRseq","extdata")
setwd(rawdata.path)
# import tab-delimited files:
# sample data are a small subset of Genotype-Tissue Expression (GTEx)
# RNA-Seq database (dbGap Study Accession: phs000424.v6.p1):
count_data <- read.delim("counts_import.txt")
variables_data <- read.delim("annotation_import.txt")
Don't setwd -
Instead
count_data <- read.delim(file.path(rawdata.path, "counts_import.txt"))
variables_data <- read.delim(file.path(rawdata.path, "annotation_import.txt"))
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <[email protected]> on behalf of Mattia Chiesa
<[email protected]>
Sent: Monday, April 23, 2018 3:32:22 AM
To: [email protected]
Subject: [Bioc-devel] Warnind DaMiRseq
Dear All,
I am the mantainer of the DaMiRseq package. I got these Warnings in the
Bioconductor Build/Check system but not locally:
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
Warning: working directory was changed to
'C:/Users/biocbuild/bbs-3.7-bioc/R/library/DaMiRseq/extdata', resetting
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: working directory was changed to
'C:/Users/biocbuild/bbs-3.7-bioc/R/library/DaMiRseq/extdata', resetting
How can I fix it?
Thanks in advance,
Mattia
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