I did not get this error on my Windows machine; ExperimentHub can find the
alzzh_gwas_top100 dataset in Bioc 3.13 (devel).
Your snapshot date is older than mine. R reported my snapshot date as
"2021-03-02"
Maybe you need to clear the cache?
You can request all available snapshot dates with possibleDates and set a
specific one if you want to with snapshotDate. See ?ExperimentHub for info.
I am not sure what best practice would be in terms of Bioc 3.13 (should you fix
a snapshot date in your package, or always use the most recent date, or allow
the user to specify a snapshot date...?). You could ask your reviewer for
advice in this regard, or maybe someone on the mailing list will comment.
Gavin
________________________________
From: Murphy, Alan E <a.mur...@imperial.ac.uk>
Sent: 02 March 2021 20:07
To: Gavin Lloyd (College of Medical and Dental Sciences);
bioc-devel@r-project.org
Subject: Re: ExperimentHub package development - Windows OS specific error
Hey Gavin,
This worked perfectly, thanks!
However, this did lead to another error where one of the datasets from the
metadata file wasn't found in the ExperimentHub dataset. Again this is Windows
specific and the dataset in question (alzh_gwas_top100) does exist:
> ### ** Examples
>
> alzh_gwas_top100()
using temporary cache D:\temp\RtmpCEujsj/working_dir\RtmpY9HMAa/BiocFileCache
snapshotDate(): 2020-04-27
Error in alzh_gwas_top100() :
resource alzh_gwas_top100 not found in ExperimentHub
This error is thrown in zzz.R here:
objs <- read.csv(system.file("extdata", "metadata.csv",
package="ewceData"),
stringsAsFactors=FALSE,fileEncoding = "UTF-8-BOM")$Title
if (!length(objs))
stop("no objects found")
## Functions to load objects by name:
ns <- asNamespace(pkgname)
sapply(objs,
function(xx) {
func = function(metadata = FALSE) {
if (!isNamespaceLoaded("ExperimentHub"))
attachNamespace("ExperimentHub")
eh <- query(ExperimentHub(), "ewceData")
ehid <- names(query(eh, xx))
if (!length(ehid))
stop(paste0("resource ", xx,
" not found in ExperimentHub"))
if (metadata)
eh[ehid]
else eh[[ehid]]
}
assign(xx, func, envir=ns)
namespaceExport(ns, xx)
})
I checked and objs does contain the correct list of titles so the issue isn't
there. Sorry about the continuation in the question but does anyone know why
this could be happening?
Kind regards,
Alan.
________________________________
From: Gavin Lloyd <g.r.ll...@bham.ac.uk>
Sent: 02 March 2021 18:10
To: Murphy, Alan E <a.mur...@imperial.ac.uk>; bioc-devel@r-project.org
<bioc-devel@r-project.org>
Subject: Re: ExperimentHub package development - Windows OS specific error
This email from g.r.ll...@bham.ac.uk originates from outside Imperial. Do not
click on links and attachments unless you recognise the sender. If you trust
the sender, add them to your safe senders
list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping
for this address.
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-boun...@r-project.org> on behalf of Murphy, Alan E
<a.mur...@imperial.ac.uk>
Sent: 02 March 2021 17:00
To: bioc-devel@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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