[Bioc-devel] Warnind DaMiRseq

[Shepherd, Lori]

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 <bioc-devel-bounces at r-project.org> on behalf of Mattia Chiesa <mattia.chiesa at hotmail.it>
Sent: Monday, April 23, 2018 3:32:22 AM
To: bioc-devel at r-project.org
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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