[Bioc-devel] ExperimentHub package development - Windows OS specific error

[Gavin Lloyd]

Your file seems to be encoded as UTF-8-BOM.


When I read it in on my Windows 10 machine the Title column has extra characters at the front ("�..Title"), which is why your function returns "no object found" when checking for the Title column.


If I resave your file with UTF-8 format your function works as expected and I am able to install your package.


Gavin


________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Murphy, Alan E <a.murphy using imperial.ac.uk>
Sent: 02 March 2021 17:00
To: bioc-devel using r-project.org
Subject: [Bioc-devel] ExperimentHub package development - Windows OS specific error

Hi all,

My apologies, I have emailed before on a related issue but now think I have found a potential cause of the issue I am having but can't seem to find a fix.

I am working on an ExperimentHub data package; ewceData<https://github.com/neurogenomics/ewceData>, which fails checks on Windows OS but passes on Linux and Mac. On Windows, the package fails to install with the following output:


Error: package or namespace load failed for 'ewceData':
 .onLoad failed in loadNamespace() for 'ewceData', details:
  call: fun(libname, pkgname)
  error: no objects found
Error: loading failed
Execution halted

It seems like this error is caused by my onload function. The onload function I use (zzz.R) should allow easy access to the stored datasets, allowing a user to call the dataset like dataset1(). The error note printed appears because the metadata.csv file did not read properly

.onLoad <- function(libname, pkgname) {
  objs <- read.csv(system.file("extdata", "metadata.csv",
                               package="ewceData"),
                   stringsAsFactors=FALSE)$Title
  if (!length(objs))
    stop("no objects found")

It would seem the issue is with either read.csv or system.file and is specific to Windows OS. Just to note I also do import read.csv from utils.

If anyone has come across an issue like this before or have good guesses for a possible fix it would be greatly appreciated?

Kind regards,
Alan,

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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